Nucleic acid for regulating the ABCA7 gene, molecules modulating its activity and therapeutic applications

[0002] The present invention relates to a nucleic acid capable of regulating the transcription of the ABCA7 gene, a gene that, under appropriate conditions, is involved in the metabolism of lipids in the hematopoietic tissues, as well as in cell signaling mechanisms linked to the immune reaction and to inflammation.

[0003] The present invention also describes polypeptides and polynucleotides, the impairment of whose sequence or expression is potentially implicated in diseases associated with the genetic locus q13 of chromosome 19.

[0004] The present invention also relates to nucleotide constructs comprising a polynucleotide encoding a polypeptide or producing a nucleic acid of interest, placed under the control of a nucleic acid for regulating the human or murine ABCA7 gene.

[0005] The invention also relates to recombinant vectors, transformed host cells, and nonhuman transgenic mammals comprising a nucleic acid for regulating the transcript ion of the human and mouse ABCA7 gene or an abovementioned nucleotide construct, as well as methods for screening molecules or substances capable of modulating the activity of the nucleic acid for regulating the ABCA7 gene.

[0006] The invention in addition relates to methods which make it possible to detect an impairment of the transcription of the ABCA7 gene and thus to diagnose a possible dysfunction in lipid metabolism at the level of hematopoietic tissues and in the cell signaling mechanisms of immunity.

[0007] Its subject is also substances or molecules modulating the activity of the nucleic acid for regulating the transcription of the ABCA7 gene as well as pharmaceutical compositions containing such substances or such molecules.

[0008] The ABC (ATP-Binding Cassette) transport proteins constitute a superfamily which is extremely well conserved during evolution, from bacteria to humans. These proteins are involved in membrane transport of various substrates, for example ions, amino acids, peptides, sugars, vitamins or steroid hormones (Higgins et al., Annu Rev. Cell Biol, 8, (1992) 67-113).

[0009] The characterization of the complete amino acid sequence of some ABC transporters has made it possible to define a common general structure comprising in particular two nucleotide binding folds (NBF) with Walker A and B type units as well as two transmembrane domains, each of the transmembrane domains consisting of six helices (Klein et al., BBA, 1461 (1999), 237-262). The specificity of the ABC transporters for the various transported molecules appears to be determined by the structure of the transmembrane domains, whereas the energy necessary for the transport activity is provided by the degradation of ATP at the level of the NBF fold (Dean et al., Curr. Opin. Genet. Dev, 5 (1995) 779-785).

[0010] Several ABC transport proteins have been identified in humans and a number of them have been associated with various diseases.

[0011] For example, cystic fibrosis is caused by mutations in the CFTR (cystic fibrosis transmembrane conductance regulator) gene, also designated ABCC7,

[0012] Moreover, some multidrug resistance phenotypes in tumor cells have been associated with mutations in the genes encoding MDR (multidrug resistance) proteins, also designated ABCB, which also have an ABC transporter structure.

[0013] Other ABC transporters have been associated with neuronal and tumor conditions (U.S. Pat. No. 5,858,719) or are potentially involved in diseases caused by impairment of the homeostasis of metals, in particular the ABC-3 protein.

[0014] Likewise, another ABC transporter, designated PFIC2 or ABCB11, appears to be involved in a form of progressive familial intrahepatic cholestasia, this protein being potentially responsible, in humans, for the export of bile salts.

[0015] A subfamily A of ABC transporters, designated ABCA, has also been identified. It is characterized by the presence of a highly hydrophobic segment (HH1: highly hydrophobic) between the two transmembrane domains, bound to the two NBF units (Broccardo et al., BBA 1461 (1999) 395-404). Four members of this subfamily have so far been characterized. They are the transporters ABCA1 and ABCA2, both located on chromosome 9, at the loci 9q22-9q31 and 9q34, respectively, as well as the transporter ABCA3 located on chromosome 16p13.3, and finally the transporter ABCA4 or ABCR located on chromosome 1p22 (Broccardo et al., 1999). The members of this subfamily are also highly conserved during evolution of multicellular eukaryotes. By way of examples, the transporters ABCA1 and ABCA4, which are the best known, exhibit 95% and 88% identity, respectively, with their murine orthologs. Members of this subfamily are in addition closely related since, for example, the transporters ABCA1 and ABCA4 exhibit a protein sequence identity of 50.9%, as well as a very similar genomic organization (Allikmets et al., Nat. Genet. (1997) 15, 236-246; Broccardo et al., Biochim. Biophys. Acta (1999) 1461, 395-404; Luciani et al., Genomics (1994) 21(1), 150-9; Remaley et al., Proc. Natl. Acad. Sci. USA (1999) 96(22), 12685-90).

[0016] Moreover, members of the subfamily A appear to exhibit a similar functional specialization at the level of the transport of membrane lipids and phospholipids. It has indeed been shown that the loss of the function of these transporters affects the renewal of the phospholipids of the cell membrane bilayer. In the case of ABCA4, there is observed, in a first instance, a normal renewal of phosphatidyl-ethanolamine (PE) in the rod cell of the membrane portion, which leads, via a succession of events, to a total loss of visual acuity (Weng et al., Cell (1999) 98(1), 13-23). In the case of ABCA1, an abnormal distribution of the membrane phospholipids in plasma membrane layers is observed, which results more precisely in the presence of a larger quantity of phosphatidylserine in the outer layer, and in a disruption of the Ca2+ concentration.

[0017] The transporters ABCA1 and ABCA4 have been particularly studied. The ABCA1 gene indeed appears to be involved in pathologies linked to a cholesterol metabolism dysfunction which induces diseases such as atherosclerosis, or familial HDL deficiencies (FHD) such a Tangier disease (FR 99/7684000; Rust et al., Nat. Genet., 22 (1999) 352-355; Brooks-Wilson et al., Nat. Genet., 22 (1999) 336-345; Bodzioch et al., Nat. Genet. 22 (1999) 347-351; Orso et al., Nat. Genet, 24 (2000) 192-196). Tangier disease would appear to be linked to a cellular defect in the translocation of cellular cholesterol which causes degradation of the HDLs, and thereby a disruption in lipoprotein metabolism. Thus, it would appear that the HDL particles which do not incorporate cholesterol from peripheral cells are not metabolized correctly but are on the contrary rapidly eliminated from the body. The plasma HDL concentration in these patients is therefore extremely reduced and the HDLs no longer ensure the return of cholesterol to the liver. This cholesterol accumulates in these peripheral cells and causes characteristic clinical manifestations such as the formation of orange-colored tonsils. Furthermore, other lipoprotein disruptions such as overproduction of triglycerides as well as increased intracellular synthesis and catabolism of phospholipids are observed.

[0018] The ABCA4 transporter has moreover been associated with degenerative and inflammatory eye diseases such as Stargardt's recessive disease (Allikmets et al., 1997) and degeneration of the macular region of the retina linked to age (AMD) (Allikmets et al., Nat. Genet. 15 (1997) 236-246; Allikmets et al., Science, 277 (1997) 1805-1807; Cremers et al., Hum. Mol. Genet. (1998), 7(3), 355-62; Martinez-Mir et al., Nat. Genet. 18 (1998) 11-12; Weng et al., Cell (1999) 98(1), 13-23).

[0019] In humans, a cDNA comprising the entire open reading frame of a new member of the A subfamily of ABC (ATP-Binding Cassette) transporters was recently cloned from human macrophage RNA, and designated ABCA7 (Kaminski et al., BBR, 273(2000), 532-538).

[0020] The characterization of the complete amino acid sequence of ABCA7 indicates that the protein product has the general structure characteristic of ABCA transporters in that it comprises the symmetrical structure comprising the two transmembrane domains and two NBF units. In addition to these characteristic units the ABCA7 protein has other units which were recently identified as being characteristic of the ABCA transporters, namely the HH1 region and the hot spot region (Broccardo et al., Biochim. Biophys. Acta (1999) 1461, 395-404).

[0021] Like the other members of the A subfamily of ABC transporters, the sequence of the ABCA7 protein is highly conserved in mice and in humans, with an inter-species identity of 79%. The ABCA7 protein exhibits furthermore an intron-exon organization characteristic of the members of the ABCA subfamily, as well as a high sequence homology in particular with the human transporters ABCA1 and ABCA4, of 54% and 49%, respectively.

[0022] Moreover, the protein transporter ABCA7 appears to exhibit a regulatory profile dependent on the flows of sterol, similar to that of the other members of the A subfamily, and in particular the ABCA1 transporter (Langman et al., BBR Com; 257(1999), 29-33; Laucken et al., PNAS, 97(2000) 817-822). There has indeed been observed by Kaminski et al. (supra) an increase in the expression of ABCA7 after incubation of human macrophages in the presence of acetylated low-density lipoproteins (AcLDL) which induce a sterol load, as well as a decrease in expression in the presence of the HDL3 cholesterol acceptor which causes a decrease in the sterol load.

[0023] Moreover, ABCA7 exhibits, like the other ABCA members, a degree of specialization of its tissue expression, the ABCA7 messenger being predominantly present in the hematopoietic tissues consisting of the lymphocytes, granulocytes, thymus, spleen, bone marrow or fetal tissues, whereas the expression of ABCA1 is predominant in the macrophages and the placenta, and that of ABCA4 is restricted in the retina (Rust et al., Nat. Genet, 22, (1999) 352-355).

[0024] All the data disclosed above, relating to the identity of the protein sequences, to the regulatory mechanism and the specificity of expression suggests that the ABCA7 gene constitutes another transporter of the A subfamily, and that it has a similar, or even redundant, function to that of the other transporters and in particular to that of the ABCA1 transporter. This transporter could therefore presumably act as mediator in the metabolism of lipids, and it is highly possible that it is, in the same way as the ABCA1 transporter, responsible for certain metabolic dysfunctions or deficiencies. Moreover, the specialization of the expression of the ABCA7 transporter presumably indicates that the latter plays a role in the transmembrane transport (export) of lipids in the hematopoietic tissues, and possibly in the lymphocyte signaling aA mechanisms of immunity, for example in the case of the pathogenesis of atherosclerosis as indicated by Kaminski et al. (Supra)

[0025] Although the expression of the human ABCA7 gene appears to be regulated according to the type of cell or the metabolic situation of a given cell type, the sequence(s) making it possible to regulate this gene were not known.

[0026] However, a need exists in the state of the art to identify these regulatory sequences for the following reasons:

[0027] a) These sequences are capable of being mutated in patients suffering from a pathology linked to a defect in the transport of lipids, possible substrates of the ABCA7 protein, or in patients who are likely to develop such pathologies.

[0028] The characterization of the regulatory sequences of the human ABCA7 gene would make it possible to detect mutations in patients, in particular to diagnose the individuals belonging to at-risk family groups. In addition, the isolation of these regulatory sequences would allow the complementation of the mutated sequence with a functional sequence capable of compensating for the metabolic dysfunctions induced by the mutation(s) diagnosed, by virtue of the construction of targeted therapeutic means, such as means intended for gene therapy.

[0029] b) The characterization of the regulatory sequences of the ABCA7 gene would make available to persons skilled in the art means capable of allowing the construction, by genetic engineering, and then the expression of defined genes in the cell types in which the ABCA7 gene is preferably expressed.

[0030] c) Moreover, some parts of the regulatory sequences of the ABCA7 gene could constitute constitutive promoter sequences with a high level of expression, of the type which will allow the construction of novel means for the expression of defined sequences in the cells, supplementing a range of means which already exist.

[0031] It has to be noted that despite the efforts undertaken, the regulatory sequences of the ABCA7 gene have so far remained completely unknown.

[0032] The inventors have now isolated and analyzed a human genomic DNA of 33.5 kb comprising the 46 exons of the open reading frame of the ABCA7 gene as well as the nontranscribed region of about 1.1 kb located on the 5′ side of exon 1, upstream of the transcriptional site +1, and comprising signals for regulating the human ABCA7 gene.

[0033] The inventors have also isolated and analyzed a murine genomic DNA of 20 Kb comprising the 45 exons of the open reading frame of the ABCA7 gene as well as the nontranscribed region of about 1.2 Kb in mice located on the 5′ side of exon 1, upstream of the transcription site +1, and comprising signals for regulating the murine ABCA7 gene.

[0034] General Definitions

[0035] The term “isolated” for the purposes of the present invention designates a biological material (nucleic acid or protein) which has been removed from its original environment (the environment in which it is naturally present).

[0036] For example, a polynucleotide present in the natural state in a plant or an animal is not isolated. The same polynucleotide separated from the adjacent nucleic acids in which it is naturally inserted in the genome of the plant or animal is considered as being “isolated”.

[0037] Such a polynucleotide may be included in a vector and/or such a polynucleotide may be included in a composition and remain nevertheless in the isolated state because of the fact that the vector or the composition does not constitute its natural environment.

[0038] The term “purified” does not require the material to be present in a form of absolute purity, exclusive of the presence of other compounds. It is rather a relative definition.

[0039] A polynucleotide is in the “purified” state after purification of the starting material or of the natural material by at least one order of magnitude, preferably 2 or 3 and preferably 4 or 5 orders of magnitude.

[0040] For the purposes of the present description, the expression “nucleotide sequence” may be used to designate either a polynucleotide or a nucleic acid. The expression “nucleotide sequence” covers the genetic material itself and is therefore not restricted to the information relating to its sequence.

[0041] The terms “nucleic acid”, “polynucleotide”, “oligonucleotide” or “nucleotide sequence” cover RNA, DNA or cDNA sequences or alternatively RNA/DNA hybrid sequences of more than one nucleotide, either in the single-chain form or in the duplex form.

[0042] The term “nucleotide” designates both the natural nucleotides (A, T, G, C) as well as the modified nucleotides which comprise at least one modification such as (1) an analog of a purine, (2) an analog of a pyrimidine, or (3) an analogous sugar, examples of such modified nucleotides being described, for example, in the PCT application No. WO 95/04 064.

[0043] For the purposes of the present invention, a first polynucleotide is considered as being “complementary” to a second polynucleotide when each base of the first nucleotide is paired with the complementary base of the second polynucleotide whose orientation is reversed. The complementary bases are A and T (or A and U), or C and G.

[0044] “Variant” of a nucleic acid according to the invention will be understood to mean a nucleic acid which differs by one or more bases relative to the reference polynucleotide. A variant nucleic acid may be of natural origin, such as an allelic variant which exists naturally, or may also be a nonnatural variant obtained, for example, by mutagenic techniques.

[0045] In general, the differences between the reference nucleic acid and the variant nucleic acid are small such that the nucleotide sequences of the reference nucleic acid and of the variant nucleic acid are very similar and, in many regions, identical. The nucleotide modifications present in a variant nucleic acid may be silent, which means that they do not alter the amino acid sequences encoded by said variant nucleic acid.

[0046] However, the changes in nucleotides in a variant nucleic acid may also result in substitutions, additions or deletions in the polypeptide encoded by the variant nucleic acid in relation to the peptides encoded by the reference nucleic acid. In addition, such nucleotide modifications in the coding regions may produce conservative or nonconservative substitutions in the amino acid sequence.

[0047] Preferably, the variant nucleic acids according to the invention encode polypeptides which substantially conserve the same function or biological activity as the polypeptide of the reference nucleic acid or, alternatively, the capacity to be recognized by antibodies directed against the polypeptides encoded by the initial nucleic acid.

[0048] Some variant nucleic acids will thus encode mutated forms of the polypeptides whose systematic study will make it possible to deduce structure-activity relationships of the proteins in question. Knowledge of these variants in relation to the disease studied is essential since it makes it possible to understand the molecular cause of the pathology.

[0049] “Fragment” will be understood to mean a reference nucleic acid according to the invention, a nucleotide sequence of reduced length relative to the reference nucleic acid and comprising, over the common portion, a nucleotide sequence identical to the reference nucleic acid.

[0050] Such a nucleic acid “fragment” according to the invention may be, where appropriate, included in a larger polynucleotide of which it is a constituent.

[0051] Such fragments comprise, or alternatively consist of, oligonucleotides ranging in length from 20 to 25, 30, 40, 50, 70, 80, 100, 200, 500,1000 or 1500 consecutive nucleotides of a nucleic acid according to the invention.

[0052] “Biologically active fragment” of a nucleic acid for regulating transcription according to the invention is understood to mean a nucleic acid capable of modulating the transcription of a DNA sequence placed under its control. Such a biologically active fragment comprises a core promoter and/or a regulatory element, as defined in the present description.

[0053] “Regulatory nucleic acid” according to the invention is understood to mean a nucleic acid which activates and/or regulates the expression of a DNA sequence selected and placed under its control.

[0054] “Promoter” is understood to mean a DNA sequence recognized by the proteins of the cell which are involved in the initiation of the transcription of a gene. The core promoter is the minimum regulatory nucleic acid capable of initiating the transcription of a defined DNA sequence which is placed under its control. In general, the core promoter consists of a genomic DNA region upstream of the site for initiation of transcription where there is very often present a CAAT sequence (where one or more transcriptional protein factors bind) as well as, except in rare cases such as in some housekeeping genes, the TATA or “TATA box” sequence or a related box. It is at the level of this box that RNA polymerase binds as well as one or more transcription factors, such as the “TATA” box binding proteins (TBPs).

[0055] A nucleotide sequence is “placed under the control” of a regulatory nucleic acid when this regulatory nucleic is located, relative to the nucleotide sequence, in such a manner as to control the initiation of transcription of the nucleotide sequence by an RNA polymerase.

[0056] “Regulatory element” or “regulatory sequence” for the purposes of the invention, is understood to mean a nucleic acid comprising elements capable of modulating transcription initiated by a core promoter, such as binding sites for various transcription factors, “enhancer” sequences for increasing transcription or “silencer” sequences for inhibiting transcription.

[0057] “Enhancer” sequence is understood to mean a DNA sequence included in a regulatory nucleic acid capable of increasing or stimulating transcription initiated by a core promoter.

[0058] “Silencer” sequence is understood to mean a DNA sequence included in a regulatory acid capable of decreasing or inhibiting transcription initiated by a core promoter.

[0059] Regulatory elements may be present outside the sequence located on the 5′ side of the site for initiation of transcription, for example in the introns and exons, including in the coding sequences.

[0060] The core promoter and the regulatory element may be “specific to one or more tissues” if they allow transcription of a defined DNA sequence placed under their control, preferably in certain cells (for example tissue-specific cells), that is to say either exclusively in the cells of certain tissues, or at different levels of transcription according to the tissues.

[0061] “Transcription factor” is understood to mean proteins which preferably interact with elements for regulating a regulatory nucleic acid according to the invention, and which stimulate or on the contrary repress transcription. Some transcription factors are active in the form of monomers, others being active in the form of homo- or heterodimers.

[0062] The term “modulation” refers to either a positive regulation (increase, stimulation) of transcription, or a negative regulation (decrease, inhibition, blockage) of transcription.

[0063] The “percentage identity” between two nucleotide or amino acid sequences, for the purposes of the present invention, may be determined by comparing two sequences aligned optimally, through a window for comparison.

[0064] The portion of the nucleotide or polypeptide sequence in the window for comparison may thus comprise additions or deletions (for example “gaps”) relative to the reference sequence (which does not comprise these additions or these deletions) so as to obtain an optimum alignment of the two sequences.

[0065] The percentage is calculated by determining the number of positions at which an identical nucleic base or an identical amino acid residue is observed for the two sequences (nucleic or peptide) compared, and then by dividing the number of positions at which there is identity between the two bases or amino acid residues by the total number of positions in the window for comparison, and then multiplying the result by 100 in order to obtain the percentage sequence identity.

[0066] The optimum sequence alignment for the comparison may be achieved using a computer with the aid of known algorithms contained in the package from the company WISCONSIN GENETICS SOFTWARE PACKAGE, GENETICS COMPUTER GROUP (GCG), 575 Science Doctor, Madison, Wis.

[0067] By way of illustration, it will be possible to produce the percentage sequence identity with the aid of the BLAST software (versions BLAST 1.4.9 of March 1996, BLAST 2.0.4 of February 1998 and BLAST 2.0.6 of September 1998), using exclusively the default parameters (Altschul et al, J. Mol. Biol. (1990) 215: 403-410; Altschul et al, Nucleic Acids Res. (1997) 25: 3389-3402). Blast searches for sequences similar/homologous to a reference “request” sequence, with the aid of the Altschul et al. (Supra) algorithm. The request sequence and the databases used may be of the peptide or nucleic type, any combination being possible.

[0068] “High stringency hybridization conditions” for the purposes of the present invention will be understood to mean the following conditions:

[0069] 1—Membrane Competition and Prehybridization:

[0070] Mix: 40 μl salmon sperm DNA (10 mg/ml)

[0071] +40 μl human placental DNA (10 mg/ml)

[0072] Denature for 5 min at 96° C., then immerse the mixture in ice.

[0073] Remove the 2× SSC buffer and pour 4 ml of formamide mix into the hybridization tube containing the membranes.

[0074] Add the mixture of the two denatured DNAs.

[0075] Incubate at 42° C. for 5 to 6 hours, with rotation.

[0076] 2—Labeled Probe Competition:

[0077] Add to the labeled and purified probe 10 to 50 μl Cot I DNA, depending on the quantity of nonspecific hybridizations.

[0078] Denature for 7 to 10 min at 95° C.

[0079] Incubate at 65° C. for 2 to 5 hours.

[0080] 3-Hybridization:

[0081] Remove the prehybridization mix.

[0082] Mix 40 μl salmon sperm DNA +40 μl human placental DNA; denature for 5 min at 96° C., then immerse in ice.

[0083] Add to the hybridization tube 4 ml of formamide mix, the mixture of the two DNAs and the denatured labeled probe/Cot I DNA.

[0084] Incubate 15 to 20 hours at 42° C., with rotation.

[0085] 4-Washes:

[0086] One wash at room temperature in 2× SSC, to rinse.

[0087] Twice 5 minutes at room temperature 2× SSC and 0.1% SDS.

[0088] Twice 15 minutes 0.1× SSC and 0.1% SDS at 65° C.

[0089] Envelope the membranes in Saran wrap and expose.

[0090] The hybridization conditions described above are adapted to hybridization, under high stringency conditions, of a molecule of nucleic acid of varying length from 20 nucleotides to several hundreds of nucleotides.

[0091] It goes without saying that the hybridization conditions described above may be adjusted as a function of the length of the nucleic acid whose hybridization is sought or of the type of labeling chosen, according to techniques known to persons skilled in the art.

[0092] Suitable hybridization conditions may for example be adjusted to the teaching contained in the manual by HAMES and HIGGINS (1985) (Nucleic acid Hybridization: A Practical Approach, Hames and Higgins Ed., IRL Press, Oxford) or in the manual by F. AUSUBEL et al (1999) (Currents Protocols in Molecular Biology, Green Publishing Associates and Wiley Interscience, N.Y).

[0093] “Transformation” for the purposes of the invention is understood to mean the introduction of a nucleic acid (or of a recombinant vector) into a host cell. The term “transformation” also covers a situation in which the genotype of a cell has been modified by an exogenous nucleic acid, and that this cell thus transformed expresses said exogenous nucleic acid, for example in the form of a recombinant polypeptide or in the form of a sense or antisense nucleic acid.

[0094] “Transgenic animal” for the purposes of the invention is understood to mean a nonhuman animal, preferably a mammal, in which one or more cells contain a heterologous nucleic acid introduced by virtue of human intervention, such as by transgenesis techniques well known to persons skilled in the art. The heterologous nucleic acid is introduced directly or indirectly into the cell or the precursor of the cell, by genetic engineering such as microinjection or infection with a recombinant virus. The heterologous nucleic acid may be integrated into the chromosome or may be provided in the form of DNA replicating extrachromosomally.

[0095] NUCLEIC ACID FOR REGULATING THE ABCA7 GENE

[0096] Using BAC-type vector libraries prepared from human and murine genomic material, the inventors succeeded in isolating a nucleic acid for regulating the human and murine ABCA7 genes.

[0097] The inventors determined, by comparative analysis of the human and murine genomic sequences, a regulatory nucleic acid comprising in particular two regulatory modules conserved in humans and mice. The inventors therefore determined that the nucleic acid for regulating transcription of the ABCA7 gene, when it is most broadly defined, consists of a polynucleotide comprising, from the 5′ end to the 3′ end:

[0098] a nontranscribed region of about 1.2 kb located upstream of the site for initiation of transcription of the ABCA7 gene, and

[0099] the partial sequence of the first exon of the ABCA7 gene.

[0100] In its broadest definition, the nucleic acid for regulating transcription of the ABCA7 gene comprises all the nucleotide regions as defined above and is identified in the sequence SEQ ID No. 1 according to the invention.

[0101] Thus, a first subject of the invention consists of a nucleic acid comprising a polynucleotide having at least 20 consecutive nucleotides of the nucleotide sequence SEQ ID No. 1, or a nucleic acid having a complementary sequence.

[0102] The region of about 1.1 Kb located upstream of the site for initiation of transcription of the ABCA7 gene, and comprising the core promoter and multiple elements for regulating transcription is also included in the sequence identified as SEQ ID No. 2 according to the invention.

[0103] More precisely, the nucleotide at position 1 of the sequence SEQ ID No. 2 is the nucleotide at position −1111, relative to the site for initiation of transcription of the ABCA7 gene.

[0104] According to a second aspect, the invention relates to a nucleic acid comprising a polynucleotide having at least 20 consecutive nucleotides having the nucleotide sequence SEQ ID No. 2, or a nucleic acid having a complementary sequence.

[0105] As already specified above, the nucleic acid for regulating the transcription of the ABCA7 gene having the sequence SEQ ID No. 1 also comprises, in addition to a nontranscribed 5′ regulatory region, the 5′ part of the first exon of the human ABCA7 gene.

[0106] The partial sequence of the first exon of the ABCA7 gene is defined as the sequence SEQ ID No. 3.

[0107] According to a third aspect, the invention relates to a nucleic acid comprising a polynucleotide having at least 20 consecutive nucleotides having the nucleotide sequence SEQ ID No. 3, or a nucleic acid having a complementary sequence.

[0108] Preferably, a nucleic acid according to the invention will be in isolated and/or purified form.

[0109] Also forming part of the invention is any “biologically active” fragment of a nucleic acid as defined above.

[0110] According to yet another aspect, the invention relates to a nucleic acid having at least 80% nucleotide identity with a nucleic acid as defined above.

[0111] In particular, this nucleic acid may be of murine origin, and consists of a polynucleotide having the nucleotide sequence SEQ ID NO: 4 comprising from the 5′ to the 3′ end:

[0112] a nontranscribed region of about 1.2 Kb located upstream of the site for initiation of transcription of the murine ABCA7 gene, and

[0113] the partial sequence of the first exon of the ABCA7 gene.

[0114] The region of about 1.2 Kb located upstream of the site for initiation of transcription of the ABCA7 gene, and comprising the core promoter and multiple elements for regulating transcription, is also included in the sequence identified as SEQ ID NO: 5 according to the invention.

[0115] The invention also includes a nucleic acid characterized in that it hybridizes, under high stringency conditions, with any of the nucleic acids according to the invention.

[0116] The invention also relates to a nucleic acid having at least 80%, advantageously 90%, preferably 95% and most preferably 98% nucleotide identity with a nucleic acid comprising at least 20 consecutive nucleotides of a polynucleotide chosen from the group consisting of the nucleotide sequences SEQ ID No. 1 to SEQ ID No. 5.

[0117] Detailed Analysis of the Sequences SEQ ID No.2 and SEQ ID No. 5

[0118] According to a principal characteristic, the nucleic acid having the sequence SEQ ID No. 2, included in the nucleic acid for regulating the human ABCA7 gene having the sequence SEQ ID No. 1, comprises the constituent elements of a core promoter, respectively a degenerate “TATA” box (TTAAG) located 30 bp upstream of the site of initiation of transcription. Likewise, a degenerate “TATA” box (TTAAA) is located 30 bp upstream of the site of initiation of transcription, on the murine nucleic acid having the sequence SEQ ID NO: 5, included in the nucleic acid for regulating the murine ABCA7 gene having the sequence SEQ ID NO: 4. The “TATA” boxes on the promoters of the human and murine ABCA7 genes as well as the position of the sites of initiation of transcription are represented in FIG. 1.

[0119] The regulatory sequences SEQ ID No. 2 and SEQ ID No. 5 also comprise numerous binding sites for various transcription factors capable of positively or negatively regulating the activity of the core promoter.

[0120] Thus, the various sequences characteristic of the sites for the binding of various transcription factors in the sequences SEQ ID No. 2 and SEQ ID No. 5 were identified by the inventors in the manner detailed below.

[0121] The sequences SEQ ID No. 2 and SEQ ID No. 5 were used as reference sequences and treated according to the algorithms of the MatInspector software packages (Quandt et al., Nucl Acid Res (1995) 23(23), 4878-4884) and compared with the data stored in several databases such as Transfac and the presence as well as the location of the various sites characteristic of the sequences SEQ ID No 2 and 5, and particularly the sites for the binding of the transcription factors were determined according to methods well known to persons skilled in the art.

[0122] More particularly, a detailed analysis was carried out using the software packages NNPP (Reese et al. J. Comput Biol. (1997) 4(3) 311-23), TSSG and TSSW (Soloryev et al., Ismb (1995), 5, 294-302), on the 1.1 kb and 1.2 Kb upstream of the site of initiation of the sequences SEQ ID No. 2 and 5, respectively, making it possible to identify 193 and 233 putative sites for binding to the transcription factors, in humans and mice during the first stage of the search. These are collated in Tables 1 and 2. After compiling and filtering as described above, and comparing the human and murine regulatory sequences, two modules common to the human and murine regulatory sequences were determined, and 5 and 3 possible sites for binding of various transcription factors were selected in the modules 1 and 2, respectively, on the human and murine sequences. The position with the filtration scores for the sites for binding to the transcription factors identified in the 1111 bp of the sequence SEQ ID No. 2 according to the invention, as well as in the 1220 bp of the sequence SEQ ID NO: 5 according to the invention, are presented in Table 3. The various binding sites are also schematically represented in FIG. 1.

[0123] The positions of the starting nucleotides in each of the sites for binding to the transcription factors are designated with reference to the numbering of the nucleotides of the sequences SEQ ID No. 2 and No: 5 relative to the site of initiation of transcription +1, contained in the sequences SEQ ID No. 1 and No. 4, as represented in FIG. 1.

[0124]
FIG. 2 represents the sequence SEQ ID NO: 1, which contains the sequence SEQ ID No. 2. The first nucleotide at position 5′ of the sequence of FIG. 2 is also the first nucleotide at position 5′ of one of the nucleotide sequences SEQ ID No. 1 and SEQ ID No. 2. In FIG. 2, the sites for binding to the transcription factors are illustrated in bold characters which delimit their respective positions, and their respective designations are indicated above each of the corresponding boxes. The numbering of the nucleotides of the sequence represented in FIG. 2 was carried out relative to the site of initiation of transcription, numbered “+1”, the nucleotide 5′ of the nucleotide +1 being itself numbered “−1”.

[0125]
FIG. 3 represents the sequence SEQ ID NO: 4, which contains the sequence SEQ ID No. 5. The first nucleotide at position 5′ of the sequence of FIG. 3 is also the first nucleotide at position 5′ of one of the nucleic sequences SEQ ID No. 4 and SEQ ID No. 5. In FIG. 3, the sites for binding to the transcription factors are illustrated in bold characters which delimit their respective positions, and their respective designations are indicated above each of the corresponding boxes. The numbering of the nucleotides of the sequence represented in FIG. 3 is relative to the site of initiation of transcription, numbered “+1”, the nucleotide in 5′ of the nucleotide +1 being itself numbered “−1”.

[0126] The genomic analysis of the nucleic acids regulating the human and murine sequences SEQ ID NO: 2 and 5, revealed two regulatory modules which were denoted module 1 and module 2, and are particularly conserved in humans and mice. These two regulatory modules comprise ubiquitous transcription factor binding sites, such as NF1, NFY and AP4, as well as sites for binding of transcription factors specific to the liver such as CEBP and HNF3B. This is compatible with the experimental expression data presented in Example 3 below, and provided by Kaminski et al. (supra), which show expression of the ABCA7 gene in human fetal hepatic tissues.

[0127] The two regulatory modules conserved in mice and humans also comprise sites for binding of transcription factors such as GFI1 and NFkappaB (NFkB), which are essentially present in the lymphatic organs.

[0128] The description of the characteristics of the sites for binding to each of the transcription factors designated in FIGS. 2 and 3 as well as in Table 3 can be easily found by persons skilled in the art. A short description of some of them is made below.

[0129] NFI factor:

[0130] The binding characteristics of the NF1 factor can be found in particular in the following entries of the Medline database: 88319941, 91219459, 86140112, 87237877, 90174951,89282387, 90151633,892618136, 86274639,87064414, 89263791. The NF1 factor recognizes the following palindromic sequence: “TGGCANNNTGCCA (NNTTGGCNNNNNNNNCCNN)” which is present in viral and cellular promoters and at the level of the origin of replication of type 2 adenoviruses. These proteins are capable of activating transcription and replication. They bind to DNA in the form of a homodimer.

[0131] NFY Factor:

[0132] The NFY factor is in particular described in entry No. P25.208 of the Swissprot database. It is a factor which recognizes a CCAAT″ unit in the promoter sequences such as those of the gene encoding type 1 collagen, albumin and -actin. It is a stimulator of transcription.

[0133] AP4 Factor:

[0134] Persons skilled in the art will be able to advantageously refer to the articles corresponding to the following entries of the Medline database: 2123466, 2833704, 8530024. The AP4 factor has a domain for binding to DNA of the “helix loop helix” (bHLH) type as well as two dimerization domains. The consensus sit e of the AP4 factor is the following “CWCAGCTGGN”, and the latter generally overlaps with a binding site for the AP1 factor.

[0135] CEBP

[0136] The characteristics for binding to the CEBP factor may be found in particular in the following entries of the Medline database: 93315489, 91248826, 94193722, 93211931, 92390404, 90258863, 94088523, 90269225 and 96133958. It is an important transcription activator in the regulation of genes involved in the immune and inflammatory responses. It binds specifically to an IL-1 response element in the gene for IL-6. It presumably plays a role in the regulation of the acute phase of the inflammation and in hematopoiesis. The consensus recognition site is the following: “T(T/G) NNGNAA(T/G)”.

[0137] HNF3B Factor:

[0138] Persons skilled in the art will be able to advantageously refer to the article by Overdier et al. (1994, Mol. Cell Biol. 14: 2755-2766), as well as to the following entries of the Medline database: 91352065, 91032994, 92345837, 89160814, 91187609, 91160974, 91029477, 94301798 and 94218249. This transcription factor acts as activator of numerous genes in the liver such as the AFT gene and the genes for albumin and tyrosine aminotransferase and interacts with cis-acting regulatory regions of these genes.

[0139] GFI1

[0140] The characteristics for binding to the GFI1 factor may be found in particular in the following entries of the Medline database: 10762661, 9931446, 9571157, 9285685, 9070650 and 7789186. The GFI1 gene encodes a zinc finger protein involved in the transcriptional regulation and more particularly in the interleukin-2 signaling pathway. The consensus recognition site is the following: “NNNNNNAAATCANNGNNNNNNN”

[0141] NFkappa-B Factor:

[0142] Persons skilled in the art will be able to advantageously refer to the articles corresponding to the following entries of the Medline database: 95369245, 91204058,94280766, 89345587, 93024383,88248039, 94173892,91088538, 91239561, 91218850,92390404, 90156535,93377072, 92097536, 93309429, 93267517, 92037544, 914266911, 91105848 and 95073993. The NFkappa-B factor is a heterodimer consisting of a first subunit of 50 kDa and a second subunit of 65 kDa. Two heterodimers may form a labile tetramer. Its binding to DNA depends on the presence of zinc (Zn++). It may be induced by numerous agents such as TNF, PKA or PKC. It is a key regulator of genes involved in responses to infection, inflammation and stress.

[0143] An essential characteristic of the regulatory nucleic acid according to the invention, and more particularly of the sequence located upstream of the site of initiation of transcription included both in the sequence SEQ ID No. 2 and in the sequence SEQ ID No. 5 is the presence of motifs characteristic of putative sites for binding to transcription factors involved in the gene expression of the T lymphocytes, such as the transcription factors CEBP, NFKB and GFI1.

[0144] GFI1 is a protooncogene which encodes a zinc finger nuclear protein involved in the cytokine signaling pathway and in the clonal amplification of the T cells (Zweidler-McKay, et al., Mol. Cell. Biol. (1966), 16(8), 4024-4034). The transcription factor GFI1 which acts as a transcriptional repressor of the genes which inhibit the activation of the T cells and oncogenesis. It is specifically present in the thymus, the spleen and the T lymphocytes.

[0145] The transcription factors CEBP and NFkappaB which are expressed in the thymus, the spleen and the T lymphocytes are well known to persons skilled in the art and act in cooperation in the mediation of the induction of the expression of the genes of the T lymphocytes (Runch et al., 1994) and of the HepB3 cells (Shimizu et al., Gene, (1994) 149, 305-310).

[0146] The positions of the starting nucleotides, relative to the site of initiation of transcription which are at −498 and −469 for the CEBP sites, and at −260 for the NFkB site, on the human regulatory module, and at −787 and −760, for the CEBP sites, and at −301 for the NFKB site, show that the two regulatory sites are more distant in the mouse promoter. However, it is probable that the two sites are closer in a three-dimensional structure so as to allow coactivation by the two factors CEBP and NFkB.

[0147] The presence of these potential sites for binding to CEBP and to NFkB in a manner conserved in humans and mice on the regulatory nucleic acids according to the invention is compatible with the observation according to which the expression of the gene encoding the human ABCA7 protein is predominant in the hematopoietic tissues and the T lymphocytes, and is thought to be most probably involved in cellular mediation of immunity, in particular in the pathogenesis of atherosclerosis (Kaminski et al., Supra).

[0148] As already mentioned above, the invention relates to a nucleic acid comprising a polynucleotide having at least 20 consecutive nucleotides of one of the nucleotide sequences SEQ ID No. 1 or 2, and SEQ ID No. 4 or 5, as well as a nucleic acid having a complementary sequence.

[0149] Included in the above definition are the nucleic acids comprising one or more “biologically active” fragments of one of the sequences SEQ ID No. 1 or 2, and SEQ ID No. 4 or 5. Persons skilled in the art can easily obtain biologically active fragments of these sequences, by referring in particular to Table 3 above as well as to FIGS. 2 and 3 in which the various characteristic units of the sequence for regulating the ABCA7 gene are present. Persons skilled in the art can thus obtain such biological active fragments by total or partial chemical synthesis of the corresponding polynucleotides or by causing restriction endonucleases to act in order to obtain desired DNA fragments, it being possible for the restriction sites present on the sequences SEQ ID No. 1 to SEQ ID No. 5 to be easily found from the sequence information, with the aid of common software packages for restriction mapping such as GCG version 9.1 map module.

[0150] The production of defined nucleic acid fragments with the aid of restriction endonucleases is for example described in the manual by Sambrook et al., (Molecular cloning: a laboratory manual, 2ed. Cold Spring Harbor Laboratory, Cold spring Harbor, N.Y. (1989).

[0151] The invention therefore also relates to a nucleic acid as defined above, which is capable of modulating the transcription of a polynucleotide placed under its control.

[0152] According to a first preferred embodiment, a biologically active fragment of a nucleic acid for regulating transcription according to the invention comprises a first conserved module (module 2) which comprises the core promoter (TATA box) ranging from the nucleotide at position −1 to the nucleotide at position −390, relative to the site of initiation of transcription, the first nucleotide transcribed being the nucleotide at position 1112 of the nucleotide sequence SEQ ID No. 1, or the nucleotide at position 1221 of the nucleotide sequence SEQ ID NO: 4.

[0153] According to a second embodiment, a biologically active fragment of a nucleic acid for regulating transcription according to the invention comprises the conserved modules 1 and 2 (FIG. 1) from the nucleotide at position −1 to the nucleotide at position −860, relative to the site of initiation of transcription, the first nucleotide transcribed being the nucleotide at position 1112 of the nucleotide sequence SEQ ID No. 1, or the nucleotide at position 1221 of the nucleotide sequence SE ID NO: 4.

[0154] According to a third embodiment, such a biologically active fragment of an acid for regulating transcription according to the invention comprises, in addition to the core promoter and the proximal regulatory elements, also other regulatory elements such as the various sites GFI1, HNF3B, CEBPB, NF1 and extends from the nucleotide at position −1 to the nucleotide at position −1111, relative to the site of initiation of transcription, the first nucleotide transcribed being the nucleotide at position 1112 of the nucleotide sequence SEQ ID No. 1, and to the nucleotide at position −1220, relative to the site of initiation of transcription, the first nucleotide transcribed being the nucleotide at position 1221 of the nucleotide sequence SEQ ID No. 4.

[0155] Analysis of Exon 1

[0156] The applicant has also identified the nucleotide sequences located downstream of the site of initiation of transcription and corresponding to the 5′ end of exon 1, human and murine genes encoding the ABCA7 protein.

[0157] More precisely, the 5′ end of exon 1, having a size of 1210 nucleotides, starts with the nucleotide at position 1112 of the sequence SEQ ID No. 1 and ends with the nucleotide at position 2322 of the sequence SEQ ID No. 1. The 5′ end of exon 1 is identified as the sequence SEQ ID No. 3 and the complete sequence of exon 1 is identified as the sequence SEQ ID No. 6.

[0158] Exon 1 contains the beginning of the open reading phase of the human ABCA7 gene, the nucleotide A of the ATG codon being located at position 1208 of the sequences SEQ ID No. 3 and 6. Exon 1 encodes the polypeptide having the sequence SEQ ID No. 7.

[0159] Exon 1 is likely to contain elements for regulating the expression of the ABCA7 gene, in particular elements of the amplifying enhancer type and/or elements of the silencer or repressor type.

[0160] Consequently, a nucleic acid for regulating transcription according to the invention may also contain, in addition to biologically active fragments of the sequence SEQ ID No. 1, also nucleotide fragments, or even the entire sequences SEQ ID No. 2 to SEQ ID No. 3 and 6.

[0161] The nucleotide sequences SEQ ID No. 1 to SEQ ID No. 3 and 6, as well as their fragments, may in particular be used as nucleotide probes or primers for detecting the presence of at least one copy of the ABCA7 gene in a sample, or for amplifying a defined target sequence in the sequence for regulating the ABCA7 gene.

[0162] The subject of the invention is therefore also a nucleic acid having at least 80% nucleotide identity with a nucleic acid as defined above, in particular obtained from one of the sequences SEQ ID No. 1 to SEQ ID No. 3 and 6.

[0163] The invention also relates to a nucleic acid which hybridizes, under high stringency conditions, with any one of the nucleic acids according to the invention, in particular a nucleic acid obtained from a sequence chosen from the sequences SEQ ID No. 1 to SEQ ID No. 3 and 6.

[0164] The invention also relates to a nucleic acid as defined above and characterized, in addition, in that it is capable of modulating the transcription of a polynucleotide of interest placed under its control.

[0165] According to a first aspect, such a nucleic acid is capable of activating the transcription of the polynucleotide of interest placed under its control.

[0166] According to a second aspect, a regulatory nucleic acid according to the invention may be characterized in that it is capable of inhibiting the transcription of the polynucleotide of interest placed under its control.

[0167] Preferably, a nucleic acid for regulating transcription according to the invention, when it is suitably located relative to a polynucleotide of interest whose expression is sought, will allow the transcription of said polynucleotide of interest, either constitutively or inducibly.

[0168] The inducible character of the transcription initiated by a regulatory nucleic acid according to the invention may be conferred by one or more of the regulatory elements which it contains, for example the presence of one or more sites as defined above in the sequence SEQ ID No. 1 or SEQ ID No. 2.

[0169] Furthermore, a tissue-specific expression of the polynucleotide of interest may be sought by placing this polynucleotide of interest under the control of a regulatory nucleic acid according to the invention which is capable, for example, of initiating the transcription of this polynucleotide of interest specifically in certain categories of cells, for example cells of the hematopoietic tissue, such as the peripheral leukocytes, thymus cells, spleen cells and bone marrow.

[0170] Preferably, a regulatory nucleic acid according to the invention may comprise one or more “discrete” regulatory elements such as enhancer and silencer elements. In particular, such a regulatory nucleic acid may comprise one or more potential sites for binding to the transcription factors as defined in FIG. 2.

[0171] A regulatory acid according to the invention also includes a sequence which does not comprise the core promoter, that is to say the sequence ranging from the nucleotide at position −1 to the nucleotide at position −25, relative to the site of initiation of transcription.

[0172] Such a regulatory nucleic acid will then preferably comprise a so-called “heterologous” core promoter, that is to say a polynucleotide comprising a “TATA” box and a “homeobox” not derived from the nucleic acid for regulating the ABCA7 gene.

[0173] Also forming part of the invention is a nucleic acid for regulating transcription comprising all or part of the sequence SEQ ID No. 1 which has been modified, for example, by addition, deletion or substitution of one or more nucleotides. Such modifications may modulate the transcriptional activity by causing an increase or on the contrary a decrease in the activity of the promoter or of the regulatory element.

[0174] Such a modification may also affect the tissue specificity of the promoter or of the regulatory element. Thus, for example, a regulatory nucleic acid according to the invention may be modified so as to stimulate transcription in only one of the tissues in which it is naturally expressed.

[0175] An acid for regulating transcription according to the invention may also be modified and be rendered inducible by a particular compound, for example by creating in the sequence an inducible site by a given therapeutic compound.

[0176] The modifications in a sequence comprising all or part of the sequence SEQ ID No. 1 and comprising the promoter or a regulatory element may be carried out with methods well known to persons skilled in the art, such as mutagenesis. The activity of the modified promoter or regulatory element may then be tested, for example by cloning the modified promoter upstream of a reporter gene, by transfecting the resulting DNA construct into a host cell and by measuring the level of expression of the reporter gene in the transfected host cell. The activity of the modified promoter can also be analyzed in vivo in transgenic animals. It is also possible to construct libraries of modified fragments which may be screened using functional tests in which, for example, only the promoters or regulatory elements having the desired activity will be selected.

[0177] Such tests may be based, for example on the use of reporter genes conferring resistance to defined compounds, for example to antibiotics. The selection of cells having a regulatory nucleic acid/reporter gene construct and containing a promoter or a regulatory element having a desired modification may then be isolated by culturing host cells transformed with such a construct in the presence of the defined compound, for example of the defined antibiotic.

[0178] The reporter gene may also encode any protein which is easily detectable, for example an optically detectable protein such as luciferase.

[0179] Consequently, the subject of the invention is also a nucleic acid comprising:

[0180] a) a nucleic acid for regulating transcription as defined above; and

[0181] b) a polynucleotide of interest encoding a polypeptide or a nucleic acid of interest.

[0182] According to a first aspect, the polynucleotide of interest whose transcription is desired encodes a protein or a peptide. The protein may be of any type, for example a protein of therapeutic interest, including cytokines, structural proteins, receptors or transcription factors. For example, in the case where transcription specifically in certain tissues is desired, such as for example in cells of the hematopoietic tissue, that is to say of the spleen, of the bone marrow, or in the peripheral leukocytes, the nucleic acid regulating transcription will advantageously comprise a nucleic acid ranging from the nucleotide at position −1 to the nucleotide at position −1111, relative to the site of initiation of transcription of the sequence SEQ ID No. 1 or 2, and ranging from the nucleotide at position −1 to the nucleotide at position −1220 SEQ ID No. 4 or 5.

[0183] In this case, the polynucleotide of interest will encode a gene involved in combating inflammation, such as a receptor for cytokines or for a superoxide dismutase. If an antitumor effect is desired, it will then be sought to stimulate the number and the activation of the cytotoxic T lymphocytes specific for a given tumor antigen.

[0184] In another embodiment, a regulatory nucleic acid according to the invention will be used in combination with a polynucleotide of interest encoding the ABCA7 protein.

[0185] As already mentioned, the polynucleotide of interest may also produce a nucleic acid, such as an antisense nucleic acid specific for a gene, the inhibition of whose translation is sought.

[0186] According to another aspect, the polynucleotide of interest whose 3 transcription is regulated by the regulatory nucleic acid is a reporter gene, such as any gene encoding a detectable protein.

[0187] Among the preferred reporter genes, there may be mentioned in particular the gene for luciferase, for -galactosidase (LacZ), for chloramphenicol acety-transferase (CAT) or any gene encoding a protein conferring resistance to a particular compound, in particular to an antibiotic.

[0188] Recombinant Vectors

[0189] The term “vector” for the purpose of the present invention will be understood to mean a circular or linear DNA or RNA molecule which is either in single-stranded or double-stranded form.

[0190] According to a first embodiment, a recombinant vector according to the invention is used in order to amplify the regulatory nucleic acid according to the invention which is inserted therein after transformation or transfection of the desired cellular host.

[0191] According to a second embodiment, it corresponds to expression vectors comprising, in addition to a regulatory nucleic acid in accordance with the invention, sequences whose expression is sought in a host cell or in a defined multicellular organism.

[0192] According to an advantageous embodiment, a recombinant vector according to the invention will comprise in particular the following elements:

[0193] (1) a regulatory nucleic acid according to the invention;

[0194] (2) a polynucleotide of interest comprising a coding sequence included in the nucleic acid to be inserted into such a vector, said coding sequence being placed in phase with the regulatory signals described in (1); and

[0195] (3) appropriate sequences for initiation and termination of transcription.

[0196] In addition, the recombinant vectors according to the invention may include one or more origins for replication in the cellular hosts in which their amplification or their expression is sought, markers or selectable markers.

[0197] By way of example, the bacterial promoters may be the Lacl or LacZ promoters, the T3 or T7 bacteriophage RNA polymerase promoters, the lambda phage PR or PL promoters.

[0198] The promoters for eukaryotic cells will comprise the HSV virus thymidine kinase promoter or alternatively the mouse metallothionein-L promoter.

[0199] Generally, for the choice of a suitable promoter, persons skilled in the art can advantageously refer to the book by Sambrook et al. (1989) cited above or to the techniques described by Fuller et al. (1996; Immunology in Current Protocols in Molecular Biology).

[0200] When the expression of the genomic sequence of the ABCA7 gene is sought, use will preferably be made of the vectors capable of containing large insertion sequences. In this particular embodiment, bacteriophage vectors such as the P1 bacteriophage vectors such as the vector p158 or the vector p158/neo8 described by Sternberg (Trends Genet., (1992) 8: 1-16; Mamm. Genome (1994) 5: 397-404) will be preferably used.

[0201] The preferred bacterial vectors according to the invention are for example the vectors pBR322(ATCC37017) or alternatively vectors such as pAA223-3 (Pharmacia, Uppsala, Sweden), and pGEM1 (Promega Biotech, Madison, Wis., UNITED STATES).

[0202] There may also be cited other commercially available vectors such as the vectors pQE70, pQE60, pQE9 (Qiagen), psiX174, pBluescript SA, pNH8A, pNH16A, pNH18A, pNH46A, PWLNEO, pSV2CAT, pOG44, pXTI, pSG(Stratagene).

[0203] These may also include the recombinant vector PXP1 described by Nordeen S K et al. (Bio Techniques, (1988), 6: 454-457).

[0204] They may also be vectors of the Baculovirus type such as the vector pVL1392/1393 (Pharmingen) used to transfect cells of the Sf9 line (ATCC No. CRL 1711) derived from Spodoptera frugiperda.

[0205] They may also be adenoviral vectors such as the human adenovirus of type 2 or 5.

[0206] A recombinant vector according to the invention may also be a retroviral vector or an adeno-associated vector (AAV). Such adeno-associated vectors are for example described by Flotte et al., Am. J. Respir., Cell Mol. Biol. (1992) 7: 349-356; Samulski et al., J. Virol. (1989) 63: 3822-3828; or McLaughlin et al., Am. J. Hum. Genet. (1996) 59: 561-569).

[0207] To allow the expression of a polynucleotide of interest under the control of a regulatory nucleic acid according to the invention, the polynucleotide construct comprising the regulatory sequence and the coding sequence must be introduced into a host cell. The introduction of such a polynucleotide construct according to the invention into a host cell may be carried out in vitro, according to the techniques well known to persons skilled in the art for transforming or transfecting cells, either in primary culture, or in the form of cell lines. It is also possible to carry out the introduction of the polynucleotides according to the invention in vivo or ex vivo, for the prevention or treatment of diseases linked to a deficiency in the transport of the ABCA7 protein.

[0208] To introduce the polynucleotides or the vectors into a host cell, persons skilled in the art can advantageously refer to various techniques, such as the technique for precipitation with calcium phosphate (Graham et al., Virology (1973) 52 456-457; Chen et al., Mol. Cell. Biol. (1987) 7: 2745-2752), DEAE Dextran (Gopal et al., Mol. Cell. Biol., (1985) 5: 1188-1190), electroporation (Tur-Kaspa et al., Mol. Cel. Biol, (1986) 6: 716-718.; Potter et al., Proc. Natl. Acad. Sci. USA (1984), 81(22), 7161-5), direct microinjection (Harland et al., J. Cell Biol (1985) 101: 1094-1095), liposomes charged with DNA (Nicolau et al., Methods Enzymol (1987) 149: 157-76; Fraley et al., Proc. Natl. Acad. Sci. USA (1979) 76: 3348-3352).

[0209] Once the polynucleotide has been introduced into the host cell, it may be stably integrated into the genome of the cell. The integration may be achieved at a precise site of the genome, by homologous recombination, or it may be randomly integrated. In some embodiments, the polynucleotide may be stably maintained in the host cell in the form of an episome fragment, the episome comprising sequences allowing the retention and the replication of the latter, either independently, or in a synchronized manner with the cell cycle.

[0210] According to a specific embodiment, a method of introducing a polynucleotide according to the invention into a host cell, in particular a host cell obtained from a mammal, in vivo, comprises a step during which a preparation comprising a pharmaceutically compatible vector and a “naked” polynucleotide according to the invention, placed under the control of appropriate regulatory sequences, is introduced by local injection at the level of the chosen tissue, for example a smooth muscle tissue, the “naked” polynucleotide being absorbed by the cells of this tissue.

[0211] Compositions for use in vitro and in vivo comprising “naked” polynucleotides are for example described in PCT Application No. WO 95/11307 as well as in the articles by Tacson et al. (Nature Med. (1996) 2(8), 888-892) and by Huygen et al., (Nat. Med. (1996) 2(8), 893-898).

[0212] According to a specific embodiment of the invention, a composition is provided for the in vivo production of a protein of interest. This composition comprises a polynucleotide encoding the polypeptide of interest placed under the control of a regulatory sequence according to the invention, in solution in a physiologically acceptable vector.

[0213] The quantity of vector which is injected into the host organism chosen varies according to the site of injection. As a guide, there may be injected between about 0.1 and about 100 μg of regulatory sequence/coding sequence polynucleotide construct into the body of an animal.

[0214] When the regulatory nucleic acid according to the invention is located on the polynucleotide construct (or vector), in such a manner as to control the transcription of a sequence comprising an open reading frame encoding the ABCA7 protein, the vector is preferably injected into the body of a patient likely to develop a disease linked to a deficiency in the ABCA7 protein.

[0215] Consequently, the invention also relates to a pharmaceutical composition intended for the prevention of or treatment of subjects affected by an ABCA7 protein dysfunction, comprising a regulatory nucleic acid according to the invention and a polynucleotide of interest encoding the ABCA7 protein, in combination with one or more physiologically compatible excipients.

[0216] Advantageously, such a composition will comprise the regulatory nucleic acid defined by one of the sequences SEQ ID No. 1 or 2, and SEQ ID No. 4 or 5, or a biologically active fragment of this regulatory nucleic acid.

[0217] The subject of the invention is, in addition, a pharmaceutical composition intended for the prevention of or treatment of subjects affected by a dysfunction in the metabolism of lipids, comprising a recombinant vector as defined above, in combination with one or more physiologically compatible excipients.

[0218] The subject of the invention is also a pharmaceutical composition intended for the prevention of or treatment of subjects affected by a dysfunction in the processes involving the immune system and inflammation, comprising a recombinant vector as defined above, in combination with one or more physiologically compatible excipients.

[0219] The invention also relates to the use of a polynucleotide construct in accordance with the invention and comprising a nucleic acid for regulating the ABCA7 gene as well as a sequence encoding the ABCA7 protein, for the manufacture of a medicament intended for the prevention of or treatment of subjects affected by a dysfunction in the metabolism of lipids or by a problem of immunological origin or of inflammatory origin.

[0220] The invention also relates to the use of a recombinant vector according to the invention, comprising, in addition to a regulatory nucleic acid of the invention, a nucleic acid encoding the ABCA7 protein, for the manufacture of a medicament intended for the prevention of or treatment of subjects affected by a dysfunction in the processes involving the immune system and inflammation.

[0221] Vectors Useful in Methods of Somatic Gene Therapy and Compositions Containing Such Vectors

[0222] The present invention also relates to a new therapeutic approach for the treatment and/or prevention of pathologies linked to the metabolism of lipids as well as for the treatment and/or prevention of pathologies linked to the dysfunction in the mechanisms of lymphocyte mediation of inflammation. It provides an advantageous solution to the disadvantages of the prior art, by demonstrating the possibility of treating pathologies, in particular pathologies linked to a dysfunction in the metabolism of lipids in myelo-lymphatic tissues, by gene therapy, by the transfer and the expression in vivo of a polynucleotide construct comprising, in addition to a regulatory nucleic acid according to the invention, a sequence encoding an ABCA7 protein which is highly presumed to be involved in the transport and/or metabolism of lipids. The invention thus offers a simple means allowing a specific and effective treatment of subjects affected by a dysfunction in the processes involving the immune system and inflammation.

[0223] Gene therapy consists in correcting a deficiency or an abnormality (mutation, aberrant expression and the like) or in bringing about the expression of a protein of therapeutic interest by introducing genetic information into the affected cell or organ. This genetic information may be introduced either ex vivo into a cell extracted from the organ, the modified cell then being reintroduced into the body, or directly in vivo into the appropriate tissue. In this second case, various techniques exist, among which various transfection techniques involving complexes of DNA and DEAE-dextran (Pagano et al., J.Virol. 1(1967) 891), of DNA and nuclear proteins (Kaneda et al., Science 243 (1989) 375), of DNA and lipids (Felgner et al., PNAS 84 (1987) 7413), the use of liposomes (Fraley et al., J.Biol.Chem. 255 (1980) 10431), and the like. More recently, the use of viruses as vectors for the transfer of genes has appeared as a promising alternative to these physical transfection techniques. In this regard, various viruses have been tested for their capacity to infect certain cell populations. In particular, the retroviruses (RSV, HMS, MMS, and the like), the HSV virus, the adeno-associated viruses and the adenoviruses.

[0224] The present invention therefore also relates to a new therapeutic approach for the treatment of pathologies linked to the transport of lipids, consisting in transferring and expressing in vivo genes encoding ABCA7 placed under the control of a regulatory acid according to the invention. It is particularly advantageous to construct recombinant viruses containing a DNA sequence comprising a regulatory nucleic acid according to the invention and a sequence encoding an ABCA7 protein involved in the metabolism of lipids, to administer these recombinant viruses in vivo, and that this administration allows a stable and effective expression of a biologically active ABCA7 protein in vivo and with no cytopathological effect.

[0225] The adenoviruses constitute particularly efficient vectors for the transfer and expression of the ABCA7 gene. In particular, the use of recombinant adenoviruses as vectors makes it possible to obtain sufficiently high levels of expression of the gene of interest to produce the desired therapeutic effect. Other viral vectors, such as retroviruses or adeno-associated viruses (AAV), allowing a stable expression of the gene are also claimed.

[0226] The present invention thus offers a new approach for the treatment and prevention of pathologies linked to dysfunctions in the metabolism of lipids and in the signaling pathways for inflammation by the lymphocytes.

[0227] The subject of the invention is therefore also a defective recombinant virus comprising a regulatory nucleic acid according to the invention and a nucleic sequence encoding an ABCA7 protein involved in the metabolism of lipids or in processes involving the immune system and inflammation.

[0228] The invention also relates to the use of such a defective recombinant virus for the preparation of a pharmaceutical composition intended for the treatment and/or prevention of dysfunctions in the signaling of inflammation by the lymphocytes.

[0229] The present invention also relates to the use of cells genetically modified ex vivo with a virus as described above, or of cells producing such as viruses, implanted in the body, allowing a prolonged and effective expression in vivo of a biologically active ABCA7 protein.

[0230] The present invention shows that it is possible to incorporate a DNA sequence encoding ABCA7 under the control of a regulatory nucleic acid as defined above into a viral vector, and that these vectors make it possible to effectively express a biologically active mature form. More particularly, the invention shows that the in vivo expression of ABCA7 may be obtained by direct administration of an adenovirus or by implantation of a producing cell or of a cell genetically modified by an adenovirus or by a retrovirus incorporating such a DNA.

[0231] The present invention is particularly advantageous because it makes it possible to induce a controlled expression, and with no harmful effect, of ABCA7 in organs which are not normally involved in the expression of this protein. In particular, a significant release of the ABCA7 protein is obtained by implantation of cells producing vectors of the invention, or infected ex vivo with vectors of the invention.

[0232] The mediator activity in the metabolism of lipids produced in the context of the present invention may be of the human or animal ABCA7 type. The nucleic sequence used in the context of the present invention may be a cDNA, a genomic DNA (gDNA), an RNA (in the case of retroviruses) or a hybrid construct consisting, for example, of a cDNA into which one or more introns would be inserted. It may also involve synthetic or semisynthetic sequences. In a particularly advantageous manner, a cDNA or a gDNA is used. In particular, the use of a gDNA allows a better expression in human cells. To allow their incorporation into a viral vector according to the invention, these sequences are advantageously modified, for example by site-directed mutagenesis, in particular for the insertion of appropriate restriction sites. The sequences described in the prior art are indeed not constructed for use according to the invention, and prior adaptations may prove necessary, in order to obtain substantial expressions. In the context of the present invention, the use of a nucleic sequence encoding a human ABCA7 protein is preferred. Moreover, it is also possible to use a construct encoding a derivative of these ABCA7 proteins. A derivative of these ABCA7 proteins comprises, for example, any sequence obtained by mutation, deletion and/or addition relative to the native sequence, and encoding a product retaining the activity of mediator of the metabolism of lipids. These modifications may be made by techniques F known to a person skilled in the art (see general molecular biological techniques below). The biological activity of the derivatives thus obtained can then be easily determined, as indicated in particular in the examples describing the measurement of the efflux of lipids from cells. The derivatives for the purposes of the invention may also be obtained by hybridization from nucleic acid libraries, using as probe the native sequence or a fragment thereof.

[0233] These derivatives are in particular molecules having a higher affinity for their binding sites, molecules exhibiting greater resistance to proteases, molecules having a higher therapeutic efficacy or fewer side effects, or optionally having new biological properties. The derivatives also include the modified DNA sequences allowing improved expression in vivo.

[0234] In a first embodiment, the present invention relates to a defective recombinant virus comprising a regulatory nucleic acid according to the invention and a cDNA sequence encoding an ABCA7 protein involved in the transport and metabolism of cholesterol. In another preferred embodiment of the invention, the DNA sequence is a gDNA sequence. The cDNA sequence encoding the ABCA7 protein, and which can be used in a vector according to the invention, is advantageously the sequence SEQ ID No. 8.

[0235] The vectors of the invention may be prepared from various types of viruses. Preferably, vectors derived from adenoviruses, adeno-associated viruses (AAV), herpesviruses (HSV) or retroviruses are used. It is most particularly advantageous to use an adenovirus, for direct administration or for the ex vivo modification of cells intended to be implanted, or a retrovirus, for the implantation of producing cells.

[0236] The viruses according to the invention are defective, that is to say that they are incapable of autonomously replicating in the target cell. Generally, the genome of the defective viruses used in the context of the present invention therefore lacks at least the sequences necessary for the replication of said virus in the infected cell. These regions may be either eliminated (completely or partially), or made nonfunctional, or substituted with other sequences and in particular with the nucleic sequence encoding the ABCA7 protein. Preferably, the defective virus retains, nevertheless, the sequences of its genome which are necessary for the encapsidation of the viral particles.

[0237] As regards more particularly adenoviruses, various serotypes, whose structure and properties vary somewhat, have been characterized. Among these serotypes, human adenoviruses of type 2 or 5 (Ad 2 or Ad 5) or adenoviruses of animal origin (see Application WO 94/26914) are preferably used in the context of the present invention. Among the adenoviruses of animal origin which can be used in the context of the present invention, there may be mentioned adenoviruses of canine, bovine, murine (example: Mav1, Beard et al., Virology 75 (1990) 81), ovine, porcine, avian or simian (example: SAV) origin. Preferably, the adenovirus of animal origin is a canine adenovirus, more preferably a CAV2 adenovirus [Manhattan or A26/61 strain (ATCC VR-800) for example]. Preferably, adenoviruses of human or canine or mixed origin are used in the context of the invention. Preferably, the defective adenoviruses of the invention comprise the ITRs, a sequence allowing the encapsidation and the sequence encoding the ABCA7 protein placed under the control of a nucleic acid according to the invention. Advantageously, in the genome of the adenoviruses of the invention, the E1 region at least is made nonfunctional. Still more preferably, in the genome of the adenoviruses of the invention, the E1 gene and at least one of the E2, E4 and L1-L5 genes are nonfunctional. The viral gene considered may be made nonfunctional by any technique known to a person skilled in the art, and in particular by total suppression, by substitution, by partial deletion or by addition of one or more bases in the gene(s) considered. Such modifications may be obtained in vitro (on the isolated DNA) or in situ, for example, by means of genetic engineering techniques, or by treatment by means of mutagenic agents. Other regions may also be modified, and in particular the E3 (WO95/02697), E2 (WO94/28938), E4 (WO94/28152, WO94/12649, WO95/02697) and L5 (WO95/02697) region. According to a preferred embodiment, the adenovirus according to the invention comprises a deletion in the E1 and E4 regions and the sequence encoding ABCA7 is inserted at the level of the inactivated E1 region. According to another preferred embodiment, it comprises a deletion in the E1 region at the level of which the E4 region and the sequence encoding ABCA7 (French Patent Application FR94 13355) are inserted.

[0238] The defective recombinant adenoviruses according to the invention may be prepared by any technique known to persons skilled in the art (Levrero et al., Gene (1991) 101: 195, EP 185 573; Graham, EMBO J. (1984) 3: 2917). In particular, they may be prepared by homologous recombination between an adenovirus and a plasmid carrying, inter alia, the DNA sequence encoding the ABCA7 protein. The homologous recombination occurs after cotransfection of said adenoviruses and plasmid into an appropriate cell line. The cell line used must preferably (i) be transformable by said elements, and (ii), contain the sequences capable of complementing the part of the defective adenovirus genome, preferably in integrated form in order to avoid the risks of recombination. By way of example of a line, there may be mentioned the human embryonic kidney line 293 (Graham et al., J. Gen. Virol. (1977) 36: 59) which contains in particular, integrated into its genome, the left part of the genome of an Ad5 adenovirus (12%) or lines capable of complementing the E1 and E4 functions as described in particular in Applications No. WO 94/26914 and WO95/02697.

[0239] Next, the adenoviruses which have multiplied are recovered and purified according to conventional molecular biological techniques, as illustrated in the examples.

[0240] As regards the adeno-associated viruses (AAV), they are DNA viruses of a relatively small size, which integrate into the genome of the cells which they infect, in a stable and site-specific manner. They are capable of infecting a broad spectrum of cells, without inducing any effect on cellular growth, morphology or differentiation. Moreover, they do not appear to be involved in pathologies in humans. The genome of AAVs has been cloned, sequenced and characterized. It comprises about 4700 bases, and contains at each end an inverted repeat region (ITR) of about 145 bases, serving as replication origin for the virus. The remainder of the genome is divided into 2 essential regions carrying the encapsidation functions: the left hand part of the genome, which contains the rep gene involved in the viral replication and the expression of the viral genes; the right hand part of the genome, which contains the cap gene encoding the virus capsid proteins.

[0241] The use of vectors derived from AAVs for the transfer of genes in vitro and in vivo has been described in the literature (see in particular WO 91/18088; WO 93/09239; U.S. Pat. No. 4,797,368, U.S. Pat. No. 5,139,941, EP 488 528). These documents describe various constructs derived from AAVs, in which the rep and/or cap genes are deleted and replaced by a gene of interest, and their use for transferring in vitro (on cells in culture) or in vivo (directly into an organism) said gene of interest. However, none of these documents either describes or suggests the use of a recombinant AAV for the transfer and expression in vivo or ex vivo of an ABCA7 protein, or the advantages of such a transfer. The defective recombinant AAVs according to the invention may be prepared by cotransfection, into a cell line infected with a human helper virus (for example an adenovirus), of a plasmid containing the sequence encoding the ABCA7 protein bordered by two AAV inverted repeat regions (ITR), and of a plasmid carrying the AAV encapsidation genes (rep and cap genes). The recombinant AAVs produced are then purified by conventional techniques.

[0242] As regards the herpesviruses and the retroviruses, the construction of recombinant vectors has been widely described in the literature: see in particular Breakfield et al., (New Biologist 3 (1991) 203); EP 453242, EP 178220, Bernstein et al. (Genet. Eng. 7 (1985) 235); McCormick, (BioTechnology 3 (1985) 689), and the like.

[0243] In particular, the retroviruses are integrating viruses, infecting dividing cells. The genome of the retroviruses essentially comprises two LTRs, an encapsidation sequence and three coding regions (gag, pol and env). In the recombinant vectors derived from retroviruses, the gag, pol and env genes are generally deleted, completely or partially, and replaced with a heterologous nucleic acid sequence of interest. These vectors may be produced from various types of retroviruses such as in particular MoMuLV (“murine moloney leukemia virus”; also called MOMLV), MSV (“murine moloney sarcoma virus”), HaSV (“harvey sarcoma virus”); SNV (“spleen necrosis virus”); RSV (“rous sarcoma virus”) or Friend's virus.

[0244] To construct recombinant retroviruses containing a sequence encoding the ABCA7 protein placed under the control of a regulatory nucleic acid according to the invention, a plasmid containing in particular the LTRs, the encapsidation sequence and said coding sequence is generally constructed, and then used to transfect a so-called encapsidation cell line, capable of providing in trans the retroviral functions deficient in the plasmid. Generally, the encapsidation lines are therefore capable of expressing the gag, pol and env genes. Such encapsidation lines have been described in the prior art, and in particular the PA317 line (U.S. Pat. No. 4,861,719), the PsiCRIP line (WO 90/02806) and the GP+envAm-12 line (WO 89/07150). Moreover, the recombinant retroviruses may contain modifications at the level of the LTRs in order to suppress the transcriptional activity, as well as extended encapsidation sequences, containing a portion of the gag gene (Bender et al., J. Virol. 61 (1987) 1639). The recombinant retroviruses produced are then purified by conventional techniques.

[0245] To carry out the present invention, it is most particularly advantageous to use a defective recombinant adenovirus. The results given below indeed demonstrate the particularly advantageous properties of adenoviruses for the in vivo expression of a protein having a lipid metabolism mediator activity. The adenoviral vectors according to the invention are particularly advantageous for a direct administration in vivo of a purified suspension, or for the ex vivo transformation of cells, in particular autologous cells, in view of their implantation. Furthermore, the adenoviral vectors according to the invention exhibit, in addition, considerable advantages, such as in particular their very high infection efficiency, which makes it possible to carry out infections using small volumes of viral suspension.

[0246] According to another particularly advantageous embodiment of the invention, a line producing retroviral vectors containing a regulatory nucleic acid according to the invention and the sequence encoding the ABCA7 protein is used for implantation in vivo. The lines which can be used to this end are in particular the PA317 (U.S. Pat. No. 4,861,719), PsiCrip (WO 90/02806) and GP+envAm-12 (U.S. Pat. No. 5,278,056) cells modified so as to allow the production of a retrovirus containing a nucleic sequence encoding an ABCA7 protein according to the invention. For example, totipotent stem cells, precursors of blood cell lines, may be collected and isolated from the subject. These cells, when cultured, may then be transfected with the retroviral vector containing the sequence encoding the ABCA7 protein under the control of its own promoter. These cells are then reintroduced into the subject. The differentiation of these cells will be responsible for cells of the hematopoietic tissue expressing the ABCA7 protein, in particular T lymphocytes which participate in the signaling of inflammation.

[0247] Advantageously, in the vectors of the invention, the sequence encoding the ABCA7 protein is placed under the control of a regulatory acid according to the invention comprising the regulatory elements allowing its expression in the infected cells, and most particularly the regulatory elements of the NFkappaB, CEBP and GFI1 type.

[0248] As indicated above, the present invention also relates to any use of a virus as described above for the preparation of a pharmaceutical composition intended for the treatment and/or prevention of pathologies linked to the metabolism of lipids or to the dysfunction linked to the processes involving the immune system and inflammation.

[0249] The present invention also relates to a pharmaceutical composition comprising one or more defective recombinant viruses as described above. These pharmaceutical compositions may be formulated for administration by the topical, oral, parenteral, intranasal, intravenous, intramuscular, subcutaneous, intraocular or transdermal route and the like. Preferably, the pharmaceutical compositions of the invention contain a pharmaceutically acceptable vehicle for an injectable formulation, in particular for an intravenous injection, such as for example into the patient's portal vein. They may relate in particular to isotonic sterile solutions or dry, in particular freeze-dried, compositions which, upon addition depending on the case of sterilized water or physiological saline, allow the preparation of injectable solutions. Direct injection into the patient's portal vein is advantageous because it makes it possible to target the infection at the level of the liver and thus to concentrate the therapeutic effect at the level of this organ.

[0250] The doses of defective recombinant virus used for the injection may be adjusted as a function of various parameters, and in particular as a function of the viral vector, of the mode of administration used, of the relevant pathology or of the desired duration of treatment. In general, the recombinant adenoviruses according to the invention are formulated and administered in the form of doses of between 104 and 1014 pfu/ml, and preferably 106 to 1010 pfu/ml. The term pfu (“plaque forming unit”) corresponds to the infectivity of a virus solution, and is determined by infecting an appropriate cell culture and measuring, generally after 48 hours, the number of plaques of infected cells. The techniques for determining the pfu titer of a viral solution are well documented in the literature.

[0251] As regards retroviruses, the compositions according to the invention may directly contain the producing cells, with a view to their implantation.

[0252] In this regard, another subject of the invention relates to any mammalian cell infected with one or more defective recombinant viruses as described above. More particularly, the invention relates to any population of human cells infected with these viruses. These may be in particular cells of blood origin (totipotent stem cells or precursors), fibroblasts, myoblasts, hepatocytes, keratinocytes, smooth muscle and endothelial cells, glial cells and the like.

[0253] The cells according to the invention may be derived from primary cultures. These may be collected by any technique known to persons skilled in the art and then cultured under conditions allowing their proliferation. As regards more particularly fibroblasts, these may be easily obtained from biopsies, for example according to the technique described by Ham (Methods Cell Biol (1980) 21a: 255). These cells may be used directly for infection with the viruses, or stored, for example by freezing, for the establishment of autologous libraries, in view of a subsequent use. The cells according to the invention may be secondary cultures, obtained for example from preestablished libraries (see for example EP 228458, EP 289034, EP 400047, EP 456640).

[0254] The cells in culture are then infected with the recombinant viruses, in order to confer on them the capacity to produce a biologically active ABCA7 protein. The infection is carried out in vitro according to techniques known to persons skilled in the art. In particular, depending on the type of cells used and the desired number of copies of virus per cell, persons skilled in the art can adjust the multiplicity of infections and optionally the number of infectious cycles produced. It is clearly understood that these steps must be carried out under appropriate conditions of sterility when the cells are intended for administration in vivo. The doses of recombinant virus used for the infection of the cells may be adjusted by persons skilled in the art according to the desired aim. The conditions described above for the administration in vivo may be applied to the infection in vitro. For the infection with retroviruses, it is also possible to coculture the cells which it is desired to infect with cells producing the recombinant retroviruses according to the invention. This makes it possible to dispense with the purification of the retroviruses.

[0255] Another subject of the invention relates to an implant comprising mammalian cells infected with one or more defective recombinant viruses as described above or cells producing recombinant viruses, and an extracellular matrix. Preferably, the implants according to the invention comprise 105 to 1010 cells. More preferably, they comprise 106 to 108 cells.

[0256] More particularly, in the implants of the invention, the extracellular matrix comprises a gelling compound and optionally a support allowing the anchorage of the cells.

[0257] For the preparation of the implants according to the invention, various types of gelling agents may be used. The gelling agents are used for the inclusion of the cells in a matrix having the constitution of a gel, and for promoting the anchorage of the cells on the support, where appropriate. Various cell adhesion agents can therefore be used as gelling agents, such as in particular collagen, gelatin, glycosaminoglycans, fibronectin, lectins and the like. Preferably, collagen is used in the context of the present invention. This may be collagen of human, bovine or murine origin. More preferably, type I collagen is used.

[0258] As indicated above, the compositions according to the invention advantageously comprise a support allowing the anchorage of the cells. The term anchorage designates any form of biological and/or chemical and/or physical interaction causing the adhesion and/or the attachment of the cells to the support. Moreover, the cells may either cover the support used, or penetrate inside this support, or both. It is preferable to use in the context of the invention a solid, nontoxic and/or biocompatible support. In particular, it is possible to use polytetrafluoroethylene (PTFE) fibers or a support of biological origin.

[0259] The present invention thus offers a very effective means for the treatment or prevention of pathologies linked to the transport of cholesterol, in particular obesity, hypertriglyceridemia, or, in the field of cardiovascular conditions, myocardial infarction, angina, sudden death, cardiac decompensation and cerebrovascular accidents.

[0260] In addition, this treatment may be applied to both humans and any animals such as ovines, bovines, domestic animals (dogs, cats and the like), horses, fish and the like.

[0261] Recombinant Host Cells

[0262] The invention also relates to a recombinant host cell comprising any one of the nucleic acids of the invention having the sequence SEQ ID No. 1 to SEQ ID No. 6, and more particularly a nucleic acid having the sequence SEQ ID NO 1 to SEQ ID No. 3.

[0263] According to another aspect, the invention also relates to a recombinant host cell comprising a recombinant vector as described above.

[0264] The preferred host cells according to the invention are for example the following:

[0265] a) prokaryotic host cells: strains of Escherichia coli (strain DH5-), of Bacillus subtilis, of Salmonella typhimurium, or strains of species such as Pseudomonas, Streptomyces and Staphylococus;

[0266] b) eukaryotic host cells: HeLa cells (ATCC No. CCL2), Cv 1 cells (ATCC No. CCL70), COS cells (ATCC No. CRL 1650), Sf-9 cells (ATCC No. CRL 1711), CHO cells (ATCC No. CCL-61) or 3T3 cells (ATCC No. CRL-6361), or cells of the Hepa 1-6 line referenced at the American Type Culture Collection (ATCC, Rockville, Md., United States of America).

[0267] c) primary culture cells obtained from an individual in whom the expression of a nucleic acid of interest, placed under the control of a regulatory nucleic acid according to the invention, is sought.

[0268] d) cells multiplying indefinitely (cell lines) obtained from the primary culture cells of c) above, according to techniques well known to persons skilled in the art.

[0269] Methods of Screening

[0270] Method of Screening in vitro

[0271] The invention provides methods for treating a subject suffering from a pathology linked to the level of expression of the ABCA7 protein. In particular, such a method of treatment consists in administering to the subject a compound modulating the expression of the ABCA7 gene, which may be identified by various methods of screening in vitro as defined below.

[0272] A first method consists in identifying compounds modulating the expression of the ABCA7 gene. According to such a method, cells expressing the ABCA7 gene are incubated with a candidate substance or molecule to be tested and the level of expression of the messenger RNA for ABCA7 or the level of production of the ABCA7 protein is then determined.

[0273] The levels of messenger RNA for ABCA7 may be determined by gel hybridization of the Northern type, well known to persons skilled in the art. The levels of messenger RNA for ABCA7 may also be determined by methods using PCR or the technique described by WEBB et al. (Journal of Biomolecular Screening (1996), vol. 1: 119).

[0274] The levels of production of the ABCA7 protein may be determined by immunoprecipitation or immunochemistry using an antibody which specifically recognizes the ABCA7 protein.

[0275] According to another method of screening a candidate molecule or substance modulating the activity of a regulatory nucleic acid according to the invention, a nucleotide construct as defined above, comprising a regulatory nucleic acid according to the invention as well as a reporter polynucleotide placed under the control of the regulatory nucleic acid, is used, said regulatory nucleic acid comprising at least one core promoter and at least one element for regulating one of the sequences SEQ ID No. 1 to SEQ ID No. 3. The reporter polynucleotide may be a gene encoding a detectable protein, such as a gene encoding a luciferase.

[0276] According to such a screening method, the cells are transfected with the polynucleotide construct containing the regulatory nucleic acid according to the invention and the reporter polynucleotide, in a stable and transient manner.

[0277] The transformed cells are then incubated in the presence or in the absence of the candidate molecule or substance to be tested for a sufficient time, and then the level of expression of the reporter gene is determined. The compounds which induce a statistically significant change in the expression of the reporter gene (either an increase, or on the contrary a decrease in the expression of the reporter gene) are then identified and, where appropriate, selected.

[0278] Thus, the subject of the invention is also a method for the in vitro screening of a molecule or substance modulating the activity of a regulatory nucleic acid according to the invention, in particular modulating the transcription of the constitutive reporter polynucleotide of a polynucleotide construct according to the invention, characterized in that it comprises the steps consisting in:

[0279] a) culturing a recombinant host cell comprising a polynucleotide of interest placed under the control of a regulatory nucleic acid according to the invention;

[0280] b) incubating the recombinant host cell with the substance or molecule to be tested;

[0281] c) detecting the expression of the polynucleotide of interest;

[0282] d) comparing the results obtained in step c) with the results obtained when the recombinant host cell is cultured in the absence of the candidate molecule or substance to be tested.

[0283] The invention also relates to a kit or box for the in vitro screening of a candidate molecule or substance capable of modulating the activity of a regulatory nucleic acid according to the invention, comprising:

[0284] a) a host cell transformed with a polynucleotide construct as defined above, comprising a reporter polynucleotide of interest placed under the control of a regulatory nucleic acid according to the invention; and

[0285] b) where appropriate, means for detecting the expression of the reporter polynucleotide of interest.

[0286] Preferably, the reporter polynucleotide of interest is the luciferase coding sequence. In this case, the regulatory nucleic acid according to the invention is inserted into a vector, upstream of the sequence encoding luciferase. This may be for example the vector pGL3-basic (pGL3-b) marketed by the company Promega (Madison, Wis., United States).

[0287] In this case, the recombinant vector comprising the luciferase coding sequence placed under the control of a regulatory nucleic acid according to the invention is transfected into the recombinant host cells whose luciferase activity is then determined after culturing in the presence or in the absence of the candidate substance or molecule to be tested.

[0288] It is possible in this case to use as controls pGL3-b vectors containing either the cytomegalovirus (CMV) promoter, the ApoAl promoter or no promoter. To test for the luciferase activity, the transfected cells are washed with a PBS buffer and lyzed with 500 μl of lysis buffer (50 mM TRIS, 150 mM NaCl, 0.02% sodium azide, 1% of NP-40, 100 μg/ml of AEBSF and 5 μg/ml of leupeptin).

[0289] 50 μl of the cell lysate obtained are then added to 100 μl of the luciferase substrate (Promega) and the measurements of activity are carried out on a spectrophotometric microplate reader, 5 minutes after the addition of the cell lysate.

[0290] The data are expressed as relative units of luciferase activity. The polynucleotide constructs producing high levels of luciferase activity in the transfected cells are those which contain a regulatory nucleic acid according to the invention contained in the sequence SEQ ID No. 1 which is capable of stimulating transcription.

[0291] For the measurements of the levels of expression of messenger RNA in a screening method according to the invention, probes specific for the messenger RNA for the reporter polynucleotide of interest are first of all prepared, for example with the aid of the multiprime labeling kit (marketed by the company Amersham Life Sciences, Cleveland, Ohio, United States).

[0292] Method of Screening in vivo

[0293] According to another aspect of the invention, compositions modulating the activity of a regulatory nucleic acid according to the invention may be identified in vivo, in nonhuman transgenic animals.

[0294] According to such a method, a nonhuman transgenic animal, for example a mouse, is treated with a candidate molecule or substance to be tested, for example a candidate substance or molecule previously selected by an in vitro screening method as defined above.

[0295] After a defined period, the level of activity of the regulatory nucleic acid according to the invention is determined and compared with the activity of an identical nonhuman transgenic animal, for example an identical transgenic mouse, which has not received the candidate molecule or substance.

[0296] The activity of the regulatory nucleic acid according to the invention which is functional in the transgenic animal may be determined by various methods, for example the measurement of the levels of messenger RNA corresponding to the reporter polynucleotides of interest placed under the control of said regulatory nucleic acid by Northern-type hybridization, or by in situ hybridization or by noninvasive biophotonic imaging (Xenogen Corporation).

[0297] Alternatively, the activity of the regulatory nucleic acid according to the invention may be determined by measuring the levels of expression of the protein encoded by the reporter polynucleotides of interest, for example by immunohistochemistry, in the case where the reporter polynucleotide of interest comprises an open reading frame encoding a protein detectable by such a technique.

[0298] To carry out an in vivo method of screening a candidate substance or molecule modulating the activity of a regulatory nucleic acid according to the invention, nonhuman mammals such as mice, rats, guinea pigs or rabbits whose genome has been modified by the insertion of a polynucleotide construct comprising a reporter polynucleotide of interest placed under the control of a regulatory nucleic acid according to the invention, will be preferred.

[0299] The transgenic animals according to the invention comprise the transgene, that is to say the abovementioned polynucleotide construct, in a plurality of their somatic and/or germ cells.

[0300] The construction of transgenic animals according to the invention may be carried out according to conventional techniques well known to persons skilled in the art. Persons skilled in the art will in particular be able to refer to the production of transgenic animals, and particularly to the production of transgenic mice, as described in U.S. Pat. No. 4,873,191 (granted on Oct. 10, 1989), U.S. Pat. No. 5,464,764 (granted on Nov. 7, 1995) and U.S. Pat. No. 5,789,215 (granted on Aug. 4, 1998), the content of these documents being incorporated herein by reference.

[0301] In brief, a polynucleotide construct comprising a regulatory nucleic acid according to the invention and a reporter polynucleotide of interest placed under the control of the latter is inserted into an ES-type stem cell line. The insertion of the polynucleotide construct is preferably carried out by electroporation, as described by Thomas et al. (1987, Cell, 51:503-512).

[0302] The cells which have been subjected to the electroporation step are then screened for the presence of the polynucleotide construct (for example by selection with the aid of markers, or by PCR or by Southern-type analysis of DNA on an electrophoresis gel) in order to select the positive cells which have integrated the exogenous polynucleotide construct into their genome, where appropriate following a homologous recombination event. Such a technique is for example described by Mansour et al. (Nature (1988) 336: 348-352).

[0303] Next, the positively selected cells are isolated, cloned and injected into 3.5-day old mouse blastocysts, as described by Bradley (1987, Production and Analysis of Chimaeric mice. In: E. J. Robertson (Ed., Teratocarcinomas and embryonic stem cells: A practical approach. IRL press, Oxford, page 113). The blastocysts are then introduced into a female host animal and the development of the embryo is continued to term.

[0304] Alternatively, positively selected ES-type cells are brought into contact with 2.5-day old embryos at an 8-16 cell stage (morulae) as described by Wood et al. (1993, Proc. Natl. Acad. Sci. USA, vol.90: 4582-4585) or by Nagy et al. (1993, Proc. Natl. Acad. Sci. USA, vol. 90: 8424-8428), the ES cells being internalized so as to extensively colonize the blastocyst, including the cells producing the germ line.

[0305] The progeny is then tested in order to determine those which have integrated the polynucleotide construct (the transgene).

[0306] The subject of the invention is therefore also a nonhuman transgenic animal whose somatic and/or germ cells have been transformed with a nucleic acid or a polynucleotide construct according to the invention.

[0307] The invention also relates to recombinant host cells obtained from a transgenic animal as described above.

[0308] Recombinant cell lines obtained from a transgenic animal according to the invention may be established in a long-term culture from any tissue of such a transgenic animal, for example by transfection of the primary cell cultures with vectors expressing oncogenes such as the SV40 large T antigen, as described for example by Chou (1989, Mol. Endocrinol. 3: 1511-1514) and Schay et al. (1991, Biochem. Biophys. Acta, 1072: 1-7).

[0309] The invention also relates to a method for the in vivo screening of a candidate molecule or substance modulating the activity of a regulatory nucleic acid according to the invention, comprising the steps of:

[0310] a) administering the candidate substance or molecule to a transgenic animal as defined above;

[0311] b) detecting the level of expression of a reporter polynucleotide of interest placed under the control of the regulatory nucleic acid;

[0312] c) comparing the results obtained in b) with the results obtained with a transgenic animal which has not received the candidate substance or molecule.

[0313] The invention also relates to a kit or box for the in vivo screening of a candidate molecule or substance modulating the activity of a regulatory nucleic acid according to the invention, comprising:

[0314] a) a transgenic animal as defined above;

[0315] b) where appropriate, the means for detecting the level of expression of the reporter polynucleotide of interest.

[0316] Pharmaceutical Compounds and Compositions

[0317] The invention also relates to pharmaceutical compositions intended for the prevention or treatment of a deficiency in the metabolism of lipids, or of a dysfunction in the processes involving the immune system and inflammation.

[0318] First, the subject of the invention is also a candidate substance or molecule modulating the activity of a regulatory nucleic acid according to the invention.

[0319] The invention also relates to a candidate substance or molecule characterized in that it increases the activity of a regulatory nucleic acid according to the invention, and most particularly of a regulatory nucleic acid comprising the sequence SEQ ID No. 1, 2, 4 or 5.

[0320] Preferably, such a substance or molecule capable of modulating the activity of a regulatory nucleic acid according to the invention was selected according to one of the in vitro or in vivo screening methods defined above.

[0321] Thus, a subject impaired in the metabolism of lipids or in immunity signaling is treated by the administration to this subject of an effective quantity of a compound modulating the activity of a regulatory nucleic acid according to the invention.

[0322] Thus, a patient having a weak ABCA7 promoter activity may be treated with an abovementioned molecule or substance in order to increase the activity of the ABCA7 promoter.

[0323] Alternatively, a patient having an abnormally high ABCA7 promoter activity may be treated with a compound capable of reducing or blocking the activity of the ABCA7 promoter.

[0324] Such a compound may be a compound which modulates the interaction of at least one transcription factor with the ABCA7 promoter or a regulatory element of a regulatory nucleic acid according to the invention.

[0325] For example, the compound may inhibit the interaction of one of the transcription factors listed in Table 1 with a regulatory nucleic acid according to the invention.

[0326] The compound may also be a compound which modulates the activity of a transcription factor which binds to the ABCA7 promoter or a regulatory element present on the latter.

[0327] A compound of therapeutic interest according to the invention may also be a compound which modulates the interaction of a first transcription factor with a second transcription factor.

[0328] As detailed in the analysis of the various transcription factors capable of binding to the sequence SEQ ID No. 1, 2, 4 or 5, some transcription factors are active only if they are combined with another transcription factor.

[0329] A compound of therapeutic interest according to the invention is preferably chosen from nucleic acids, peptides and small molecules. For example, such a compound may be an antisense nucleic acid which specifically binds to one region of the ABCA7 promoter or to a regulatory element of a nucleic acid for regulating ABCA7 and inhibiting or reducing the activity of the promoter.

[0330] This compound of therapeutic interest may also be an antisense nucleic acid which interacts specifically with a gene encoding a transcription factor modulating the activity of the ABCA7 promoter, in a manner such that the interaction of the antisense nucleic acid with the gene encoding the transcription factor binding to the ABCA7 promoter reduces the production of this transcription factor, resulting in an increase or a decrease in the activity of the ABCA7 promoter, depending on whether the transcription factor increases or on the contrary reduces the activity of the ABCA7 promoter.

[0331] The toxicity and the therapeutic efficacy of the therapeutic compounds according to the invention may be determined according to standard pharmaceutical protocols in cells in culture or in experimental animals, for example in order to determine the lethal dose LD50 (that is to say the dose which is lethal for 50% of the population tested) as well as the effective dose ED50 (that is to say the dose which is therapeutically effective in 50% of the population tested).

[0332] For all the compounds of therapeutic interest according to the invention, the therapeutically effective dose may be initially estimated from tests carried out in cell cultures in vitro.

[0333] The subject of the invention is also pharmaceutical compositions comprising a therapeutically effective quantity of a substance or molecule of therapeutic interest according to the invention.

[0334] Such pharmaceutical compositions may be formulated in a conventional manner using one or more physiologically acceptable vectors or excipients.

[0335] Thus, the compounds of therapeutic interest according to the invention, as well as their physiologically acceptable salts and solvates, may be formulated for administration by injection, inhalation or by oral, buccal, parenteral or rectal administration.

[0336] Techniques for the preparation of pharmaceutical compositions according to the invention can be easily found by persons skilled in the art, for example in the manual Remmington's Pharmaceutical Sciences, Mead Publishing Co., Easton, Pa., United States.

[0337] For a systemic administration, injection will be preferred, including intramuscular, intravenous, intraperitoneal and subcutaneous injections. In this case, the pharmaceutical compositions according to the invention may be formulated in the form of liquid solutions, preferably in physiologically compatible solutions or buffers.

[0338] Method for the Detection of an Impairment in the Transcription of the Human ABCA7 Gene

[0339] The subject of the invention is in addition methods for determining if a subject is at risk of developing a pathology linked to a deficiency in the metabolism of lipids, or in the processes involving the immune system and inflammation.

[0340] Such methods comprise the detection, in cells of a biological sample obtained from the subject to be tested, of the presence or of the absence of a genetic impairment characterized by impairment of the expression of a gene whose expression is regulated by the ABCA7 promoter.

[0341] By way of illustration, such genetic impairments may be detected in order to determine the existence of a deletion of one or more nucleotides in the sequence of a nucleic acid for regulating ABCA7, of the addition of one or more nucleotides or of the substitution of one or more nucleotides in said sequence SEQ ID No. 1, 2, 3 or 6.

[0342] According to a specific embodiment of a method for the detection of an impairment of the transcription of the ABCA7 gene in a subject, the genetic impairment is identified according to a method comprising the sequencing of all or part of the sequence SEQ ID No. 1, or alternatively of all or part of at least the sequence SEQ ID No. 2.

[0343] Sequencing primers may be constructed so as to hybridize with a defined region of the sequence SEQ ID No. 1. Such sequencing primers are preferably constructed so as to amplify fragments of about 300 to about 500 nucleotides of the sequence SEQ ID No. 1 or of a complementary sequence.

[0344] The fragments amplified, for example by the PCR method, are then sequenced and the sequence obtained is compared with the reference sequence SEQ ID No. 1 in order to determine if one or more deletions, additions or substitutions of nucleotides are found in the sequence amplified from the DNA contained in the biological sample obtained from the subject tested.

[0345] The invention therefore also relates to a method of detecting an impairment of the transcription of the ABCA7 gene in a subject, comprising the following steps:

[0346] a) sequencing of a nucleic acid fragment amplifiable with the aid of at least one nucleotide primer hybridizing with the sequence SEQ ID No. 1 or SEQ ID No. 2, according to the invention;

[0347] b) aligning the sequence obtained in a) with the sequence SEQ ID No. 1 or SEQ ID No. 2;

[0348] c) determining the presence of one or more deletions, additions or substitutions of at least one nucleotide in the sequence of the nucleic acid fragment, relative to the reference sequence SEQ ID No. 1 or SEQ ID No. 2.

[0349] In addition, also forming part of the invention are oligonucleotide probes hybridizing with a region of the sequence SEQ ID No. 1 or of the sequence SEQ ID No. 2 in which an impairment in the sequence has been determined during the implementation of the method of detection described above.

[0350] Alternatively, also forming part of the invention are oligonucleotide probes hybridizing specifically with a corresponding region of the sequence SEQ ID No. 1 or of the sequence SEQ ID No. 2 for which one or more deletions, additions or substitutions of at least one nucleotide has been determined in a subject.

[0351] Such oligonucleotide probes constitute means of detecting impairments in the sequence for regulating the ABCA7 gene and therefore also means for detecting a predisposition to the development of a pathology linked to a deficiency in the metabolism of lipids or to dysfunction in the processes involving the immune system and inflammation.

[0352] The subject of the invention is therefore also a kit or box for the detection of an impairment of the transcription of the ABCA7 gene in a subject, comprising:

[0353] a) one or more primers hybridizing with a region of the sequence SEQ ID No. 1 or of the sequence SEQ ID No. 2;

[0354] b) where appropriate, the means necessary for carrying out an amplification reaction.

[0355] The subject of the invention is also a kit or box for the detection of an impairment of the transcription of the ABCA7 gene in a subject, comprising:

[0356] a) one or more oligonucleotide probes as defined above;

[0357] b) where appropriate, the reagents necessary for carrying out a hybridization reaction.

[0358] The nucleic acid fragments derived from any one of the nucleotide sequences SEQ ID No. 1-6 are therefore useful for the detection of the presence of at least one copy of a nucleotide sequence for regulating the ABCA7 gene or a fragment or a variant (containing a mutation or a polymorphism) thereof in a sample.

[0359] The nucleotide probes or primers according to the invention comprise at least 8 consecutive nucleotides of a nucleic acid chosen from the group consisting of the sequences SEQ ID NO 1-5, or of a nucleic acid having a complementary sequence.

[0360] Preferably, nucleotide probes or primers according to the invention will have a length of 10, 12,15, 18 or 20 to 25, 35,40, 50, 70, 80, 100, 200, 500, 1000, 1500 consecutive nucleotides of a nucleic acid according to the invention, in particular a nucleic acid having a nucleotide sequence chosen from the sequences SEQ ID NO. 1-5.

[0361] Alternatively, a nucleotide probe or primer according to the invention will consist of and/or comprise the fragments having a length of 12, 15, 18, 20, 25, 35, 40, 50, 100, 200, 500, 1000, 1500 consecutive nucleotides of a nucleic acid according to the invention, more particularly of a nucleic acid chosen from the sequences SEQ ID No. 1-5, or of a nucleic acid having a complementary sequence.

[0362] The definition of a nucleotide probe or primer according to the invention therefore covers oligonucleotides which hybridize, under the high stringency hybridization conditions defined above, with a nucleic acid chosen from the sequences SEQ ID NO 1-5, 6 or 8 or with a sequence complementary thereto.

[0363] Examples of primers and pairs of primers which make it possible to amplify various regions of the ABCA7 gene are represented below.

[0364] This includes for example the pair of primers represented by the primer having the sequence SEQ ID No. 9: AGCCAGCAACGCAATCCTCC and the primer having the sequence SEQ ID No. 10: CGCACCATGTCAATGAGCCC.

[0365] A nucleotide primer or probe according to the invention may be prepared by any suitable method well known to persons skilled in the art, including by cloning and action of restriction enzymes or by direct chemical synthesis according to techniques such as the phosphodiester method by Narang et al., (Methods Enzymol (1979) 68:90-98) or by Brown et al. (Methods Enzymol (1979) 68:109-151), the diethylphosphoramidite method by Beaucage et al. (Tetrahedron Lett (1980) 22: 1859-1862) or the technique on a solid support described in patent EP 0,707,592.

[0366] Each of the nucleic acids according to the invention, including the oligonucleotide probes and primers described above, may be labeled, if desired, by incorporating a marker which can be detected by spectroscopic, photochemical, biochemical, immunochemical or chemical means.

[0367] For example, such markers may consist of radioactive isotopes (32P, 33P, 3H, 35S), fluorescent molecules (5-bromodeoxyuridine, fluorescein, acetylaminofluorene, digoxigenin) or ligands such as biotin.

[0368] The labeling of the probes is preferably carried out by incorporating labeled molecules into the polynucleotides by primer extension, or alternatively by addition to the 5′ or 3′ ends or by “nick translation”.

[0369] Examples of nonradioactive labeling of nucleic acid fragments are described in particular in French patent No. 78 109 75 or in the articles by Urdea et al. (Nucleic Acid Res (1988) 11: 4937-4957) or Sanchez-pescador et al. (J. Clin Mircrobiol (1988) 26(10) 1934-1938).

[0370] Advantageously, the probes according to the invention may have structural characteristics of the type to allow amplification of the signal, such as the probes described by Urdea et al.(Mol. Cell. Biol., (1991) 6:716-718), or alternatively in European patent No. EP-0,225,807 (CHIRON).

[0371] The oligonucleotide probes according to the invention may be used in particular in Southern-type hybridizations with genomic DNA or alternatively Northern-type hybridizations with RNA.

[0372] The probes according to the invention may also be used for the detection of products of PCR amplification or alternatively for the detection of mismatches.

[0373] Nucleotide probes or primers according to the invention may be immobilized on a solid support. Such solid supports are well known to persons skilled in the art and comprise surfaces of wells of microtiter plates, polystyrene beds, magnetic beds, nitrocellulose bands or microparticles such as latex particles.

[0374] Consequently, the present invention also relates to a method of detecting the presence of a nucleic acid as described above in a sample, said method comprising the steps of:

[0375] 1) bringing one or more nucleotide probes according to the invention into contact with the sample to be tested;

[0376] 2) detecting the complex which may have formed between the probe(s) and the nucleic acid present in the sample.

[0377] According to a specific embodiment of the method of detection according to the invention, the oligonucleotide probe(s) are immobilized on a support.

[0378] According to another aspect, the oligonucleotide probes comprise a detectable marker.

[0379] The invention relates, in addition, to a box or kit for detecting the presence of a nucleic acid according to the invention in a sample, said box comprising:

[0380] a) one or more nucleotide probes as described above;

[0381] b) where appropriate, the reagents necessary for the hybridization reaction.

[0382] According to a first aspect, the detection box or kit is characterized in that the probe(s) are immobilized on a support.

[0383] According to a second aspect, the detection box or kit is characterized in that the oligonucleotide probes comprise a detectable marker.

[0384] According to a specific embodiment of the detection kit described above, such a kit will comprise a plurality of oligonucleotide probes in accordance with the invention which may be used to detect target sequences of interest or alternatively to detect mutations in the coding regions or the noncoding regions of the nucleic acids according to the invention, more particularly of the nucleic acids having the sequences SEQ ID NO 1-5, 6 and 8 or the nucleic acids having a complementary sequence.

[0385] Thus, the probes according to the invention, immobilized on a support, may be ordered into matrices such as “DNA chips”. Such ordered matrices have in particular been described in U.S. Pat. No. 5,143,854, in PCT applications No. WO 90/150 70 and 92/10092.

[0386] Support matrices on which oligonucleotide probes have been immobilized at a high density are for example described in U.S. Pat. No. 5,412,087 and in PCT application No. WO 95/11995.

[0387] The nucleotide primers according to the invention may be used to amplify any one of the nucleic acids according to the invention, and more particularly all or part of a nucleic acid having the sequences SEQ ID NO 1-5, or alternatively a variant thereof.

[0388] Another subject of the invention relates to a method of amplifying a nucleic acid according to the invention, and more particularly a nucleic acid having the sequences SEQ ID NO 1-5 or a fragment or a variant thereof contained in a sample, said method comprising the steps consisting in:

[0389] a) bringing the sample in which the presence of the target nucleic acid is suspected into contact with a pair of nucleotide primers whose hybridization position is located respectively on the 5′ side and on the 3′ side of the region of the target nucleic acid whose amplification is sought, in the presence of the reagents necessary for the amplification reaction; and

[0390] b) detecting the amplified nucleic acids.

[0391] To carry out the amplification method as defined above, use will be advantageously made of any one of the nucleotide primers described above.

[0392] The subject of the invention is, in addition, a box or kit for amplifying a nucleic acid according to the invention, and more particularly all or part of a nucleic acid having the sequences SEQ ID NO 1-5, said box or kit comprising:

[0393] a) a pair of nucleotide primers in accordance with the invention, whose hybridization position is located respectively on the 5′ side and on the 3′ side of the target nucleic acid whose amplification is sought;

[0394] b) where appropriate, the reagents necessary for the amplification reaction.

[0395] Such an amplification box or kit will advantageously comprise at least one pair of nucleotide primers as described above.

[0396] The invention is in addition illustrated, without however being limited, by the figures and examples below.

[0397]
FIG. 1 is a schematic representation of the sites for transcription factors found in humans and mice in the promoter region of the ABCA7 genes.

[0398]
FIG. 2 illustrates the sequence SEQ ID No. 1. The position of each of the characteristic units for binding to various transcription factors is represented in bold characters, the designation of the transcription factor specific for the corresponding sequence being indicated above the nucleotide sequence.

[0399]
FIG. 3 illustrates the sequence SEQ ID No. 4. The position of each of the characteristic units for binding to various transcription factors is represented in bold characters, the designation of the transcription factor specific for the corresponding sequence being indicated above the nucleotide sequence.

[0400]
FIG. 4 illustrates the pattern of expression of the human ABCA7 gene on Northern blots of various adult and fetal tissues (Clontech) hybridized with an amplimer produced with the primers SEQ ID No. 9 and 10 (Table 4).

[0401]
FIG. 5 illustrates the pattern of expression of the murine ABCA7 gene on a Northern blot of various adult tissues hybridized with an amplimer produced with primers specific for the murine transcript.

[0402]
FIG. 6 shows a section of artery showing atherosclerosis and acute inflammation obtained at a below-the-knee amputation from a 92-year-old male. Macrophages in the organizing thrombus and within the inflammatory infiltrate in the adventitia were faintly positive for hybridization.

[0403]
FIG. 7 shows a section of bronchus obtained at autopsy from a 63-year-old asthmatic female. Respiratory epithelium showed faint hybridization. In the submucosal inflammatory infiltrate, small subsets of lymphocytes showed faint hybridization. Occasional, faint hybridization was visible in macrophages.

[0404]
FIG. 8 shows a section of colon obtained at surgery from an 81-year-old female with a clinical diagnosis of Crohn's disease. In the lamina propria, hybridization was identified in macrophages, subsets of lymphocytes, and occasional plasma cells.

[0405]
FIG. 9 shows a section of normal lymph node obtained at surgery from a 48-year-old male. Subsets of lymphocytes showed faint hybridization. In reactive germinal centers, subsets of cells showed faint to occasionally moderate hybridization. Scattered throughout the lymph node, cells resembling macrophages were positive.

[0406]
FIG. 10 shows a section of synovium obtained from a 25-year-old female with a clinical diagnosis of rheumatoid arthritis. In most areas, subsynovial histiocytes and macrophages appeared to show stronger hybridization than superficial synoviocytes. In reactive lymphoid follicles, faint to moderate hybridization was also identified in subsets of lymphocytes within germinal centers and within the corona.

[0407]
FIG. 11 shows a section of skin obtained at biopsy from a 55-year-old female with a diagnosis of psoriasis. Epidermal keratinocytes showed faint, positive hybridization. In the perivascular inflammatory infiltrate, macrophages were moderately positive. Scattered perivascular lymphocytes also appeared to be positive.

EXAMPLES

Example 1

Determination of the 5′ end of the cDNA for ABCA7

[0408] Amplification of the end of the mRNA by RT-PCR (RACE) was carried out using the SMART RACE cDNA amplification kit (Clontech, Palo Alto, Calif.). (PolyA) mRNAs extracted from human spleen tissues were used as template in order to produce a SMART 5′ cDNA library according to the manufacturer's instructions. The first amplification primers and the internal primers were chosen from the cDNA sequence. The amplifications carried out with the internal primers for PCR amplification were cloned. Specific clones were then amplified using primers whose sequences are respectively (CAGGAAACAGCTATGAC) and (GCCAGTGTGATGGATAT) and sequenced on the two strands. Finally, the primers ABCA7 L1 GCGGAAAGCAGGTGTTGTTCAC (SEQ ID No. 11) and ABCA7L2 CGATGGCAGTGGCTTGTTTGG (SEQ ID No. 12) were used to identify the end of the human ABCA7 cDNA.

Example 2

Analysis of the Promoter of the Human and Murine ABCA7 Genes

[0409] The site of initiation of transcription was located on the promoters of the human and murine genes for ABCA7 using the following three software packages: TSSG and TSSW (Solovyev et al., Ismb (1997) 5, 294-302) and NNPP (Reese M G, et al., 1999). A prediction of the binding sites for the human and murine transcription factors was made using the MatInspector program for searching for motifs (Quandt et al., Nucl. Acid Research (1995) 23(23) 4878-84). The calculation of the scores for each binding site for the transcription factors was made using the following formula: (Of−Tf)/(Tf)1/2, in which “Of” is the frequency of observation of a motif and “Tf” is the calculated frequency of a consensus motif. In order to separate the motifs which are not considered to be relevant, a first filtration step was performed by adjusting the Matlnspector program “template similarity” score above 0.85 and the “core similarity” score above 0.99. Finally, a comparative analysis of the inter-species promoters was made as described by Werner T (Models for prediction and recognition of eukaryotic promoters, Mammalian Genome (1999) 10: 168-175) in order to define the transcription modules comprising sites having a similar motif and present both on the human and murine sequences of the sequence upstream of the ABCA7 gene.

Example 3

Preferential Expression of Human and Murine ABCA7 Genes in Hematopoietic Tissues

[0410] The profile of expression of the polynucleotides according to the present invention was determined according to the protocols for PCR-coupled reverse transcription and Northern blot analysis described in particular by Sambrook et al. (ref. C S H Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989). “Molecular Cloning: A Laboratory Manual,” 2nd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.).

[0411] For example, in the case of an analysis by reverse transcription, a pair of primers was synthesized from each of the complete cDNAs of the human and murine ABCA7 genes in order to detect the corresponding cDNAs. The sequences of these primers are presented in Table 4.

[0412] The polymerase chain reaction (PCR) was carried out on cDNA templates corresponding to reverse transcribed polyA+ mRNAs. The reverse transcription to cDNA was carried out with the enzyme SUPERSCRIPT II (GibcoBRL, Life Technologies) according to the conditions described by the manufacturer.

[0413] The polymerase chain reaction was carried out according to standard conditions, in 20 μl of reaction mixture with 25 ng of cDNA preparation. The reaction mixture was composed of 400 μM of each of the dNTPs, 2 units of Thermus aquaticus (Taq) DNA polymerase (Ampli Taq Gold; Perkin Elmer), 0.5 μM of each primer, 2.5 mM MgCl2, and PCR buffer. Thirty PCR cycles (denaturing 30 s at 94° C., annealing of 30 s divided up as follows during the 30 cycles: 64° C. 2 cycles, 61° C. 2 cycles, 58° C. 2 cycles and 55° C. 28 cycles and an extension of one minute per kilobase at 72° C.) were carried out after a first step of denaturing at 94° C. for 10 min in a Perkin Elmer 9700 thermocycler. The PCR reactions were visualized on agarose gel by electrophoresis. The cDNA fragments obtained may be used as probes for a Northern blot analysis and may also be used for the exact determination of the polynucleotide sequence.

[0414] In the case of a Northern Blot analysis, a cDNA probe produced as described above was labeled with 32P by means of the DNA labeling system High Prime (Boehringer) according to the instructions indicated by the manufacturer. After labeling, the probe was purified on a Sephadex G50 microcolumn (Pharmacia) according to the instructions indicated by the manufacturer. The labeled and purified probe was then used for the detection of the expression of the mRNAs in various tissues.

[0415] The Northern blot containing samples of RNA of various human tissues (Multiple Tissue Northern or MTN; references (Human II, 7759-1, Human 7760-1, and Human Fetal II 7756-1, Clontech) was hybridized with the designated specific labeled probe for ABCA7 (2637-4881 bp).

[0416] The protocol followed for the hybridizations and washes may be either directly that described by the manufacturer (Instruction manual PT1200-1) or an adaptation of this protocol using methods known to persons skilled in the art and described for example in F. Ausubel et al. (Currents Protocols in Molecular Biology, Green Publishing Associates and Wiley Interscience NY (1989). It is thus possible to vary, for example, the prehybridization and hybridization temperatures in the presence of formamide.

[0417] For example, it may be possible to use the following protocol:

[0418] 1—Membrane Competition and PREHYBRIDIZATION:

[0419] Mix: 40 μl salmon sperm DNA (10 mg/ml)

[0420] +40 μl human placental DNA (10 mg/ml)\

[0421] Denature for 5 min at 96° C., then immerse the mixture in ice.

[0422] Remove the 2× SSC and pour 4 ml of formamide mix in the hybridization tube containing the membranes.

[0423] Add the mixture of the two denatured DNAs.

[0424] Incubate at 42° C. for 5 to 6 hours, with rotation.

[0425] 2—Labeled Probe Competition:

[0426] Add to the labeled and purified probe 10 to 50 μl Cot I DNA, depending on the quantity of repeat sequences.

[0427] Denature for 7 to 10 min at 95° C.

[0428] Incubate at 65° C. for 2 to 5 hours.

[0429] 3—Hybridization:

[0430] Remove the prehybridization mix.

[0431] Mix 40 μl salmon sperm DNA+40 μl human placental DNA; denature for 5 min at 96° C., then immerse in ice.

[0432] Add to the hybridization tube 4 ml of formamide mix, the mixture of the two DNAs and the denatured labeled probe/Cot I DNA.

[0433] Incubate 15 to 20 hours at 42° C., with rotation.

[0434] 4—Washes:

[0435] One wash at room temperature in 2× SSC, to rinse.

[0436] Twice 5 minutes at room temperature 2× SSC and 0.1% SDS.

[0437] Twice 15 minutes 0.1× SSC and 0.1% SDS at 65° C.

[0438] After hybridization and washing, the blot was analyzed after overnight exposure in contact with a phosphorus screen revealed with the aid of Storm (Molecular Dynamics, Sunnyvale, Calif.).

[0439] The results presented in FIG. 5 show that the mouse ABCA7 gene is expressed in the adult tissues. A larger quantity of murine ABCA7 mRNA was detected in the hematopoietic tissues such as the spleen and thymus, which is consistent with the expression of ABCA7 that was observed in the myelomonocytic and lymphocytic lines. No expression of the ABCA7 gene was detected in the fibroblastic cell lines.

[0440]
FIG. 4 shows a similar pattern of expression of the human ABCA7 gene with however a strong hybridization signal in the fetal liver.

Example 4

Analysis of the Gene Expression Profile for Dysfunctions in the Metabolism of Lipids, or in Inflammation Signaling

[0441] The verification of the impairment of the level of expression of the ABCA7 gene may be determined by hybridization of these sequences with probes corresponding to the mRNAs obtained from hematopoietic tissues from subjects who are affected or otherwise, according to the methods described below:

[0442] 1. Preparation of the Total RNAs, of the poly(A)+ mRNAs and of cDNA Probes

[0443] The total RNAs are obtained from hematopoietic tissues from normal or highly affected subjects by the guanidine isothiocyanate method (Chomczynski et al., Anal Biochem (1987) 162:156-159). The poly(A)+ mRNAs are obtained by affinity chromatography on oligo(dT)-cellulose columns (Sambrook et al., (1989) Molecular cloning: a laboratory manual. 2ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.) and the cDNAs used as probes are obtained by RT-PCR (DeRisi et al., Science (1997) 278:680-686) with oligonucleotides labeled with a fluorescent product (Amersham Pharmacia Biotech; CyDye T M).

[0444] 2. Hybridation and Detection of the Expression Levels

[0445] The glass slides containing the sequences according to the present invention corresponding to the ABCA7 gene are hydridized with the nucleotide probes prepared from the messenger RNA of the cell to be analyzed. The use of the Amersham/molecular Dynamics system (Avalanche Microscanner TM) allows the differential quantification of the expressions of the products of sequences on healthy or affected cell type.

Example 5

Test Intended for the Screening of Molecules Activating or Inhibiting the Expression of the ABCA7 Gene

[0446] The screening test makes it possible to identify a sequence capable of modulating the activity of synthesis of the ABCA7 protein.

[0447] 5.1 Construction of the Expression Plasmids Containing a Nucleic Acid for Regulating the Human ABCA7 Gene

[0448] The region of the acid for regulating the human ABCA7 gene ranging from the nucleotide at position −1111 up to the nucleotide at position −1, relative to the site of initiation of transcription, may be amplified by the PCR technique with the aid of the pair of primers specific for the region described above from human genomic DNA present in a BAC vector of a human BAC vector collection.

[0449] The amplified DNA fragment is digested with restriction endonuclease Sal 1, then inserted into the vector PXP1 described by Nordeen et al. (Bio Techniques, (1988) 6:454-457), at the level of the Sal 1 restriction site of this vector. The insert is then sequenced.

[0450] 5.2 Cell Culture and Transfection

[0451] Cells of the CHO or HELA line (ATCC, Rockville, Md., USA) are cultured in the E-MEM (Minimum Essential Medium with Earle's Salts) medium supplemented with 10% (v/v) fetal calf serum (BioWhittaker, Walkersville, Md.). Approximately 1.5×105 cells are distributed into each of the wells of a 12-well culture plate (2.5 cm), and are cultured up to about 50-70% confluence, and then cotransformed with 1 μg of plasmid Sal-Lucif and 0.5 μg of the control vector pBetagal (CloneTech Laboratories Inc., Palo Alto, Calif., USA) using the Superfectin Reagent Kit (QIAGEN Inc., Valencia, Calif., USA). Two hours after the addition of the DNA, the culture medium is removed and replaced with complete AMEM (Minimum Essential Medium Eagle 's Alpha Modification) medium. After a period of twenty hours, the cells are placed in fresh medium of the DMEM (Dulbecco's Minimum Essential Medium) type supplemented with 2 μg/ml of glutamine, 100 units/ml of streptomycin and 0.1% of bovine serum albumin (BSA, Fraction V), in the presence or otherwise of molecules at various concentrations.

[0452] The cells are recovered 16 hours after the last change of medium using a Lysis Solution obtained from the Tropix Luciferase Assay Kit (Tropix Inc., Bedford, Mass., USA). The cellular lysate is divided into aliquot fractions which are used to quantify the proteins using the MicroBCA Kit (Pierce, Rockford, Ill., USA) as well as to quantify the production of luciferase and beta-galactosidase using the Tropix Luciferase Assay Kit and Galacto-Light Plus Kit, respectively. The tests are carried out according to the manufacturer's recommendations. The molecules active on the ABCA7 promoter are then selected according to the ratio “luciferase activity/beta-galactosidase activity”

Example 6

In situ Hybridization Study Using ABCA7 Probe

[0453] Serial tissue sections from archival paraffin samples were hybridized with radiolabeled cRNA probes corresponding to an ABCA7 fragment. The ABCA7 fragment, which corresponds to nucleotides 594 through 1055 of GenBank sequence NM—019112, was subcloned into pCRII (Invitrogen) and transcribed in vitro with SP6 (antisense) and T7 (sense) RNA polymerases in the presence of 35S-uridine 5′-triphosphate. After transcription, the probes were column-purified and separated by electrophoresis on a 5% polyacrylamide gel to confirm size and purity.

[0454] Tissue sections were digested with proteinase K and hybridized with the probes at a concentration of approximately 3.5×107 dpm/ml for 18 hours at 65° C. Following hybridization, the slides were treated with RNAse A and washed stringently in 0.1× SSC at 70° C. for 2 hours. The slides were then coated with Kodak NTB-2 emulsion, exposed 7 days at 4° C., and developed using Kodak D-19 Developer and Fixer. Slides were stained with hematoxylin and eosin (H&E) and imaged using a DVC digital photo camera coupled to a Nikon microscope.

[0455] Hybridization signals appeared increased in markedly inflamed tissue, and were identified consistently in subsets of macrophages and lymphocytes across all samples. In macrophages, only subsets of cells showed hybridization. For example, in asthmatic samples, the submucosal inflammatory infiltrate contained positive macrophages (FIG. 7). Macrophages were also positive within inflammatory infiltrates and granulomas of Crohn's disease (FIG. 8), in psoriasis samples (FIG. 11), and in subsynovial histiocytes of rheumatoid arthritis (FIG. 10). Similarly, subsets of lymphocytes were also positive within lymphoid aggregates, germinal centers (FIG. 9), inflammatory infiltrates of Crohn's disease (FIG. 8), in psoriasis (FIG. 11), and in rheumatoid arthritis samples (FIG. 10).

1TABLE 1Sites, scores, consensus and positions relative to the site of initiation oftranscription (TSS) predicted by the NNPP, TSSG and TSSW software packages in humansCorePosition/simi-TemplateFiltrationSiteConsensusSequenceZ scoreTSS(bp)laritysimilarityComparativeGFI1_01NNNNNAAATCANNGNNNNgccactatAATCgaqayackaga3 669779−5691 000 88analysisNNNNbetweenHNF3B_01NNNTRTTTRYTYgaaTGTTggccc3 978804−5470 990 85speciesCEBPB_01RNRTKNNGMAAKNNcgttcglGGAAlga1 857489−4980 870 85CEBPB_01RNRTKNNGMAAKNNatctaglGGAAccc1 857489−4690 870 85NFI_Q6NNTTGGCNNNNNCCNNNgccTGGCagcccrgggg1 651312−4021 000 86AP4_Q6CWCAGCTGGNlgCAGCcggl12 133646−3401 000 85NFKAPPAB_01GGGAMTTYCCGGGAcctgcc9 285691−2601 000 90NFY_Q6TRRCCAATSRNcgcCCAlagc6 200634−1061 000 89Z score >=AHRARNT_01KNNKNNTYGCGTGCMScgalyagggCGTGctt10 450420−10651 000 871.96CDPCR3HD_01NATYGATSSSggGATCaagg2 474120−10041 000 87IK1_01NNNTGGGAATRCCcaagGGGAaaatg14 484154−9991 000 87NFY_Q6TRRCCAATSRNaccaIIGGgag6 200634−9781 000 87LYF1_01TTTGGGAGRattGGGAgg7 208594−9751 000 91BARBIE_01ATNNAAAGCNGRNGGagcaAAAGctgaagc32 363969−9631 000 91E47_02NNNMRCAGGTGTTMNNagccaCAGGlgaglcl15 631450−9511 000.68MYOD_01SRACAGCTGKYGccaCAGGlyagl32 908282−9491 000 89LMO2COM_01SNNCAGGTGNNNccaCAGGlagt2 232208−9491 000 95TH1EA7_01NNNNGNRTCTGGMWTTaggtgagtCTGGgt16 677521−9451 000.91GFI1_01NNNNNNAAATCANNGNNNNgglggatqaatGATTtqaggg3 609729−9341 000 93NNNNNRF2_01ACCGGAACNSggcTTCCtgg6 109000−8831 000 85NFKB_Q6NGGGGAMTTTCCNNgaggcagtTCCClc26 126380−8611 000 88CREL_01SGGRNWTTCCaggcagTTCC2 943267−8601 000 90NFKAPPAB_01GGGAMTTYCCggcaglTCCC9 285691−8501 000 91IK1_01NNNTGGGAATRCCgcaglTCCClcaa14 484154−8581 000 89STAT_01TTCCCRKAATTCCctcaa6 2814978541 000 91BARBIE_01ATNNAAAGCNGRNGGccatgagCTTTggct32 363969−8381 000 90USF_Q6GYCAGGTGNGgtctCGTGgc5 390268−8021 000 94AP2_Q6MKCCCSCNGGCGIcCCCGttggcg7 064136−7771 000 86VMYB_01AAYAACGGNNcccCGTTgggc4 360540−7761.000 89TATA_01STATAAAWRNNNNNNaaccctaTTTAtcc7 166360−7651 000.87GATA_CNGATAAGNMNNrctatTTATCc2 004465−7611 000 93GATA1_03NNNNNGAAANNGNctaltTATCctcaa2 7763547001 000 94VMYB_01AAYAACGGNNcccAACGgca4 3605487431 000 91AP2_Q6MKCCSCNGGCGctgccgCGGGag7 064136−7231 000 87AHRARNT_01KNNKNNTYGCCTGCMScccCACGcctckact10 450429−7071 000 85BARBIE_01ATNNAAAGCNGRNGGcttcAAAGctgtgga32 363969−6801 000 88AP4_Q6CWCAGCTGGNcaaaGCTGg13 133646−6771 000 87AHRARNT_01KNNKNNTYGCGTGCMSccaCACGctccattt10 450429−6641 000 87HFH1_01MAWTGTTATWIaagaGTTattt51 812065−6291 000 88IK1_01NNTGGAATRCCgagtGGGAaacgg14 484154−6031 000 89VMY8_01AAYAACGGNNggaAACGggt4 360548−5981 000 89CREL_01SGGRNYWTCCcgggttTTCC6 194143−5931 000 98JFKAPPAB65_01GGGRATTTCCcgggttTTCC28 315415−5931 000 95GFI1_01NNNNNNNNAAATCANNGNNNtlcctcaaAATCagggtagcatt3 669729−5871 000 95NNNNSTAT_01TTCCCRKAATTCCtcaaa6781497−5871 000 88STAT_01TTCCCRKAAttcgGCAA6 281497−4961 000 92BARBIE_01ATNNAAAGCNGRNNGGaccctaCTTacag32 363909−4591 000 85TH1E47_01NNNNGNRTCTGGMWTTagtcCCAGagtctgga16 677521−4321 000 88TH1E47_01NNNNGNRTCTGGMWTTcccagagtCTGGacta16 677521−4291 000 90AP4_Q6CWCAGCTGGNgaCAGCgggg12 133646−3851 000 90IK1_01NNNTGGGAATRCCcagaGGGAactcc14 484154−3741 000.90CHOP_01NNRIGCAATMCCtccTGCAattcgg22 328386−3641 000.87AP4_Q6CWCAGCTGGNcggcGCTGcg24 429942−3541 000.88AP4_Q5NNCAGCTGNNcggaGCTGcg3 791000−3541 000 92CHOP_01NNRTGCAATMCCCcggtatTGCAgcc22 328386−3461 000 93HLF_01RTTACRYAATGTTAacaac12 961423−3321 000 85IK1__01NNNTGGGAATRCCctcgTTCCCggag14 4841542851 000 88SP1_Q6NGGGGCGGGGYNggagGGCGgcctg11 119144−2761 000 86NFKB_Q6NGGGGAMTTTCCNNctGGGAcctgccgg26 126380−2621 000.87AP4_Q6CWCAGCTGGNcgCAGCtacg24.429942−1461 000 88AP4_Q5NNCAGCTGNNcgCAGCtccg3 791000−1461 000 92ATF_01CNSTGACGTNNNYCgagTGACgggcagg8 675151−1211 000 86AP1FJ_Q2RSTGACTNNNWagTGACgggca5 905504−1201 000 91AP1_Q2RSTGACTNMNWagTGACgggca5 9055041201 000 89CAAT_01NNNRRCCAATSAgtcgcCCAAtag4 415584−1081 000 86AHRARNT_01KNNNKNTYGCGTGCMScaatagcagCGTGcag10.450429−1021 000 90AHRARNT_01KNNKNNTYCGCTGCMSaggcaggggCGTGccc10 450429−861 000 92GC_01NRGGGCCGGGGCNKaaggCGCGgcggagc15.933816−281 000 92SP1_Q6NGGGGCGGGGYNaaggCGCGgcgcg11 119144−281 000 93AP4_Q6CWCAGCTGGNgcctGCTGct12 133646−91 000 86SP1_Q6NGGGGGCGGGGYNgctgGGCGgagag11 119141−21 000 90GC_01NRGGGGCGGGGCNKgctgGGCGqagga15 933816−21 000 87IK1_01NNNTGGGAATRCCcggaGGGAaggcg14 48115141 000 87AP4_Q6GWCAGCTGGNaagaCCTGLag12 133646191 000 89IK1_01NNNTGGGAATRCCgagaGGGAagacag14 484151561 000 87IK1_01NNNTGGGAATRCCcaagTCCCtggg14 4811511101 000 87IK1_01NNNTGGGAATRCCccctCGGAattag14 4841541161 000 92TST1_01NNKGAWTWANANTNNtgggAATThagggggl6 8829111191 000 87NKX25_02CWTAATTGgaATTAqg5 6750051221 000 91AP1_Q2RSTGACTNMNWtcTGACctccl5 9055041401 000 86AP1FJ_02RSTGACTNNNWtcTGACctccl5 9055041401 000 90RORA1_01NWAWNNAGGTCANctGACCtccttcc15 3812411411 000 94RORA2_01NWAWNTAGGTCANctGACCtccttcc33 9051181411 000 85NRF2_01ACCGGMGNStccTTCCggI6 1090801471 000 96ATF_01CNSTGACGTNNNYGIgITGACgacggcl8 6751511601 000 91CREB_04NSTGACGTTTMANNgITGACgacggc5 5439141611 000 87AP1_Q2RSTGACTNMNWglTGACgacgg5 9065041611 000 89AP1FJ_02RSTGACINMNWgtTGACgacgg5 9055041611 000 90GFI1_01NNNNNNAAATCANNGNNNNgaattgatcactGATTclcaagg3 6607291741 000 92NNNNCDPCR3HD_01NATYGATSSSaattGATCac2 4741201751 000 97TH1E47_01NNNNGNRTCTGGMW11tcggacaCTGGgacc16 6775212031 000 89TAL1ALPHAE47—NNNAACAGATCGKTNNNtcggacaTCTGggacc43 1621082031 000 8601TAL1BETAE47—NNNAACAGATGKTNWNtcgggacaTCTCggacc43 1621082031 000 8701E47_02NNNMRCAGGTGTTMNNtcacaacaCCTGagcc15 6314502391 000 90E47_01NSNGCAGGTGKNGNNtcacaacCTGCagc6 7081242391000 97LMO2COM_01SNNCAGGTGNNNacacaCCTGcag2 2322882411 000 97MYOD_01SRACAGGTGKYGcacaCCTGcag32 9082822411 000 87VMYB_01AAYAACGGNNgccCGTTaga4 36115482591 000 92SRY_02NWWAACAAWANNIcIlACAAaIgg8 4734582931 000 86TH1E47_01NNNNGNRTCTGGMWTTtcccCCAGatcctaag16 6775213201 000 88E4BP4_01NRTTAYGTAAYNcttgalGTAAag12 6785343411 000 86VBP_01GTTACRTNANttgatGTAAa5 0532443421.000 92CREL_01SGGRNWTTCCGGAAagaacc2 9432673521 000 85VBP_01GTTACRTNANctggcGTAAg5 0532443621 000 86TH1E47_01NNNNGNRTCTGGMWITgtacagggtCTGGgtct16 6775213671 000 92AP1FJ_Q2RSTGACTNMNWqctgGICAcc9 0188553081 000 92AP1_Q2RSTGACTNMNWgctgGTCAcc9 0188553981 000 89AP1_Q4RSTCACTMANNgcctgGTCAcc13 1485803981 000.86ER_Q6NNARGNNANNNTGACCWNNcctgGTCAcctttagaca11 6772904901 000 88ELK1_01NNNACMGGAAGTNGNNagcaaTTCCggccc15 16145254121 000 86AP1FJ_Q2RSTGACTNMNWcctcGTCAgr9 0188554201 000 93API_Q2RSTGACTNMNWcctctGTCAgr9 0188554261 000 92AP1_Q4RSTGACTMANNcctctGTCAgr13 1485864261 000 89GFI1_01NNNNNNAAATCANNGNNNNctgtcagcgtaGATTctccatct3 6607294291 000 86NNNNATF_01CNSTGACGINNNYCtgtcagcGTCAgal8 8671514301 000 90CREB_Q4NSTGACGTMANNgtcagcGTCAga11 2626904311 000 88CREB_Q2NSTGACGTAANNgtcagcGTCAga17 7828924111 000 86AP1FJ_Q2RSTGACTNMNWIrcagcGTCAga5 9055044321 000 90AP1_Q2RSTGACTNMNWIcagcGTCga5 9056044321 000 88TAL1BETAE47—NNNAACAGATGKTNNNttctccaTCTGtgta64 7663084131 000 8801TAL1BETAITF2—NNNMCAGATGKTNNNttctccgTCIGgtra64 7663064431 000 8701TAL1ALPHAE47—NNAACAGATGKTNNNttctccatCTGgtca64 7653064431 000 6901AP1FJ_Q2RSTGACTNMNWtctgtGTCAga9 0188554501 000 93AP1_Q4RSTGACTNMANNtctgCTCAga13 1485864501 000 88AP1_Q2RSTGACTMANNtctgtGTCAga9 0188554501 000 91CDPCR3HD_01NATYGATSSSaalaGATCag2 4741204801 000 95GFI1_01NNNNNAAATCANNGNNNNagctcggAATCgcgactccag3 6697294831 000 89NNNNgAP1_Q2RSTGACNMNWgcTGACIccag9 0188564951 000 94AP1FJ_Q2RSTGACTNMNWgcTGACIccag9 0158554951 000 94AP1_Q4RSTGACTMANNgcTGACIccag13 1485864951 000 91GATA1_03NNNNNGATAANNGNgtctcTATCccagc2 7763545081 000 89AP1FJ_Q2RSTGACTNMNWccTGACtctt9 018855520 1 000 92AP1_Q2RSTGACTNMNWccTGACtctt9 0188555291 000 91BARBIE_01ATNNAAAGCNGRNGGcctgactCTTctct32 3630696291 000 86AP1_Q4RSTGACTMANNccTGACtctt13 1485885291 000 88TH1E47_01NNNNGNRTCTGGMWTTctctCTGGctcc16 6775215341 000 85CP2_01GCNMNAMCMAGCTGGctcccgc3 2457335421 000 90AP2_Q6MKCCCSCNGGCGctCCCGcggtcc7 0641365461 100 88GFI1_01NNNNNNMATCANNGNNNgtccctctgagGATTaatgtacd3 6697295541 000 85NNNNAP4_Q6CWCAGCTGGNcagaGCTgg12 1336465901 000 87AP4_01WGARYCAGCTGYGGNCNKgtgcctccaGCTGggcaa178 5243296031 000 86RFX1_01NNGTNRCNNRGYAACNNctccagclygGCAActg7 2268286071 000 89AP4_Q6CWCAGCTGGNtccaGCTGgg182817946081 000 97AP4_Q5NNCAGCTGNNtccaGCTGgg2 6282446081 000 96AP4_Q6GWCAGC1GGNtcCAGCtggg16 2817946001 000 93AP4_Q5NNCAGCTGNNtcCAGCtggg2 6282446081 000 94E47_01NSNGCAGGTGKNCNNclgggcaaCTGCctg6 7081246131 000 87SREBP1_02KATCACCCCACgtgggGTGAta30 4992016821 001 00GATA1_03NNNNNGATAANNGNgggglGATAgIcca2 7763546841 000 91OLF1_01NNCNATCCCYNGRGARNagcaclTCCCctgggcylgtga64 6012706071 000 89KGNIK1_01NNNTGGGAATRCCgcacITCCCctgg14 4841540981 000 87NRF2_01ACCGGAAGNScacTTCCcct6 1090006991 000 86ANRARNT_01KNNKNNTYGCGTGCMStccctgggCGTGtga10 1504297031 000 85NFY_Q6TRRCCAATSRNctgCCAAIatt6 2006347301 000 87CDP_01CCAATAATCGATccAATAttcgtt147 4307297331 000 86GATA_CNGATAAGNMNNtgctgTTATCt2 0044657441 000 93GATA1_03NNNNNGATAANNGNgctgtTATCttcgg2 7763547451 000 98GFI1_01NNNNNNAAATCANNGNNNNgggaaaggAATCcttgcclgggc3 6897297701 000 89NNNNCP2_01GCNMNAMGMAGCTCGgctgggc3 2457337871 000 90RORA1_01NWAWNNAGGTCANggctggGGTCag76 160648071 000.85AP1_Q2RSTGACTNMNWtgpppGTCAgg5 9055048101 000 88AP1FJ_Q2RSTGACTNMNWtggggGTCAgg5 9085048101 000 91NRF2_01ACCGGAAGNScctGGAAgag6 1090805221 000 86E47_02NNNMRCAGGTGTTMNNgcttcCCAGGtgaggct15 6314508321 000 86ATF_01CNSTGACGTNNNYCIggTGACpgaaagcg8 6751518601 000 92CREB_Q4NSTGACGTMANNggTGACgaaagc16 9814678611 000 94AP1_Q2RSTGACTNMNWggTGACgaaag9 0186558611 000 92CREB_Q2NSTGACGTAANNggTGACgaaagc26 7302218611 000 95APIFJ_Q2RSTGACTNMNWggTGACgaaag9 0188558611 000 95CREBP1_Q2NSTGACGTMASNggTGACgaaagc22 1277148611 000 89API_Q4RSTGACTMANNggTGACgaaag13 1405868611 000 91CREB_01TGACGTMATGACgaaa4 1762038631 000 86AP4_01WGARYCAGCTGYGGNCNKaagtcccaGCTGtcagc178 5243299171 000 88AP4_Q6CWCAGCTGGNcccaGCTGtc182817949271 000 97AP4_Q6CWCAGCTGGNccCAGCtgtc182817949221 000 94AP4_Q5NNCAGCTGNNcccaGCTGtcc2 6282449221 000 98AP4_Q5NNCAGCTGNNccGAGClglc2 6282449221 000 96AP1FJ_Q2RSTGACTNMNWcagclGTCAgc5 9055049241 000 91AP1_Q2RSTGACTNMNWcagctGTCAgc59055049241 000 89GF1_01NNNNNNAAATCANNGNNNNtggcagccAATCagatgcga3 6607299551 000 90NNNNcCAAT_01NNNRRCCAATSAggcagCCAAtca4 4155849561 000 98NFY_CNCTGATTGGYTASYggcagCCAATcaga69 8367039561 000 96NFY_Q6TRRCCAATSRNcagCCAAtcag6 2006349581 000 96AP4_Q6CWCAGCTGGNgacgGCTGcg12 1336469761 000 86AP2_Q6MKCCCSCNGGCGcggctgCGGGtt7 0641369781 000 91NFY_Q6TRRCCAATSRNcccaTTGGttt6 2006319951 000 95CAAT_01NNNRRCCAATSAccaTTGGtttac4 4155849961 000 91TATA_01STATAAAWRNNNNNNggagcctcTTTAtcg7 16636010251 000 86GATA_CNGATAAGNMNNcctcITTATCg2 00446510291 000 92GATA1_03NNNNNGATAANNGNdcttTATCgaglg2 77635410301 000 93AP1_Q2RSTGACTNMNWagTGACtactg901885510401 000 93AP1_Q4RSTGACTMANNagTGACtactg13 14858610401 000 93AP1FJ_02RSTGACTNMNWagTGAClaclg9 01885510401 000 94GFI1_01NNNNNNAAATCANNGNNNNctcgdctAATCagagrttagg3 60072010561 000 94NNNNSTAT1_01NNNSANTTCCGGGMNTGNcagagcttccaGGAAccctgc155 09417510671 000 85SNSTAT_01TTCCCRKAATTCCaggaa6 28149710731 000 95STAT_01TTCCCRKAAttccaGGAA628149710731 000 97GATA1_03NNNNNNGATAANNGNIgIggGATAaaga2 77635410901 000 95GATA_CNGATAAGNMNNgGATAAaggaa2 00446510941 000 94BARBIE_01ATNNMAGCNCRNGCGIcagAAAGgggcagg32 36396911111 000 86NFKB_Q6NGGGGAMTTTCCNNcaGGGAgttgcgcg26 12638011221 000 88NFKAPPAB_01 GGGAMTTYCCGGGAgtlgcc9 28569111241 000 93AP2_Q6MKCCCSCNGGCGtgCCCGcagccg7 05413611301 000 90AP4_Q6CWCAGCTGGNcgCAGCcgca12 13364611341 000 86XBP1_01NNGNTGACGTGKNNNWTgcaccgcACGTcttcag21 30233811411 000 85VMYB_01AAYAACGCNNgacCGTTgtc4 36054811611 000 93ER_Q6NNARGNNANNNTGACCYNNgaccgttgtccTGACctct11 67729011611 000 86AP1FJ_Q2RSTGACTNMNWccTGACctctc2 79215311701 000 90RORA1_01NWAWNNAGGTCANctGACCtctctgt7 61606411711 000 92NF1_Q6NNTTGGCNNNNNNCCNNNaagagaaggtgGCCAaga1 651312−10931 000 94DELTAEF1_01NNNCACCTNANagaAGGTggcc0 830664−10901 000 93CoreCMYB_01NNNNNNGNCNGTTGNNggccagagaGTTGgcgt0 187475−10831 000 86similarity >=NF1_Q6NNTTGGCNNNNNNCCNNNagtTGGCgtcatgagg1.651312−10741 000 910.99MZF1_01NGNGGGGAtgtGGGGa−0 225601−10351 000 99TemplateIK2_01NNNYGGGAWNNNtgtgGGGAgaga−1 019855−10351 000 60similarity >=M2F1_01NGNGGGGAttgGGGGa−0 225601−10161 000 960.851K2_01NNNYGGGAWNNNttggGGGAtggg1 0119855−10161 000 89MZF1_01NGN6GGGAtggGGGGa0 225601−10081 000 98IK2_01NNNYGGGAWNNtgGGGAtcca−1019855−10081 000 89MZF1_01NGNGGGGAcgaGGGGa0 225901−9991 000 95IK2_01NNNYGGGAWNNNcaagGGGA4cgat−1 019655−9991 000 91DELTAEF1_01NNNCACCTNANgtccACCTcaa0 830664−9871 000 961K2_01NNNYGGGAWNNNNcattGGAggag−10199559761 000 93AP4_Q5NNCAGCTGNNaaaaGCTGaa0 302731−9601 000 88MYOD_Q6NNCANCTGNYcacGGGTGag0 740149−9481 000 90DELTAEF1_01NNNCACCTNANcacAGGTgcgt0 8306049481 000 97IK2_01NNNVGGGAWNNNggccGGGActtg−1019895−9131 000 90IK2_01NNNYGGGAWNNtagaGGAgagg1019855−8981 000 86NF1_Q6NNTTGGCNNNNNNCGNNNIgggrttctgGCGAttt1 651312−8851 000 86IK2_01NNNYGGGAWNNNcagTCCCtcaa−1 019855−8571 000 91NF1_Q6NNTTGGCNNNIINNCCNNNcttTGGCtgcactcacc1 6513128311 000 93DELTAEF1_01NNNCACCTNANctctACCTtac0 830664−8201 000 88NMYC_01NNNCACGTGNNNagtctCGTGgcc0 3036068031 000 88CMYB_01NNNNNNGNCNGTTGNNatgtctccccGTTGgrga0 187475−7821 000 90IK2_01NNNYGGGAWTNNNtgtcTCCCcgtt−1019856−7811 000 88MZF1_01NGNGGGGAICCCCgtt−0 229801−7771 000 96VMYB_02NSVAACGGNccCGTTggc0 427098−7751 000 96NF1_Q6NNTTGGCNNNNNNCCNNNcgTGGCgaactcctctt1 651312−7731 000 94GATA1_04NNCWGATARNNNNctattTATCccta1 126824−7601 000 92GATA1_02NNNNNGATANKGNNctcTTATCctcaa1 132907−7601 000 89LMO2COM_02NMGATANSGattTATCct0 679503−7581 000 88CMYB_01NNNNNNGNCNGTTGNNgtccCAACggctgcca0 187475−7461 000 94VMYB_02NSYAACGGNcccAACGgc0 327098−7431 000 99DELTAEF1_01NNNCACCTNANIgcACCTcct0 830664−7321 000 93IK2_01NNNYGGGAWNNNccgcGGGAgccg1 019955−7201 000 89IK2_01NNNYGGGAWNNNgcrgTCCCcacg−1 019955−7121 000 91MZF1_01NGGGGAIKCCCCarg0 6679407081 000 99IK2_01NNNYGGAWNNNactctCCCagc−1 0199556941 000 88MZF1_01NGNGGGAtCCCCagc0 687940−6901 000 97AP4_Q5NNCAGCTGNNccCAGCgcct0 302731−6881 000 86AP4_Q5NNCAGCTGNNcaaaGCTtg14654876771 000 90IK2_01NNNYGGGAWNNNacgcTCCCatt−1019855−6601 000 91AP4_Q5NNGAGCTGNNttCAGCttca0 302731−6601 000 87DELTAEF1_01NNNCACCTNANcttcACCTCcca0 830684−6451 000 95IK2_01NNNYGGGAWNNNgagtGGAaacg1 019855−6031 000 96VMYB_02NSYAACGGNggaAACGgg0 327098−9581 000 9088_01NNNNNYAATTNactaTAATcggagact−0 676908−5861 000 86NF1_Q6NNTTGGCNNNNNNCCNNNNIgTGGCcccctcccct1 651312−5441 000 95IK2_01NNNYGGGAWNNNccccTCGCcctc−10198555371 000 87MZF1_01NGNGGGGAtCCCCctr0 225601−5311 000 96IK2_01NNNYGGGAWNNgtagTCCCagag−1010865−4341 000 961K2_01NNNYGGGAWNNtagaGGGAgcct−1 019055−4101 000 88NF1_Q6NNTTGGCNNNNNNCCNNNgaggagcctgGCCAgtc1 851312−4081 000 88MZF1_01NGNGGGGAcccGGGGa0 2256013911 000 95IK2_01NNINYGGGAWNNNcccgGGGAcagc1 0108553911 000 89AP4_Q5NNCAGCTGNNgaCAGCgggg1 465487−3851 000 92IK2_01NNNYGGGAWNNNagcgGGGAcaga−1 010855−3821 000 88MZF1_01NGNGGGGAagcGGGGa−0 225601−3821 000 99IK2_01NNNYGGCAWNNNcagaGGGAactc−1 019855−3741 000 94CEBPB_01RNRTKNNGMAAKNNaactcctGGAAttc1 857489−3671 000 88AP4_Q5NNCAGCTGNNtgCAGCcggt1 465487−3401 000 90ARNT_01NNNNNCACGTGNNNNNtatacaaCGTGgggag0 305357−3301 000 88MZF1_01NGNGGGGAcgtGGCGa0 607040−3231 000 99IK2_01NNNYGGCAWNNNcgtgGGGAggca−1 019855−3231 000 88IK2_01NNNYGGGAWNNNlggcTGCCcaaa−1 019855−3081 000 89MZF1_01NGNGGGGAtCCCCaaa−0 225601−3041 000 96AP4_Q5NNCAGCTGNNgaCAGCgcag0 302731−2961 000 86IK2_01NNNYGGGAWNNNtcgttCCCggag−1 019855−2841 000 94CETS1P54_01NCMGGAWGYNccCGGApggc1 0327722791 000 89IK2_01NNNYGGGAWNNNgccIGGGActg−1 019855−2641 000 92NF1_06NNTTGGCNNNNCCNNNCNNNccgggcactacGCCAccc1 651312−2521 000 87CEBPB_01RNRTKNNGMAAKNNtgatcaGCAAgag1 8574892291 000 90IK2_01NNNYGGGAWNNNgcaggTCCCtta−1 0108552111 000 91IK2_01NNNYGGGAWNNNgtgaTCCCgtct−1 018855−1721 000.93IK2_01NNNYGGGAWNNNclccrCCCltgg−1 019855−1621 000 88NF1_06NNTTGGCNNNNNNCCNNNccTGGCccgcgcagctc1 651312−1561 000 92NF1_06NNTTGGCNNNNNNCCNNNcgacggagcagGCCAgtg1 651312−1381 000 86CREB_02NNGNTGACGYNNtgagTGACgggc0 972541−1221 000 88AP4_Q5NNGAGCTGNNcggcGCTGct0 302731−701 000 88DELTAEF1_01NNNCACCTNANtgttACCTgcg0 830604−641 000 85AP4AP4 Q5NNCAGCCTGNNctCAGCgac0 302731−451 000 87NKX25_05TYAAGTGcACTTgg1 905547−381 000 93NF1_Q6NNTTGGCNNNNNNCCNNNactTGGCttaaggggcgg1 651312−371 000 92IK2_01NNNYGGGAWNNNgcgcTCCCTgcc−1 010855−181 000 90AP4_Q5NNCAGCTGNNgcctGCTGct1 405487−91 000.92AP4_Q5NNCAGCTGNNIgctGCTGyy0 302731−61 000 90IK2_01NNNYGGGAWNNNcggnGGAAaggc−1 01986541 000 83AP4_Q5NNCAGCIGNNaagaGCTGag1 465487191 000 93DELTAEF1_01NNNCACCTNANggaAGGTtgaga0 830864371 000.97IK2_01NNNYCGGAVWNNNgagaGGGAagaa−1 019855581 000 93IK2_01NNNYGGGAWNNNggccGGGAggga−1 019855961 000 90IK2_01NNNYGGGAWNNNgggaGGGAtgca−1 0198551001 000 91IK2_01NNNYGGGAWNNNaagtTCCGtggg−1 0198551111 000 91SB_01NNNNNYAATTNccctgggaATTAgggg−0 6768081161 000 93IK2_01NNNYGGGAWNNNccctGGGAatta−1 0198551161 000 96CETSIP54 _01NCMGGAWGYNtcctTCCGgt1 0327721471 000 95CMYB_01NNNNNNNGNCNGTTGNNtccggtgaatGTTGacga0 1874751511 000 85CREB_02NNGNTGACGYNNatgTGACgacg0 9725411591 000 93AP4_Q5NNCAGCTGNNgacgGCTGaa0 3027311671 000 89IK2_01NWNYGGGAWNNNatctGGAacct−1 10198552091 000 93DELTAEF1_01NNNCACCTNANacacACCTgca0 8360612411 000 96MYOD_Q6NNCANCTGNYcaCACCIgra0 1758052421 000 91VMYB_02NSYAACGGNccCGTTaga0 3270982601 000 96IK2_01NNNYGGGAWNNNgcacTCCCcctt−1 0198552751 000 90MZF1_01NGNGGGGAICCCCctt−0 2258012791 000 97IK2_01NNNYGGGAWNNNccacTCCCccag−1 0198553161 000 88MZF1_01NGNGGGGAIGCCCcag−0 2256013201 000 96IK2_01NNNYGGGAWNNNNtaagTCCCgctt−1 0198553321 000 91IK2_01NNNYGGGAWNNNgaggTCCCagtt−1 0198553831 000 94CETSIP54_01NCMGGAWGYNcagtTCCGgc10327723901 000 93DELTAEF1_01NNNCACCTNANggtcACCTtta0 8306644021 000 95CEBPB_01RNRTKNNGMAAKNNacctttaGCAActt1 8574894061 000 93DELTAEF1_01NNNCACCTNANcagAGTggac0 8306644571 000.94GATA1_02NNNNNGATANKGNNgtctcTATCccagc11320075081 000 92GATA1_04NNCWGATARNNNNgtctgTATCccag11280245081 000 90LMO2COM_02NMGATANSGctcTATCcc0 6705935101 000 93IK2_01NNNYGGGAWNNNtctaTCCCagcc−10108555111 000 95IK2_01NNNYGGGAWNNNtggcTCCCgcgg−1 0108555431 000 89IK2_01NNNYGGGAWNNNgcggTCCCtctg−1 0198555511 000 91SB_01NNNNNYAATTNtctgagcgATTAtgc−0 6768085591 000 86DELTAEF1_01NNNCACCTNANataGGTgtgg0 8308845781 000.97AP4_Q5NNCAGCTGNNcagaGCTGgg1 4654875901 000.91CMYB_01NNNNNNGNCNCTTGNNtgggCAACtgcctgtctc0 1874756141 000 94NKX25_01TYAAGTGCACTTct1 9055476701 000 88GATA1_02NNNNNGATANKGNNggggtGATAtcca1 1329076041 000 93GAT1_04NNCWGATARNNNNgggIGATAgtcca1 1289246851 000.92LMO2COM_02NMGATANSGgtGATAgtc0 6795936871 000 92IK2_01NNNYGGGGAWNNNcactTCCCCtgg−1 0108556991 000 89NKX25_01TYAAGTGcACTTcc1 9055476901 000 88MZF1_01NGNGGGGAICCCCIgg−0 2236017011 000 95NFl_Q6NNTTGGCNNNNNNCCNNNtgtccagacatGCCAata1 0513127211 000 92GATA1_04NNCWGATARNNNNgctgtTATCttcg1 1289247451 000 95GTA1_02NNNNNGATANKGNNgctgtTATCttrgg1 1329077451 000 92LMO2COM_02NMGATANSGtgtTATCtt0 6795837471 000 94MZF1_01NGNGGGGAIgaGGGGa−0 2250017061 000 97IK2_01NNNYGGGAWNNNtgagGGGAaagg−1 0198557661 000 90NF1_Q6NNTTGGCNNNNNNCCNNNgcctgggctggGCCAggc1 6513127851 000 85LMOC0M_01SNNCAGGTGNNNttcCAGGtgagg0 7734148341 000 94DELTAEF1_01NNNCACCTNANtccAGGTgagg0 8306648351 000 98MYOD_Q8NNCANCTGNYtccaGGTGag0 7401498351 000 90CREB_02NNGNTGACGYNNctggTCACgaaa0 97254185191 000 94IK2_01NNNYGGGAWNNNtcggTCCCtggca−1 0198558861 000 89NKX25_01TYAAGTGttAAGTc1 9055479151 000 86IK2_01NNNYGGGAWNNNtaagTCCCcagc1 0198559161 000 90MZF1_01NGNGGGGGAtGCCCagc0 6679409201 000 97AP4_Q5NNCAGCTGNNgtCAGCCCcctg0 3027319291 000 66NF1_Q6NNTTGGCNNNNNNCCNNNcagtcctggcaGCCAatc1 6513129491 000 92NF1_Q6NNTTGGCNNNNNNCCNNNtccTGGCagccaatcaga1 6513129521 000 89AP4_Q5NNCAGCTGNNgacgGCTGcg1 4654879761 000 91IK2_01NNNYGGGAWNNNgcgcTCCCattg−1 0198559901 000 94GATA1_04NNCWGATARNNNNctcttTATCgagt1 12092410301 000 92GATA1_02NNNNNGATANKGNNctcttTATCgagtg1 13290710301 000 92LMO2COM_02NMGATANSGctTATCga0 67959310321 000.95S8_01NNNNNYAATTNActcTATcagagctt−0 67880810591 000 85AP4_Q5NNCAGCTGNNctgcGCTGtg0 30273110641 000.87IK2_01NNNYGGGAWNNNctgtGGGAtaaa1 0108551 0091 000.95GATA1_02NNNNNGATANKGNNtgtggGAIAaagga1 13290710901 000.93GATA1_04NNCWGATARNNNNgtggGATAaagga1 12892410911 000 93LMO2COM_02NMGATANSGggGATAaag0 67959310931 000.93CMYB_01NNNNNNGNCNGTTGNNggggcagggaGTTGcccg0 18747511181 000.88IK2_01NNNYGGGAWNNNggcaGGGAgttg−1 01985511201 000 89AP4_Q5NNCAGCTONNcgCAGCcgca1 46548711341 000 90ARNT_01NNNNNCACGTGNNNNNcaccgCACGtcttcag0 30535711421 000 86CMYB_01NNNNNNGNCNGTTGNNcagcccgaccGTTGtcct0 18747511551 000 93VMYB_02NSYAACGGNacGTTgtc0 32709811621 000 97IK2_01NNNYGGGAWNNtctgTCCCgtcc−1 01085511791 000.91IK2_01NNNYGGGAWNNNccgTCCCctgc−1 01985511841 000 87MZF1_01NGNGGGGAICCCCtgc−0 22560111881 000 95HNF3B_01NNNTRTTTRYTYctcTGTTtgtac3 978804−11060 990 84NoneCDPCR3HD_01NATYGATSSScgtcGATGag2 474120−10680 930 85(MatIspectorUSF_Q6GYCACGTGACgcCACAggtg5 390268−9500 880 87defaultE47_01NSNGCAGGTGKCNNgccACAGgtgagtct6 708124−9500 830 86parameters)USF_Q6GYCACGTGNCcacaGGTCag10 960075−9480 820 87USF_CNACACTGTNacAGGTCa0 301857−9470 860 92CETS1P54_01NCMGGAWGYNggctCCTgg1 0327728830 930.95CAAT_01NNRRCCAATSAcctggCCATttg4 415584−8780 860 86CEBPB_01RNRTKNNGMAAKNNcagTTCCctcaaat1 857489−8570 870 86AP2_Q6MAKCCCSCNGGCGgcCCCCcatgcg7 064136−8430 980 86USF_CNCACGTGNITCGTgg0 301857−8010 810 86CETS1P54_01NCMGGAWGYNccTGGAtgtc1 0327727870 850 92CETS1P54_01NCMGGAWGYNcaccTCCTgc1 032772−7290 930 92CETS1P54_01NCMGGAWGYNcaccTCCAgc1 032772−6420 850 89CETS1P54_01NCMGGAWGYNttctTCCAga1 032772−6110 850 90CEBPB_01RNRTKNNGNAAKNNggtTTCctcaaaa1 857489−5910 990 88CEBPB_01RNRTKNNGNAAKNNgttTTCCcaaaat1 857489−5900 870 90GC_01NRGGGGCGGGGCNKggccccCTCCccct15 933816−5400 880 91SP1_Q6NGGGGCGGGGYNgccccCTCCcccct11 119144−5390 840 93CETS1P54_01NCMGGAWGYNccccTCCTgc1 032772−5310 930 87AP2_Q6MKCCCSCNGGCGagCCCCggggac7 064136−3940 980 86AP2_Q6MKCCCSCNGGCGagccccGGGac7 064136−3940 980 88RFX1_02NNGTNRCNNNRGTAACNNcggggcacgagGGAActc7 228454−3800 880 90NFKAPPAB85_01CGGRATTTCCGGGAactcct14 122479−3700 830 69CETS1P54_01NCMGGAWGYNgaacTCCTgc2 674616−3680 930 85VMYB_01AAYAACGGNNgccGGTTata4 365048−3360 810 86TATA_01STATAAAWRNNNNNNttaTACAacgtgggg7 166360−3310 800 86LYF1_01TTTCGGAGRctCCCaaa7 208594−3050 820 85CEBPB_01RNRTKNNGMAAKNNccttaaGAAAccc1 857489−2050.990 89PAD5_CNGTGGCTCIGTGATccc4 266174−1730 900 86CAAT_01NNNRRCCAATSAgcaggCCAGga4 416584−1310 850 90USF_Q6GYCACGTGNCggccaACTGag5 390268−1280 860 89AP1_CNTGASTCANgTGAGTGac1 751881−1230 850 87AP1_CNTGASTCANgTGAGTGac1 751881−1230 860 86NFKAPPAB_01GGGAMTTYCCGGGGcgtgcc9 285691−810 900 87USF_Q6GTCACGTGNCcgCACTggc5 390268−400 860 89USF_CNCACGTGNgCACTTgg0 301857−390.840 91CETS1P54_01NCMGGAWGYNccTGGAaggt1 032772340 850 88RFX1_01NNGTNRCNNRGTAACNNaagTTCCctgggaatta7 2288281110 880 89CLOX_01NNTATCGATTANYNWtgaATTGatcactga81 9798261730 870 89CDP_02NNATCGATTANYNNtgaATTGatcactga37 3467241730 850 89LMO2COM_01SNNCAGGTGNNNggacaTCTGgga0 7734142050 820 90MYOD_Q6NNCANCTGNYgaCATCtggg0 1758052060 920 89USF_CNCACGTCNaCACCTgc0 3018572430 860 92AP2_Q6MKCCCSCNGGCGagCCCCctgccc70641362010 960 88CMYB_01NNNNNNGNCNGTTGNNccccctgcccGTTAgaac0 1874752530 840 85CETS1P54_01NCMGGAWGYNgaacTCCTgc2 6746152670 930 85AP2_Q6MKCGCSCNGGCGctCCCCCctgcc7 0641362780 980.88CEBPB_01RNRTKNNGMAAKNNaaatggaGAAActg1 8574892990 990 92VMYB_01AAYAAGGGNNagaAACTgag4 3605483050 880 87CEBPD_01RNRTKNNGMAAKNNgcttgatGTAAagg1 8574893400 930 89CEDP8_01RNRTKNNGMAAKNNatgtaaaGGAAaga1 8574893450 870 86CEBPB_01RNRTKNNGMMKNNccctggcGTAAggg1 8574893600 930 88CETS1P54_01NCMGGAWGYNaactTCCTgc1 0327724160 930 96LMO2COM_01SNNCAGGTGNNNctccaTGTGtgt0 7734144450 820.90MYOD_Q6NNCANCTGNYtcCATCtgtg−0 1758054460 920.91AP1_CNTGASTCANcTGTGTCAg1 7516814510 860 88CLOX_01NNTATCGATTANYNWaaaATAGatcaggaa81 9789364780 810 85CDP_02NWNATCGATTANYNNaaaATAGatcaggaa37 3467244780 810 88CETS1P54_01NCMGGAWGYNtcgAGGAatcg1 0327724860 930 88GATA_CNGATMGNMNNagtctCTATCc2 0044655070 890 92GC_01NRGGGGCGGGGCNKIgtgGGCAgagctg15 9338165840 810 86CETS1P54_01NCMGGAWGYNtgccTCCAgc1 0327726040 850.89LMO200M_01SNNCAGGTGNNNctccaGCTGggc0 7734146070 880 94LMO2COM_01SNNCAGGTGNNNctcCAGCIgggc0 7734146070 880 93MYOD_Q6NNCANCTGNYtcCAGCIggg1 6561026080 920 90MYOD_Q6NNCANCTGNYtccaGCTGgg1 6561026080 920 90LMO2COM_01SNNCAGGTGNNNgggcaACTGcct0 7734148150 800.91VMYB_01MYAACCGNNggcAACTgcc4.3605486160.880.86VMYB_02NSYAACGGNggcAACTgc0.3270986160 820 89MYOD_Q6NNCANCTGNYggCAACtgcc−0 1758056160.870.97GATA_CNGATAAGNMNNIGATAGtccag2 0044656880 890 88AP2_Q6MKCCCSCNGGCGttCCCCtgggcg7 0641367020 980 88USF_Q6GYCACGTGNCggcgTGTGaa5 3902887100 860.87CHOP_01NNRTGCAATMCCCgtgTGAAagtcc223263807130 800.86CETS1P54_01NCMGGAWGYNaatgTCCAgc1 0327727190 650 86OCT1_02NNGAATATKCANNNNgccaatATCgttgc11 8654477320 980 91COPCR3_01CACCRATANNTATNGCAATattcgttgctg92 3760687340 970 86VMYB_01AAYAACGGNNIgcTGTTatc4 3605487440 820 89STAT_01TTCCCRKAAttcggAGAA6 2814977540 810 88CETS1P54_01NCMGGAWGYNgcACGAggct1 0327728010 930 90AP2_Q6MKCCCSCNGGGCGaggctgGGGt7 0641368060 980 85CETS1P54_01NCMGGAWGYNtcAGGAcctg1 0327728160 930 87CETS1P54_01NCMGGAWGYNccTGGAagag1 0327728220 850 89CETS1P54_01NCMGGAWGYNgggctCCAgg1 0327728310 850 92USF_Q6GYCACGTGNCtccaGGTGag10 9601758350 820.86USF_CNCACGTGNccAGGTGa0 3018578360 860 92SP1_Q6NGGGGGCGGGGYNttggGGTGgagcc11 1191448470 820 87GC_01NRGGGGCGGGGCNKttggGGTGgagcct15 9338168470 870 91USF_Q6GYCACGTGNCgcctGGTGac5 3902888570 820 90CEBPB_01RNRTKNNGMAAKNNtggtgacCAAAgcg1 8574898500 990 91MYOD_01SRACAGGTGKYGcccaGCTGtca32 9052826210 830 86LMO2COM_01SNNCAGGTGNNNcacaGCTGtca2 2322889210 880 92LMO2COM_01SNNCAGGTGNNNcccCAGCgtca0 7734149210 880.93MYOD_Q6NNCANCTGNYCCCAGCtgtc1 6561029220 920 98MYOD_Q6NNCANCTGNYcccaGCTGtc1 6551029220 920 89LMO2COM_01SNNCAGGTGNNNaatCAGAtgcga0.7734149630 820 89MYOD_Q6NNCANCTGNYatcaGATGcg−0.1758059640 920 94CEBPB_01RNRTKNNGMAAKNNggITTACIccaccc1 85748910010 930 90GC_01NRGGGGCGGGGCNKttactcCACCcctg15 93381610040 870 87SP1_Q6NGGGGGCGGGGYNtactcCACCcctg11 11914410050 820 85USF_Q6GYCACGTGNCatcgAGTGac5 39026810360 860 88HNF3B_01NNNTRTTTRYTYtacTGTTtgcct3 97880410460 990 92CETS1P54_01NCMGGAWGYNagctTCCAgg1 03277210700 850 92CETS1P54_01NCMGGAWGVNccAGGAaccc1 03277210750 930 89CEBPB_01RNRTKNNGMAAKNNgggataaaGCAAtga1 85748910940 870 89CEBPB_01RNRTKNNGMAAKNNagttcaGAAAggg1 85748911070 990 94GC_01NRGGGGCGGGGCNKaggGCCAgggagt15 93381611160 810 85NFKB_CNGCGACTTTCCAaGGGAGttgccc42 3137211230 880.90

[0456]

2

TABLE 2

Sites, scores, consensus and positions relative to the site of initiation of

transcription (TSS) prectictect by the NNPP, TSSG anct TSSW software packages in mice

Core

Position/
simi-
Template

Filtration
Site
Consensus
Secquence
Z score
TSS(bp)
larity
similarity

Comparative
GFI1_01
NNN
ttgcctacAATCaggcaactatt
2 393233
−842
1 00
0 66

analysis

NNOMNNAAATCANNGNNNN

between
HNF3B_01
NNNTRTTTRYTY
aacTATTgattc
2 929849
−825
1 00
0 85

species
CEPB_01
RNHTKNNGMAAKNN
tgattctGAAAttg
1 460836
−787
0 99
0 94

CEBPB_01
RNRTKNGMAAKNN
atgTTGCtaaatg
1 460836
−760
1 00
0 91

NF1_Q6
NNTTGGCNNNNNWCCNN
ttcTGGCtggtggcagga
2 199282
−668
1 00
0 88

AP4_Q6
CWCAGCTGGN
caCAGCgtg
14 114395
−386
1 00
0 87

NFKAPPAB_01
GGGAGCTGCC
gggaGCTGcc
11 12
−301
1 00
0 88

NFY_Q6
TRRCCAATSRN
cctCCAAtggc
5 181309
−156
1 00
0.89

Z score >=
HFH2_01
NAWTGTTTRTTT
aaaaAACAaaa
56 365713
−1211
1 00
0 94

1.96
SRY_02
NWWAACAAWANW
aaaaACAAaaac
7 964442
−1209
1 00
0 94

HFH2_01
NAWTGTTTRTTT
acactaAAGAaaa
56 365713
−1205
1 00
0 87

SRY_02
NWWAACAAWANN
aaaaACAAaaca
3.860390
−1203
1 00
0 95

HFH2_01
NAWTGTTTRTTT
aacaaAACAaaa
28 165126
−1200
1 00
0 89

SRY_02
NWWAAACAAWANN
caaaACAAaaac
3 800390
−1198
1 00
0 94

HFH2_01
NAWTGTTTRTTT
accaaaAACAaaa
56 365713
−1194
1 00
0 87

SRY_02
NWWMCAAWANN
aaaaACAAaaac
7 064442
−1192
1 00
0.94

HFH2_01
NAWTGTTTRTTT
acaaaAAGAata
28 165126
−1188
1 00
0.91

HFH1_01
NAWTGTTTATWT
acaaAAACaata
28 079407
−1188
1 00
0 87

SRY_02
NWWAACAAWANN
aaaaACAAtaaa
3 860390
−1186
1 00
0 98

TATA_01
STATAAAWRNNNNNN
ctaTAAAaacctctg
3 965815
−1181
1 00
0 89

NF1_Q6
NNTTGGCNNNNNNCCNNN
gtITGGCcgtgatggagg
2 199282
−1140
1 00
0 93

CHOP_01
NNRTGCAATMCCC
aggTGCAagccct
20 432681
−1104
1 00
0 85

SRY_02
NWWAACAAWANN
ctgcAAaagt
3 860390
1093
1 00
0 85

LYF1_01
TTTGGGAGR
ttaGGGAga
7 842719
1082
1 00
0 90

E2F_02
TTTSGCGC
gcgaCAAA
3 546279
1071
1 00
0.91

GATA1_03
NNNNNGATAANNGN
tgtgaGATAgtcg
2 031644
−1042
1 00
0 88

CDPCR3HD_01
NATYGATSSS
gataGATCgg
2 349950
−1037
1 00
0 97

NFE2_01
TGCTGASTCAY
ggCTGAgtctc
21 950203
−1009
1 00
0 87

CHOP_01
NNRTGCAATMCCC
atcTGCAaaaccc
20 432681
−969
1 00
0 86

NF1_Q6
NNTTGGCNNNNNNCCNNN
aactcacgttGGCAggg
2.199282
−938
1 00
0 85

SRY_02
NWWAACAAWANN
tgctTTGTgaaa
3 860399
−891
1 00
0 85

HFH1_01
NAWTGTTTATWT
aaatAAACcagt
28 019407
−888
1 00
0 96

POLY_C
CAATAAANGCNYYYKCTN
aAATAAAccgtttttt
177 2679419
688
1 00
0 68

ISRE_01
CAGTTTCWCTTTYCC
caGTTTttttttcc
384 173196
880
1 00
0 80

TALBETAE47_01
NNNAACAGATGKTNNN
gcagacaICIGagaat
15 998313
−859
1 00
0 85

GFI1_01
NNNNNAAATCANNGNNNNNN
catcgagAAICttgrctacaatc
2 393233
−854
1 00
0 68

SRY_02
NWWAACAAWANN
gcctACAArca
3 860390
−840
1 00
0 85

RFX1_01
NNGTNRCNNRGYAACNN
tacaatccagGCAArta
7 172878
−837
1 00
0 87

GFI_01
NNNNNAAATCANNGNNNNNN
caggccaactattGATTctactctt
2 393233
−830
1 00
0 89

GFI1_01
NNNNNAAATCANNGNNNNNN
tlgallcIAATCllaggatattgg
2 393233
−820
1 00
0 89

GATA1_03
NNNNNGATAANNGN
cttagGATAttggg
2 031644
809
1.00
0 90

NFY_Q6
TRRCCAATSRN
galaTTGGgcl
5 187369
804
1 00
0 88

GFI1_01
NNNNNAAATCANNGNNNNNN
gggctgccaclGATIclgaaatt
2 393233
−790
1 00
0 89

E47_02
NNNMRCAGGTGTTMNN
gclgccaCCTGallct
15 432640
796
1 00
0 88

LMO2COM_01
SNNCAGGTGNNN
lgccaCCTGatt
3 041567
−794
1 00
0 93

MYOD_01
SRACAGGTGKYG
IgccaCCTGatt
40 698075
−794
1 00
0 92

SRY_02
NWWNAACAAWANN
gaaaTTGTctag
3 888390
−780
1 00
0 87

TH1E47_01
NNNNGNRTCTGGMWTT
gtacattCTGCtgg
16 434030
−694
1 00
0 85

CP2_01
GCNMNAMCMAG
CTCGctggtgg
3 137246
−686
1 00
0 88

GATA1_03
NNNNNGATMNNGN
cacagGATAcaaag
2 031644
−565
1 00
0 88

SRY_02
NWWAACAAWANN
ggaIACAAagac
3 860390
−661
1 00
0 85

NRF2_01
ACCGGAAGNS
accTTCCgac
6 701850
−640
1 00
0.87

ER_Q6
NNARGNNANNNTGACCYNN
aaalgglcctcTGACctrc
10 374054
573
1 00
0 69

AP1FJ_Q2
RSTGACTNMNW
tcTGACctcca
5 142253
−564
1 00
0 90

AP1_Q2
RSTGACTNMNW
lclGACctcca
5 142253
564
1 00
0.86

RORA1_01
NWAWNNAGGTCAN
cIGACCIccacg
5 437913
563
1 00
0.93

GATA1_03
NNNENNGATAANNGN
ccacaGATAlgcca
2 031644
−556
1 00
0 87

OCT1_06
CWNAWTKWSATRYN
agalalgrcATGCa
8 438364
−552
1 00
0 85

OCT_C
CTNATTTGCATAY
alaagCAAATlaa
70 265881
−520
1 00
0 88

NKX25_02
CWFAATTG
aaATTAat
3 983418
−514
1 00
0 86

TSI1_01
NNKGAWTWANANTNN
aattAATTaaattta
4 120840
−513
1 00
0 87

NKX25_02
CWTAATTG
atTAATta
3 983418
−512
1 00
0 87

NKX25_02
CWTAATTG
taATTAaa
3 983418
−510
1 00
0 87

SRY_02
NWWAACAAWANN
aaaACAAaggt
3 860390
−499
1 00
0 93

NF1_06
NNTTGCCNNNNNCCCNNN
tggTGGCacacgcctta
2 199282
−481
1 00
0 85

AHRARNT_01
KNNKNNTYGCGTGCMS
gcaCACGcctllaatc
14 600483
−476
1 00
0 86

GFI1_01
NNNNAAATCANNNGNNNNNN
acgcctttAATCccagcactcagg
2 393233
−472
1 00
0 91

GFI1_01
NNNNAATCANNGNNNNNNNN
ggtctaaglGATTlccaggcc
2 393233
−413
1 00
0 97

NKX25_02
CWTAATTG
aaATTAaa
3 083418
−363
1 00
0 88

LYF1_01
TTTGGGAGR
llgcGGAga
7 842719
−333
1.00
0 89

NF1_Q6
NNTTGGCNNNNNNCCNNN
IglgggggclGCCAlll
2 190262
−305
1 00
0 88

NFKB_Q6
NGGGGAMTTTCCNN
IGGGAgctccal
30 067003
−303
1 00
0 87

NFKAPPAB_01
GGGAMTTYCC
GGGAgctgc
10 361187
−301
1 00
0 88

ER_Q6
NNARGNNANNNNNGACCTNN
gaactcacaggtGACcgt
10 374054
−279
1 00
0 86

E47_02
NNNRCAGGTCTMNN
actcaCAGGgacccg
15 432640
277
1 00
0 90

LMO2COM_01
SNNCAGGTGNNN
tcaCAGGgaca
3 041587
−275
1 00
0 94

MYOD_01
SRACAGGTGKYG
tcaCAGGgacc
40 696075
−275
1 00
0 89

SREBP1_01
NATCACGTGAY
cacagTGTAcc
15 355630
−274
1 00
0 86

AP1_Q4
RSTGACTMANN
ggTGACccgtt
11 246163
−270
1 00
0 86

AP1_Q2
RSTGACTNNNW
ggTGACcgtt
7 895015
−270
1 00
0 91

AP1FJ_Q2
RSTGACTMMNW
ggTGACccgtt
7 895015
−270
1 00
0 93

VMYB_01
AAYAACGGNN
aaccCGTTgtc
3 427439
−266
1 00
0 93

HF1_Q6
NNTTGGCNNNNNNCCNNN
gtcccagtgaaGCCAaac
2 199282
−242
1 00
0 90

PADS_C
NGTGGTCTC
IGIGGIccc
5 230232
−169
1 00
0 89

GC_01
NRGGGGCGGGGGCNK
lgglccGCGGtcct
35 805311
−167
1 00
0.87

SP1_Q6
NGGGGGCGGGGYN
ggtccGCCCccct
25 529462
−166
1 00
0 88

NF1_Q6
NNTTGGCNNNNNNCCNN
caaTGGCaaagtcgcctg
2 190282
−152
1 00
0 85

E47_02
NNNMRCAGGTGTMMN
aglagCAGGtgcaata
15 432640
131
1 00
0 92

E47_01
NSNGCAGGTGKNCN
gtaGCAGgtgcaata
9 748242
−133
1 00
0 88

LMO2COM_01
SNNCAGGTGNN
tagCAGCgcaa
3 041567
−132
1 00
0 96

MYOD_01
SRACAGGTGKYG
tagCAGGgcaa
40 699075
−132
1 00
0 86

CHOP_01
NNRTGCAATMCCC
aggTGCAalalcc
20 432681
−128
1 00
0 95

CAAT_01
NNNRRCCAATSA
aatcatCCAAag
3 434507
−122
1 00
0 90

NFY_Q6
TRRCCAATSRN
tatCCAAtagt
5 187369
−120
1 00
0 92

GC_01
NRGGGGCGGGGCNK
agggGGCGgggctg
35 805311
−103
1 00
1 00

SP1_Q6
NGGGGGCGGGGYN
agggGGCGgggcl
25 529462
−103
1 00
0 99

BARBIE_01
ATNNAAAGCNGRNGG
agcgAAAGtggatgg
29 452018
6
1 00
0 91

NKX25_01
TYAAGTG
gaAAGTg
3 534570
9
1 00
0 88

VMYB_01
AAYAACGGNN
cagAACGgtg
3 427439
34
1 00
0 90

GFI1_01
NNNNNAAATCANNGNNNNN
ggtgagaaAATCcccgaggagggtg
2 393233
40
1 00
0 90

NFKB_Q6
NGGGGAMTTTCCNN
tgagaaaaTCCCcg
30 067903
42
1 00
0 86

ZID_01
NGGTCYATCAYC
gaaggtgGAGCct
41 225196
64
1 00
0 91

TH1E47_01
NNNGNRTCTGGMMTT
ctggagatCTGGggat
16 434630
75
1 00
0 88

SREBP1_02
KATCACCCAC
gtgggGTGAgg
27 710802
94
1 00
0 94

NFE2_01
TGCTGASTCAY
ggCTGAgacac
21 950203
108
1 00
0 87

USF_Q6
GTCACGTGNC
gcCACGttcc
6 857788
114
1 00
0.87

IK1_01
NNNTGGGAATRCC
cagtTCCCtgat
14 853568
116
1 00
0 88

GATA1_03
NNNNNGATAAANNGN
tcctGATAatttg
2 031644
121
1 00
0 93

NKX25_02
CWTAATTG
gaTAATtt
3 983418
125
1 00
0 86

E47_02
NNNRCAGGGTGMNN
ggttcCAGCtgcctac
15.432640
136
1 00
0 87

LMO2COM_01
SNNCAGGTGNN
ttgCAGGtgcct
3 041567
138
1 00
0 96

MYOD_01
SRACAGGTGKYG
ttcCAGGtgccl
40 699075
138
1 00
0 86

GATA1_03
NNNNNGAtAANNGN
ttCCtTATCcttcc
2 031644
164
1 00
0 95

NRF2_01
ACCGGAAGNS
tccTTCCtggg
6 701850
171
1 00
0 91

STAF_02
NNTTCCCAKMATKCMWNCNN
cttcggggagtgTGCGaaaa
341 255024
173
1 00
0 86

IK1_01
NNNTGGGAATRCC
gtgtGGCAaaaat
14 853568
183
1 00
0 92

LYF1_01
TTTGGGAGR
tgtGGActct
7 842719
101
1 00
0 86

AP4_Q6
CWCAGCTGGN
caCAGCggtc
14 114306
210
1 00
0 90

AP1_Q2
RSTGACTNMNW
cagcgGTCAtc
5 142253
212
1 00
0 88

AP1FJ_Q2
RSTGACTNMMNW
cagcgGTCAtc
5 142253
212
1 00
0 90

TALBETAE47_01
NNNAACAGATGKTNNN
gcggtcaTCTGgtac
48 119467
214
1 00
0 89

TAL1ALPHAE47—
NNNAACAGATGKTNNN
gccggtcaTCTGgtcac
48 119407
214
1 00
0 88

01

TAL1BETAITF2_
NNNAACAGATGKTNNN
gcaggtcaTCTGgtcac
48 119467
214
1 00
0 88

01

TH1E47_01
NNNNGNRTCTGGMWTT
gcggtcatCTGGcac
16 434630
214
1 00
0 86

AP1F_02
RSTGACTNMNW
atctgGTCAcc
7 895015
220
1 00
0 93

API_Q4
RSTGACTMANN
atctgGTCAcc
11 246163
220
1 00
0 86

API_Q2
RSTGAGTNMNW
actcgGTCAcc
7 898015
220
1 00
0 90

ER_Q6
NNARGNNANNTGACGYNN
tctgGTCAcctgaggac
10 374054
221
1 00
0 86

NF1_Q6
NNTTGGCNNNNNNCCNNN
gagggacctctGCCAacc
2 199282
233
1 00
0 95

NKX25_01
TYAAGTG
cACTTIc
3 534570
267
1 00
0 88

AP1FJ_02
RSTGACTNMNW
ggcclGTCAcc
5 142253
281
1 00
0 91

AP1_Q2
RSTGACTNMNW
ggcctGTCAcc
5 142253
281
1 00
0 88

SREBP1_02
KATCACCCCAC
tgTCACccccc
27 710802
285
1 00
0 87

TH1E47_01
NNNNGNRTCTGGMWTT
ccccGCAGatctaaa
16 434630
297
1 00
0 86

IRF1_01
SNAAAGYGAAACC
aaTTTCactttat
81 006772
311
1 00
0 87

1RF2_01
GAAAGYGAAASY
aaTTTCactttat
59 661305
311
1 00
0 85

NF1_Q6
NNTTGGCNNNNNNCCNNN
gagtggaagcccGCAatt
2 199262
341
1 00
0 93

NFY_Q6
TRRCCAATSRN
ccgCCkAAttc
5 187360
350
1 00
0 89

OCT1_Q6
NNNNATGCAAATNAN
ccaATTccatgtag
11 430842
353
1 00
0 87

OCT1_08
CWNAWTKWSATRYN
ccaatllccATGTa
8 438364
353
1 00
0 92

OCT1_07
TNTATGNTAATT
AATTIccatgta
27 048281
355
1 00
0 88

CEBP_C
NGWNTKNKGYAAKNNAYA
aaacttgGCAATttccc
23 615437
374
1 00
0 86

NF1_Q6
NNTTGGCNNNNNNCCNNN
ctTGGCaatttccctct
2 199282
377
1 00
0.95

NFKAPPABBS_01
GGGRATTTCC
ggcaaITTCC
30 669184
381
1 00
0 86

CREL_01
SGGRNWTTCC
ggcaatTTCC
7 203414
381
1 00
0 86

NFKAPPAB_01
GGGAMTTYCC
gcaattTCCC
10 361187
382
1 00
0 85

IK1_01
NNNTGGGAATRCC
caatlTCCCctc
14 883568
383
1 00
0 86

AP1_Q4
RSTGACTMANN
tctrtGTCAgc
11 246163
302
1 00
0 90

AP1FJ_Q2
RSTGACTNMNNW
tctctGTCAgc
7 895015
302
1 00
0 95

AP1_Q2
RSTGACTNMNW
tctctGTCAgc
7 895015
392
1 00
0 95

ISRE_01
CAGTTTCWCTTTYCC
caGTTTccctatcgg
384 173196
405
1 00
0 85

IK1_01
NNNTGGGAATRCC
cagtTCCCatc
14 853568
405
1 00
0.87

GATA1_03
NNNNNGATAANNGN
ttccTATCggtat
2 031641
409
1 00
0 91

GATA1_03
NNNNNGATAANNGN
atcggTATCatgaa
2.031644
415
1 00
0 88

NF1_Q6
NNTTGGCNNNNNNCCNNN
tcatgaagcagGCCAag
2 199282
422
1 00
0 86

TATA_01
STATAAAWRNNNNNN
aaaTAAAataacgaa
3 965615
458
1 00
0.85

GFI1_01
NNNNAAATCANNGNNNNNNN
aataacgaAATCaggatggcgtg
2 393233
464
1 00
0 92

VMYB_01
AAYAACGGNN
aatAACCaaa
3 427439
454
1 00
0 85

AHRARNT_01
KNNKNNTYGCGTGCMS
caggaatggCGTGctc
14 600483
475
1 00
0 93

AP1_Q4
RSTGACTMANN
ccTGACtcctc
11 246163
503
1 00
0 89

API_Q2
RSTGACTNMNW
ccTGACtcctc
7 895015
503
1 00
0 90

AP1FJ_Q2
RSTGACTNMNW
ccTGACtcctc
7 595015
503
1 00
0 93

BARBIE_Q2
ATNNAAAGCNGRNGG
taccctcCTTTlgac
29.452018
532
1 00
0 86

AP1FJ_Q2
RSTGACTNMNW
ttTGACtccgg
7.896015
541
1 00
0 90

AP1_Q2
RSTGACTNMNW
ttTGACtccgg
7 805015
541
1 00
0 88

AP1_Q4
RSTGACTMANN
ttTGACIccgg
11 246163
541
1 00
0 88

GC_01
NRGGGGCGGGGCNK
ggagGGCGggccct
35 805311
550
1 00
0 91

SP1_Q6
NGGGGGCGGGGYN
ggagGGCGggccc
25 529462
550
1 00
0 93

TH1E47 01
NNNNGNRTCTGGMaWTT
cttcttctCTGGtttc
16 434630
565
1 00
0 86

AHRARNT_01
KNNKNNTYGCGTGCMS
ccttgggagCGTGact
14 600483
580
1 00
0 86

LYF1_01
TVTGGGAGR
cttGGGAgc
7 842719
581
1 00
0 86

AP1FJ_Q2
RSTGACTNMMNW
cgTGACttgc
7 895015
589
1 00
0 92

AP1_Q2
RSTGACTNMNW
cgTGACtttgc
7.895015
589
1 00
0.89

AP1_Q2
RSTGACTMANW
cgTGACtttgc
7.895015
589
1 00
0.89

AP1_Q4
RSTGACTMANN
cgTGACtttgc
11 246163
589
1 00
0 89

IK1_01
HNNTGGGAATRCC
tcagtTCCCatct
14 853508
613
1 00
0 88

E47_01
NSNGCAGGTGKWCNN
aaggccagCTCCaaa
9 748242
638
1 00
0 89

AP4_Q6
GWCAGCTGGN
gcCAGCtgca
21 241746
641
1 00
0 91

AP4_Q5
NNCAGCTGNN
gcCAGCtgca
3 060778
841
1 00
0 94

AP4_Q6
CWCAGGTGGN
gccaGCTGca
21 241746
641
1 00
0 94

AP4_Q5
NNCAGCTGNN
gccaGCTGca
3 060778
641
1 00
0 95

OCT1_Q65
NNNNATGCAAATNAN
ccagctgrAAATgac
11 430842
642
1.00
0 88

AP1_Q2
RSTGACTNMNW
aaTGACacaga
7 895015
651
1 00
0 94

AP1FJ_Q2
RSTGACTNNWW
aaTGACacaga
7 805015
651
1 00
0 94

AP1_Q4
RSTGACTMANN
aaTGACacaga
11 246163
651
1 00
0 91

E47_Q2
NNNMRCAGGTGTTMNN
ggggcaCCTGgggcg
15 432840
677
1 00
0 88

LMO2COM_01
SNNCAGGTGNNN
ggccaCCTGggg
3 041567
679
1 00
0 96

MYOD_01
SRACAGGTGKYG
ggccaCCTGggg
40 698075
679
1 00
0 89

VMYB_01
AAYAACGGNN
gcgAACGgaa
3 427439
690
1 00
0 91

TH1E47_01
NNNNGNRTCTGGMWTT
accccggICTGGIatg
16 434630
705
1 00
0 90

AP1FJ_Q2
HSTGACTNMNW
gcTGACcgtgg
5 142253
723
1 00
0 89

AP1_Q2
RSTGACTNMNW
gcTGACcgtgg
5 142253
723
1 00
0 68

ZID_01
NGGCTCYATCAYC
gaccgtgGACCcc
41 225196
120
1 00
0 89

BARBIE_01
ATNNAAAGCNGRNGG
acccaagCTTaaac
29 452018
750
1 00
0 92

GC_01
NRGGGGGCGGGGCNK
aagctcCGCCccct
35 805311
267
1 00
0 97

SP1_Q6
NGGGGGCGGGGYN
agctcCGCCccct
25 520462
708
1 00
0 95

CREL_01
SGGRNWTCC
agggtcTTCC
3 467858
703
1 00
0 92

TH1E47_01
NNNGNRTCTGGMWTT
tcttCCAGaccccagc
16 434630
797
1 00
0 94

CDP_02
NWNATCGATTANYNN
gccttcatCGATagc
21 123980
811
1 00
0 91

CLDX_01
NNTATCGATTANYNW
gccttcatCGATagc
50 240688
811
1 00
0 90

GATA1_03
NNNNGATAANGN
tcatcGATAgcccl
2 031644
815
1 00
0 88

NF1_Q6
NNTTGGCNNNNNNNCCNNN
tagcccttccaGCCAatc
2 199282
822
1 00
0 93

NRF2_01
ACCGGAAGNS
accttCCagc
6.701850
825
1 00
0 85

GFI1_01
NNNNAAATCANNGNNNNN
ttccagccAATCagctagaggac
2 393233
828
1 00
0 88

HFY_C
NCTGATTGGYIASY
tccagCCAATcagc
65 593286
829
1 00
0 96

CAAT_01
NNNRRCCAATSA
tccagCCAAtca
3 434507
829
1 00
0 99

NFY_Q6
TRRCCAATSRN
cagCCAAtcag
5 187369
831
1 00
0 96

AP4_Q6
CWCAGCTGGN
gacgGCTGg
14 114396
849
1 00
0 86

IK1_01
NNNTGGGAATRCC
cgggttCCattg
14 853668
862
1 00
0 91

NFY_Q6
TRRCCAATSRN
ccaTTGGtca
5 187369
868
1 00
0 95

CAAT_01
NNNRRCCAATSA
ccaTTGGtcact
3 434507
869
1 00
0 91

AP1FJ_Q2
RSTGACTNMNW
cattgGTCAct
7.895015
870
1 00
0 94

AP1_Q4
RSTGACTMANN
cattgGTCAact
11 246163
870
1 00
0 91

AP1_Q2
RSTGACTNMNW
cattgGTCAact
7 895015
870
1 00
0 91

OLF1_01
NCNANTCCCYNGRGARNKGN
gtcactTCCCtagtgattttct
77 977123
875
1 00
0 86

IK1_01
NNNTGGGAATRCC
tcactTCCCagt
14 853568
876
1 00
0 87

SRY_02
NWWWAACAAWANN
tgccTTGttgc
3 860390
905
1 00
0 89

GFI1_01
NNNNNAAATCANNGNNNNNN
ctctttgcgggaGATIattgagg
2 393233
921
1 00
0 88

TATA_01
SIATAAAWRNNNNN
gcgggagaTTAttg
3 965815
927
1 00
0 85

AP2_Q6
MKCCSCNGGGG
gaCCCGcagaca
12 284970
978
1 00
0 86

TH1E47_01
NNNNGNRTCTGGMWTT
acattgttCTGGagcc
16 434630
987
1 00
0 89

HF1_Q6
NNTTGGCNNNNNCCNN
atttgtctggaGCCacac
2 199282
989
1 00
0 86

AP4_Q6
CWCAGCTGGN
caCAGCtcac
14 114396
1004
1.00
0 88

AP4_Q6
CWCAGCTGGN
ctccGCTGtt
14 114396
1040
1 00
0 85

Th1E47_01
NNNGNRTCTGGMWTT
cggtCCAGagtcatca
16 434630
1052
1 00
0 88

VMAF_01
NNNTGCTGACTCAGCANNN
cgggtccagaGTCAcatgg
168513881
1052
1.00
0 87

AP1_Q2
RSTGACTNMNW
ccagaGTCAtc
7 895015
1056
1 00
0 93

Core
AP1_Q4
RSTGACTMANW
ccagaGTCAtc
11 246163
1056
1.00
0 90

similarity >=
AP1FJ_Q2
RSTGACTNMNW
ccagaGTCAtc
7 895015
1056
1 00
0 92

0.99
SOX5_01
NNAACAATNN
aaaaCAATaa
0 681190
−1185
1 00
0 99

Template
AP4_Q5
NNCAGCTGNN
gggcGTGt
0 508566
−1122
1 00
0 85

similarity >=
DELTAEF1_01
NNNCACCTNAN
gcaAGCTgcaa
0 538360
−1107
1 00
0 96

0.85
IK2_01
NNNYGGGAWNNN
gtatGGGAgag
0 854442
−1083
1 00
0 91

CMYB_01
NNNNNNGNCNGTTGNN
aacgacacGTTGatg
0 594660
1065
1 00
0.92

GATA1_02
NNNNNGATANKGNN
IglgGATAgalcg
0 930257
−1042
1 00
0 91

GATA1_04
NNCWGATARNNNN
gtgaGAtAgatcg
0 653180
−1041
1 00
0 94

LMO2COM_02
NMGATANSG
gaGATAgat
0 569272
−1030
1 00
0 91

IK2_01
NNNYGGGAWNNN
agtcTCCTtcac
−0 854442
−1014
1 00
0 89

AP4_Q5
NNCAGCTGNN
acCAGCttcc
0 508566
−994
1.00
0 86

IK2_01
NNNYGGGAWNNN
catcTCCCtta
−0 854442
−909
1 00
0 88

SOX5_01
NNAACAATNN
cctaCAATcc
0 681190
−839
1 00
0 80

GATA1_02
NNNNNGATANKGNN
cttagGATAttggg
0 930257
−809
1 00
0 93

GATA1_04
NNCWGATARNNNN
ttagGATAttggg
0 653180
−808
1 00
0 89

LMO2COM_02
NMGATANSG
agGATAttg
0 569272
−806
1 00
0 92

DELTAEF1_01
NNNCACCTNAN
lgccACCTgat
0 538380
−794
1 00
0 97

MYOD_Q6
NNCANCTGNY
gaCACCtgat
0 781061
−793
1 00
0 95

SOX5_01
NNAACAATNN
aaATTGlcla
0 681190
−779
1 00
0 86

SOX5_01
NNAACAATNN
ggtaCAATtc
0 681190
−695
1 00
0 86

GATA1_02
NNNNNGATANKGNN
cacagGATAcaaag
0 930257
−665
1 00
0 89

GATA1_04
NNCWGATARNNNN
acagGATACaaag
0 853180
−664
1 00
0 88

LMO2COM_02
NMGATANSG
agGATAcaa
0 569272
−682
1.00
0 88

CEBPB_01
RNRTKNNGMAAKNN
accttgtGCAAacc
1 480836
−851
1 00
0 94

DELTAEF1_01
NNNCAGCTNAN
tccgACCTaaa
0 538300
−838
1 00
0.87

CEBPB_01
RNRTKNNGMAAKNN
lcTTGCclgaggl
1 400836
−620
1 00
0 87

IK2_01
NNNYGGGAWNNN
gaggTCCCacat
0 854442
−611
1 00
0 95

DELTAEF1_01
NNNCACCTTNAN
tctgACCTcca
0 538360
−564
1 00
0 85

GATA1_02
NNNNNGATANKGNN
ccacaGATAgcca
0 930257
−556
1 00
0.93

GATA1_04
NNCWGATARNNNN
cacaGATAlgcca
0 653180
−555
1 00
0 94

LMOZCOM_02
NMGATANSG
caGATAtgc
0 569272
−553
1 00
0 96

S8_01
NNNNNYAATTN
acccTAATaagcaat
−1 397267
−526
1 00
0 86

S8_01
NNNNNYAATTN
ataagcaaTTAatta
−1 397287
520
1 00
0 95

S8_01
NNNNNYAATTN
gcaaattATTAaatt
−1 397287
−516
1 00
0 97

S8_01
NNNNNYAATTN
aactTAATtaaattta
−1 397287
−514
1 00
0 99

IK2_01
NNNYGGGAWNNN
ttaaTCCCagca
−0 854442
−466
1 00
0 95

AP4_Q5
NNCAGGTGNN
rcCAGCactc
0 508568
−461
1 00
0 85

AP4_Q5
NNCAGCTGNN
caCAGCagtg
1 794672
−386
1 00
0 93

SB_01
NNNNNYAATTN
ctctaaaaATTAaaaa
1 397287
−369
1 00
0 93

MZF1_01
NGNGGGGA
cttGGGGa
0 437162
−334
1 00
0 96

IK2_01
NNNYGGGAWNNN
cttgGGGAgagg
−0 884442
−334
1 00
0 89

IK2_01
NNNYGGGAWNNN
tgtgGGGAgctg
−0 854442
−305
1 00
0 87

MZF1_01
NGNGGGGA
IGctGGa
0 437162
−305
1 00
0 99

AP4_Q5
NNCAGCTGNN
gggcaGCTcc
1 794672
−301
1 00
0 91

MYOD_Q6
NNCANCTGNY
cacaGGTGac
0 781061
−274
1 00
0 91

DELTAEF1_01
NNNGACCTNAN
cacAGGIgacc
0 538380
−274
1 00
0 95

CMYB_01
NNNNNNGNCNGTTGNN
caggtgaccccGTTGtccc
0 594660
272
1 00
0 90

VMYB_02
NSYAACGGN
ccCGTTgtc
0 465812
−265
1 00
0 95

IK2_01
NNNYGGGAWNNN
gttgTCCCcctc
−0 854112
−262
1 00
0 91

MZF1_01
NGNGGGA
ICCCCctc
0 437162
−258
1 00
0 96

IK2_01
NNNYGGGAWNNN
cgtgTCCCagtg
−0 854442
−245
1 00
0 93

AP4_Q5
NNCAGCTGNN
IgCAGCagga
0 508566
221
1 00
0 90

CMYB_01
NNNNNNGNCNGTTGNN
caggaatcctGTTGtccc
0 594660
−216
1 00
0 89

IK2_01
NNNYGGGAWNNN
gttgTCCCtta
0 854442
−206
1 00
0 91

AP4_Q5
NNCAGCTGNN
gcggGCTGtg
0 508666
−175
1 00
0 86

IK2_01
NNNNYGGGAWNNN
gtggTCCCgcct
−0 854442
−168
1 00
0 92

DELTAEF1_01
NNNCACCTNAN
agcAGGTgcaa
0 530360
−131
1 00
0 95

MYOD_Q8
NNCANCTGNY
agcaGGTGca
0 147777
−131
1 00
0 96

GATA1_02
NNNNNGATANKGNN
lgcaaTATCcaata
−0 046677
−125
1 00
0 92

GATA1_04
NWCWGATARNNNN
lgcaaTATCcaal
0 653180
−125
1 00
0 87

LMO2COM_02
NMGATANSG
caaTATCca
0 569272
−123
1 00
0 92

NKX25_01
TYAAGTG
cACTTaa
1 519193
−33
1 00
0 98

IK2_01
NNNYGGGAWNNN
gcgcTCCCccgc
−0 854442
−19
1 00
0 89

MZF1_01
NGNGGGGA
ICCCCcgc
0 437162
−15
1 00
0 96

VMYB_02
NSYAACGGN
cagAACGgl
0 465812
34
1 00
0 92

IK2_01
NNNYGGCAWNNN
aaaaTCCCgag
−0 854442
46
1 00
0 90

MZF1_01
NGNGGGGA
ICCCCgag
1 679353
50
1 00
0 95

DELTAEF1_01
NNNCACCTNAN
ggaAGGTggag
0 538360
83
1 00
0 95

IK2_01
NNNYGGGAWNNN
IctgGGGAtgct
−0 854442
82
1 00
0 89

MZF1_01
NGNGGGGA
IcIGGGGa
0 437162
62
1 00
0 96

AP4_Q5
NNCAGCTGNN
gtggGCTGag
0 508566
105
1 00
0 86

ARNT_01
NNNNNCACGTGNNNNN
tgagCACGttccctg
0 511281
111
1 00
0 88

IK2_01
NNNYGGGAWNNN
acglTCCCgat
−0 894442
117
1 00
0 92

GATA1_02
NNNNNGATANKGNN
IccclGATAatttg
0 930257
121
1 00
0 91

GATA1_04
NNCWGATARNNNN
ccctGATActtttg
0 653180
122
1 00
0 95

SB_01
NNNNNYAATTN
ctgaTAATllgggglt
−1 397287
124
1 00
0 95

LMO2COM_02
NMGATANSG
ctGATAatt
0 569272
124
1 00
0 91

GATA_C
NGATAAGNMNN
IGATAAIIIgg
1 411097
125
1 00
0 90

MYOD_Q6
NNCANCTGNY
tccaGGTGcc
−0 141777
139
1 00
0 91

DELTAEF1_01
NNNCACCTNAN
tccAGGTgcct
0 538360
139
1 00
0 95

IK2_01
NMNYGGGAWNNN
actcTCCCttgc
−0 854442
150
1 00
0 88

GATA C
NGATAAGNMNN
cttccTTATCc
1 411097
163
1 00
0 97

GATA1_04
NNCWGATARNNNN
ttccIIAICcttc
0 653180
164
1 00
0 94

GATA1_02
NNNNNGATANKGNN
ttccTATCcttcc
0 930257
164
1 00
0 95

IMO2COM_02
NNGATANSG
ccTATCcl
0 560272
1 66
1 00
0 96

CETS1P54_01
NCMGGAWGYN
tccttCCGgg
1 244487
171
1 00
0 94

IK2_01
NNNYGGGAWNNN
tccgGGGAgtgt
0 854442
175
1 00
0 86

MZF1_01
NGNGGGGA
tccGGGGa
0 437162
175
1 00
0 95

IK2_01
NNNYGGGAWNNN
gtgtGGGAaaca
0 854442
183
1 00
0 97

AP4_Q5
NNCAGCTGNN
caCAGcggtc
1 794672
210
1 00
0 92

DELTAEF1_01
NNNCACCTNAN
ggttACCTcga
0 538360
224
1 00
0 94

IK2_01
NNNYGGGAWNNN
tcgaGGGAcctc
−0 854442
231
1 00
0 90

CMYB_01
NNNNNNGNCNGTTGNN
ctgcCAACctacccctcc
0 694690
242
1 00
0 85

DELTAEF1_01
NNNCACCTNAN
ctacACCTcca
0 538360
250
1 00
0 94

IK2_01
NNNYGGGAWNNN
agtgTCCCactt
−0 854442
260
1 00
0 93

MZF1_01
NGNGGGGA
cCCCCacc
0 437162
291
1 00
0 85

NKX25_01
TYAAGTG
cACTTa
1 519193
316
1 00
0 94

IK2_01
NNNYGGGAWNNN
aaagTCCCcgag
−0 854442
332
1 00
0 88

MZF1_01
NGNGGGGA
ICCCCgag
1 670353
336
1 00
0 95

CEBPB_01
RNRTKNNGMAAKNN
aactttgGCAAtttt
1 460830
375
1 00
0 96

IK2_01
NNNYGGGAWNNN
aattTCCCtctc
−0 854442
384
1 00
0 92

IK2_01
NNNYGGGAWNNN
agIITCCCatc
−0 854442
406
1 00
0 94

GATA1_04
NNCWGATARNNNN
ttcccTATCggta
0 653180
409
1 00
0 93

GATA1_02
NNNNNGATANKGNN
ttcccTATCggtat
0 930257
409
1 00
0 97

LMO2COM_02
NMGATANSG
ccccTATCgg
0 560272
411
1 00
0 99

GATA1_02
NNNNNGATANKGNN
atcggTATCatgaa
0 930251
415
1 00
0 92

GATA1_04
NNCWGATARNNNN
atcggTTCatga
0 653180
415
1 00
0 91

LMO2COM_02
NMGATANSG
cggTATCat
0 569272
417
1.00
0 98

CETS1P54_01
NCMGGAWGYN
cagTCCGgg
1 244487
445
1 00
0 92

MZF1_01
NGNGGGGA
cggGGGGa
0 437182
451
1 00
0 98

IK2_01
NNNYGGGAWNNN
cgggGGGAaata
−0 854442
451
1 00
0.91

IK2_01
NNNYGGGAWNNN
cctgTCCTgac
−0 854442
497
1 00
0 90

CETS1P54_01
NCMGGAWGYN
IgacTCCGga
1 244457
543
1 00
0 87

CETS1P54_01
NCMGGAWGYN
tcCGGAgggc
1 244487
547
1 00
0 90

IK2_01
NNNYGGGAWNNN
ccttGGGAgcgt
−0 854442
580
1 00
0 92

IK2_01
NNNYGGGAWNNN
cagITCCC9atct
−0 854442
614
1 00
0 94

CETS1P54_01
NCMGGAWGYN
agacTCCGgg
1 244487
659
1 00
0 86

DELTAEF1_01
NNNCACCTNAN
ggcACCTggg
0 538360
079
1 00
0 95

MYOD_Q6
NNCANCTGNY
gcCACCtggg
0 781061
680
1 00
0 91

VMYB_02
NSYAACGGN
gcgAACGga
0 465812
690
1 00
0 93

GATA1_02
NNNNNGATANKGNN
tcatcGATAgccct
0 930257
815
1 00
0 91

GATA1_04
NNCWGATARNNNN
catcGATAgcct
0 653180
816
1 00
0 88

LMO2COM_02
NMGATANSG
tcGATAgcc
0 569272
818
1 00
0 95

AP4_Q5
NNCAGCTGNN
atCAGCtacg
0 508566
837
1 00
0 89

AP4_Q5
NNCAGCTGNN
gacgGCTGcg
1 794677
849
1 00
0 91

IK2_01
NNNYGGGAWNNN
gggtTCCCattg
0 854442
863
1 00
0 97

IK2_01
NNNYGGGAWNNN
cactTCCCtagt
0 854442
877
1 00
0 92

NKX25_01
TYAAGTG
cACTTcc
1 519193
877
1 00
0 88

IK2_01
NNNYGGGAWNNN
ttgCGGAgatt
−0 854442
925
1 00
0 89

AP4_Q5
NNCAGCTGNN
ctCAGCccga
0 508566
945
1 00
0 87

AP4_Q5
NNCAGCTGNN
caCAGtlcac
1 794672
1004
1 00
0 92

AP4_Q5
NNCAGCTGNN
ctcCGCTGtt
1 794672
1040
1 00
0 91

CETS1P54_01
NCMGGAWGYN
tgttTCCGgt
1 244481
1046
1 00
0 95

None
HFH2_01
NAWTGTTTRTTT
aaacaAAAAaaa
58.365713
−1219
0.62
0 89

(MatIspec-
HNF3B_01
NNNTRTTTRYTY
aaacaAAAAaaa
6.168471
−1219
0.85
0 90

tor) default
HFH3B_01
NAWTGTTTRTTT
aacaAAAAAcaa
28.166126
−1215
0 82
0 88

(parameters)
HNF3B_01
NNNTRTTTRYTY
aaaaAACAaaaa
6.168471
1211
0 99
0 88

HNF3B_01
NNNTRTTTRYTY
aaacaAAAAcaa
9 407093
−1207
0 85
0 80

HNF3B_01
NNNTRTTTRYTY
aaacaAAAAraa
9 407093
−1196
0 85
0 89

HNF3B_01
NNNTRTTTRYTY
aaacaAAAAcaa
9.407093
−1190
0 85
0 89

HFHZ_01
NAWTGTTTRTTT
aaaacAATAaaa
28.165126
−1185
0 90
0 85

TATA_C
NCTATAAAAR
acAATAAAAa
0 111772
−1182
0 89
0 93

VMYB_01
AAYAACGGNN
ctcTGTTtct
3 427439
−1171
0 82
0 85

VMYB_01
AAYAACGGNN
agaAACAgac
3 427439
−1068
0 82
0.86

LMO2COM_01
SNNCAGGTGNNN
acaCAGTtgaat
1 242813
−1060
0 80
0 87

MYOD_06
NNCANCTGNY
cacaGTTGaa
−0 147777
−1059
0 87
0 89

OCT1_08
CWNAWTKWSATRYN
cacagttgaATGAa
8 438364
−1059
0 83
0 86

VMYB_02
NSYAACCGN
acAGTTgaa
0 465812
−1058
0 82
0 88

GATA_C
NGATAAGNMNN
aGATAGatcgg
1 411097
−1038
0 89
0 90

CEBPB_01
RNRTKNNNGMAARNN
gggtggaGAAAgag
1 460836
−1022
0 99
0 93

LMO2COM_01
SNNCAGGTGNNN
atgcaTCTGcaa
1.242813
−973
0 82
0 91

MYOD_06
NNCANCTGNY
tgCATCIgca
−0.147777
−972
0 92
0.91

AP1_C
NTCASTCAN
cTAACTCAc
1 430304
−940
0 86
0 87

AP1_C
NTGASTCAN
cTAACTCAc
1 430304
−940
0 85
0 87

PADS_C
NGTGGTGTC
gGTGATcta
5 230232
−922
0 90
0 89

CEBP_C
NGWNTKNKGYAAKNNAYA
tgctttgIGAAATaaacc
23 615437
−897
0 80
0 89

CEBPB_01
RNRTKNNGMAAKNN
gcttgIGAAAIaa
1 460836
−896
0 99
0 95

VMYB_01
AAYAACGGNN
accAGTTtttt
3.427439
−882
0 88
0.88

HFH2_01
NAWTGTTTRTTT
cagTTTtttt
28 165126
−680
0 82
0 86

CETS1P54_01
NCMGGAWGYN
tttTCCAga
1 244481
−872
0 85
0 86

LMO2COM_01
SNNCAGGTGNNN
agaacaTCTGaga
1 242813
−857
0 82
0 89

MYOD_06
NNCANCTGNY
gaCATCgag
−0 147777
−856
0 92
0 89

SRY_02
NWWAACAAWANN
actaTTGAttct
3 860390
−824
0 81
0 85

CDPCR3HD_01
NATYGATSSS
tattGATTctt
2 349950
−822
0 89
0 93

OCI1_02
NNGAATATKCANNN
tcttaGGATattggg
8 030815
−810
0 86
0 86

GATA_C
NGATAAGNMNN
gGATAttggc
1 411097
805
0 87
0 86

USF_Q6
GYCAGGTGNC
gcGACCtgat
13 868419
793
0 82
0 89

USF_C
NCACGTGN
cCACCTga
0 607662
−792
0 86
0 93

USF_Q6
GYCACGTGNC
ggctGGTGgr
6 857788
684
0 82
0 87

CETS1P54_01
NGMGGAWGYN
gcAGGAgatg
1 244487
−676
0 93
0 88

USF_Q6
GYCAGGTGNC
ggCACAggat
6 857788
−667
0 86
0 85

CETS1P54_01
NCMGGAWGYN
aCAGGAtaca
1 244487
−664
0 93
0 91

GATA_C
NGATAAGNMNN
qGATACaaga
1 411097
−661
0 88
0 89

CETS1P54_01
NCMGGAWGYN
ccAGGAaatg
1 244487
−578
0 93
0 92

GATA_C
NGATAAGNMNN
aGATATgccat
1 411097
−552
0 87
0 94

OCT1_06
CWNAWTKWSATRYN
gTATgccatgcat
0 438364
−551
0 94
0 85

LMO2COM_01
SNNCAGGTGNNN
algCATGtgtcc
1 242813
−539
0 62
0 89

USF_Q6
GYCACGTGNC
tgcaTGTGtc
6 857788
538
0 86
0 86

USF_C
NCACGTGN
gcATGTGt
0 507662
−537
0 88
0 93

USF_C
NCACGTGN
gCATGTgt
0 507662
−537
0 82
0 85

OCT1_06
CWNAWTKWSATRYN
attaattaATTTa
8 438364
−512
0 89
0 90

TATA_C
NCTATAAAAR
aaTTTAAAAa
8 11772
−504
0 93
0 87

MYCMAX_02
NANCACGTGNNW
ttactTGTGgtg
3 484391
−488
0 90
0 86

USF_Q6
GYCACGTGNC
ggCACAcgcc
6 857788
−477
0 86
0 86

CETS1P54_01
NCMGGAWGYN
tcAGGAggca
1 244487
−453
0 93
0 91

PADS_C
NGTGGTCTC
aGTGATttc
5 230232
−404
0 90
0 91

CETS1P54_01
NCMGGAWGYN
gattTCCAg
1 244487
−401
0 85
0 89

CAAT_01
NNNRRCCAATSA
gtcagCCACtct
3 434807
−371
0 83
0 85

NFY_Q6
TRRCCAATSRN
gagCCACtctc
5 187369
−375
0 81
0 85

TATA_C
NCTATAAAAR
ITTTTAAAaa
16 345002
−350
0 93
0 88

TATA_C
NCTATAAAAR
ITTTTAAAaa
16 345002
−350
0 93
0 88

AP2_Q6
MKCCCSCNGGCG
gtccttGGGGag
12 284970
−337
0 98
0 85

CETS1P54_01
NCMGGAWGYN
acAGGAatgt
1 244487
−320
0 93
0.85

OCT1_06
CWNAWTKWSATRYN
gCCATttcaagatg
8 438364
294
0 83
0 86

CEBPB_01
RNRTKNNGMAAKNN
ccaTTTCaagatgt
1 480838
293
0 99
0 92

E47_01
NSNGCAGGTGKNCNN
ctcACAGgtgacccg
9 748242
−275
0 83
0 85

USF_Q6
GYCACGTGNC
ctCACAggtg
6 857788
−276
0 86
0 86

USF_Q6
GYCACGTGNC
cacaGGTGar
13 858419
−274
0 82
0 89

USF_C
NCACGTGN
acAGGTGa
0 507662
−273
0 86
0 92

ARP1_01
TGACCYTTGANCCYW
tgacccGTTGtccccc
123 979855
−268
0 83
0 87

CETS1PS4_01
NCMGGAWGYN
gcAGGAatcc
1 244487
−217
0 93
0 88

CETS1P54_01
NCMGGAWGYN
ggaaTCCTgt
1 244487
−214
0 93
0 88

VMYB_01
AAYMCGGNN
tccTGTTgtc
3 427439
−210
0 82
0 86

CEBPB_01
RNRTKNNGMAAKNN
cctttaaGAAAccc
1 460836
−200
0 99
0 89

USF_C
NCACGTGN
gcAGCTCc
0 507662
−181
0 86
0 92

GATA_C
NGATAAGNNNN
gtgcaATATCc
1 411097
126
0 87
0 89

OCT1_02
NNGAATATKCNNNN
tgcctATCCaatag
8 039815
−125
0 86
0 92

NFKB_C
NGGGACTTTCCA
gagaaaATCCCc
42 843021
43
0 93
0 88

NFKAPPAB_01
GCGAMTTYCC
gaaaaICCC
10 361187
45
0 90
0 86

CETS1P54_01
NCMGGAWGYN
aTGGAgatc
1 214487
74
0 85
0 85

RFX1_01
NNGTNRCNNRGTAACNN
acgTTCCctgataatt
7 172818
117
0 88
0 85

CETS1P54_01
NCNGGAWCYN
gggTCCAgg
1 244487
135
0 85
0 86

USF_C
NCACCGTGN
ccAGGTGc
0 507662
140
0 86
0 92

CEBPB_01
RNRTKNGMAAKNN
gagtgtgGGAAaaa
1 460306
181
0 87
0 88

LMO2COM_01
SNNCAGGTGNN
ggtcaTCTGgtc
1 242813
216
0 82
0 88

MYOD_Q6
NNCANCTGNY
gtCATCggt
−0 147777
217
0 92
0 93

CETS1P54_01
NCMGGAWGYN
caccTCCAgt
1 244487
253
0 85
0 91

USF_Q6
GTCACGTGNC
ctcaAGTCr
6 857788
256
0 86
0 86

CEBPB_01
RNRTKNNGMAAKNN
cacTTCaaatga
1 460836
267
0 99
0 93

SRF_Q6
GNCCAWATAWGGWN
ttCCAAatgaggrr
30 107806
771
0 97
0 91

GC_01
NRGGGGCGGGGCNK
accccccCACCcccc
35 805311
289
0 87
0 91

SP1_Q6
NGGGGGCGGGYN
cccccCACCcccc
25 529482
290
0 92
0 92

OCT1_06
CWNAWTKWSATRYN
cAAATctcatta
8 438364
309
0 89
0 85

CEBPB_01
RNRTKNNGMAKNN
acttatGAAgaa
1 460836
317
0 99
0 94

OCT1_05
MKNATTTGCATAYY
ccaatttCCATgta
49 364942
363
0 85
0 86

CEBPB_01
RNRTKNNGMAKNN
cagTTTCatcg
1 460836
405
0 99
0 87

GATA_C
NGATAAGNNNN
ttttccCTACg
1 411097
408
0 89
0 93

GATA_C
NGTAAGMNN
tatgcGTATCa
1 411097
414
0 88
0 89

USF_Q6
GYCACGTGNC
gcCACAggca
6 857788
433
0 86
0 85

AP2_Q6
MKCCCSCNGCCC
ttccggGGGaa
12 284970
448
0 98
0 85

OCT1_06
CWNAWTKWSATRYN
gAAATaaaatacg
8 438364
457
0 89
0 86

CEBPB_01
RNRTKNNGMAAKN
aaataacGAAAtca
1 460836
463
0 99
0 91

AP2_Q6
MKCCCSCNGGG
ctccggAGGGcg
12 284970
546
0 86
0 91

RFX1_02
NNGTNRCNNNNRGYAACNN
tggTTTCcttgggagcyt
7 174515
574
0 88
0 89

FRX1_01
NNGTNRCNNRGYAACNN
tggTTTCcttgggagcg
7 172878
574
0 88
0 88

LMO2COM_01
SNNCAGGTGNN
ggcCAGCgaaa
1 242813
640
0 88
0 94

LMO2COM_01
SNNCAGGTGNN
ggcCAGCgaaa
1 242813
640
0 88
0 91

MYOD_Q6
NNCANCTGNY
gcraGCTGca
1 709698
641
0 92
0 97

MYOD_Q6
NNCANCTGNY
gcraGCTGca
1 709698
641
0 92
0 90

AP1_C
NTGASTCAN
atGACACAg
1 430304
652
0 86
0 85

USF_Q6
GYCACGTGNC
ctCACCgggg
6 857788
670
0 82
0 85

USF_Q6
GYCACGTGNC
ctCACCgggg
13 858419
680
0 82
0 89

USF_C
NCACGTGN
cCACCTgg
0 507662
681
0 86
0 92

RFX1_02
NNGTNRCNNNRGYAACNN
ctggggcgaacGGAAccg
7 174515
685
0 88
0 89

AP2_Q6
MKCCCSCNGGCG
agCCCCgagccc
12 284970
734
0 98
0 85

OCT1_Q6
NNNNATGCMATNAN
aagaatgcAAACagg
11.430842
781
0 80
0.88

HNF3B_01
NNNTRTTTRYTY
atgcaAACAggg
2 929849
785
0 99
0 92

CETS1P54_01
NCMGGAWGYN
gtctTCCAga
1 244487
796
0 85
0.89

CDPCR3HD_01
NATYGATSSS
ttCATCgata
2 349950
814
0 93
0 93

CDPCR3HD_01
NATYGATSSS
catcGATAgc
2 340950
816
0 84
0.95

GATA_
NGATMGNMNN
cGATAGCccctt
1 411097
819
0 89
0 88

CETS1P54_01
NCMGGAWGYN
ccctTCCAgc
1 244487
825
0 85
0 89

HNF3B_01
NNNTRTTTRYTY
cctTGTTgccg
2.929849
907
0 99
0.88

CETS1P54_01
NCMGGAWGYN
tttgTCCTgt
1 244487
1027
0 93
0 86

[0457]

3

TABLE 3

Promoter
Site
Transcripton Factor
Core Similarity
Matrix Similarity
Z_score
Position/TSS (bp)
motif
consensus

ABCA7 Human
A
GFI-01
1,00
0,88
4,43
−569
GCCACTATAATCGGAGACTCTAGA
NNNNNNAAATCANNGNNNNNNNN

B
HNF3B_03
0,99
0,85
4,37
−547
GAATGTTGGCCC
NNNTRTTTRYTY

C
CEBP_01
0,87
0,85
2,13
−498
CGTTCGTGGAATGA
RNRTKNNGMAAKNN

D
CEBP_01
0,87
0,85
2,13
−469
ATCTAGTGGAACCC
RNRTKNNGMAAKNN

E
NF1_Q6
1,00
0,86
2,00
−402
GCCTGGCCAGCCCCGGGG
NNTTGGCNNNNNNCCNNN

F
AP4_Q5
1,00
0,90
1,68
−340
TGCAGCCGGT
NNCAGCTGNN

G
NFKAPPAB_01
1,00
0,90
9,96
−260
GGGACCTGCC
GGGAMTTYCC

H
NF1_Q6
1,00
0,89
2,00
−106
CGCCCAATAGC
TRRCCAATSRN

ABCA7 Mouse
A
GFI-01
1,00
0,88
2,96
−842
TTGCCTACAATCCAGGCAACTATT
NNNNNNAAATCANNGNNNNNNNN

B
HNF3B_03
0,99
0,85
3,25
−825
AACTATTGATTC
NNNTRTTTRYTY

C
CEBP_01
0,99
0,94
1,72
−787
TGATTCTGAAATTG
RNRTKNNGMAAKNN

D
CEBP_01
1,00
0,91
1,72
−760
ATGTTGCTAAAATG
RNRTKNNGMAAKNN

E
NF1_Q6
1,00
0,88
2,61
−688
TTCTGGCTGGTGGTGGCAGGA
NNTTGGCNNNNNNCCNNN

F
AP4_Q5
1,00
0,93
2,03
−386
CACAGCAGTG
NNCAGCTGNN

G
NFKAPPAB_01
1,00
0,88
11, 12
−301
GGGAGCTGCC
GGGAMTTYCC

H
NFY_Q6
1,00
0,89
5,63
−156
CCTCCAATGGC
TRRCCAATSRN

[0458]

4

TABLE 4

Oligonucleotides Specific

for the Human ABCA7 Gene

Name
Sequence (5′-3′)
Orientation

ABCA7_U2
CTTCAGCCCGACCGTTG
Sense

ABCA7_AJ
AGAATTTCATGTATCGCC
Sense

ABCA7_L2
CGATGGCAGTGGCTTGTTTGG
Antisense

ABCA7_L1
GCGGAAAGCAGGTGTTGTTCAC
Antisense

ABCA7_AL
CTGGAGTTGCTGTCAGAG
Sense

ABCA7_AK
GGGTAAAAGGTGTATCTGG
Antisense

ABCA7_AN
TCACGAGGACCAATAAGATC
Sense

ABCA7_AM
TGTCAGTGTCACGGAGTAG
Antisense

ABCA7_AP
CCTGGAAGCTGTGTGC
Sense

ABCA7_AO
ACGGAGACGCCAGGAC
Antisense

ABCA7_AR
GTCCTGGCGTCTCCGTTC
Sense

ABCA7_AQ
CTCGTCCAGGATAACAAC
Antisense

ABCA7_AT
GTGCTGCCCTACACGG
Sense

ABCA7_AS
CAGTGCCCAGCCCTGTAC
Antisense

ABCA7_AV
ACCCCAGAGTCTCCATCC
Sense

ABCA7_AU
GAGAAGCCTCCGTATCTGAC
Antisense

ABCA7_AX
CTGCTCTCCTGCTGTTGC
Sense

ABCA7_AW
GCACCATGTCAATGAGCC
Antisense

ABCA7_AZ
CCTCAGCATGGGATACTG
Sense

ABCA7_AY
GCTTGCGTTTGTTCCCTC
Antisense

ABCA7_BA
ACCACGGCTTCTCTCC
Antisense

ABCA7_Q
AGCCAGCAACGCAATCCTCC
Sense

ABCA7_B
CGCACCATGTCAATGAGCCC
Antisense

ABCA7_L3
TGAAGACGTGCGGTGCG
Antisense

ABCA7_L4
TGTCTCCGGCGATACATGAAATTC
Antisense

ABCA7_L5
ACCTCAGACCCAGACCCTTACGC
Antisense

ABCA7_U4
GGAATGAGGTTCAGAAAGGG
Sense

ABCA7_U5
ATGCAAGTTCCCTGGGAGTTAG
Sense

ABCA7_U6
CTCCTTCCGGTGAATGTTGACG
Sense

[0459]

Nucleic acid for regulating the ABCA7 gene, molecules modulating its activity and therapeutic applications

Information

Publication Number

Date Filed

Date Published

Inventors

CPC

US Classifications

International Classifications

Abstract

Description

Claims

Parent Case Info

Provisional Applications (1)