Mammalian regulator of nonsense-mediated RNA decay

FIELD OF THE INVENTION
This invention relates generally to compositions and methods for inhibiting nonsense-mediated RNA decay in a cell.
BACKGROUND OF THE INVENTION
Description of Related Art
The following is a general description of art relevant to the present invention. None is admitted to be prior art to the invention.
All organisms possess the ability to detect and degrade RNA transcripts that contain a premature translation stop codon. Such RNA transcripts are termed "nonsense" transcripts, and the cellular process of degrading these transcripts is termed nonsense-mediated RNA decay (NMRD). Although has been studied extensively in yeast mammalian factors that participate in NMRD have not been described previously. In yeast, the protein Upf1, encoded by the Upf1 gene, is thought to be involved in NMRD(Leeds et al., 1992, Csaplinski et al., 1995). Upf1 shares a high degree of sequence homology with Sen1 of S. cerevisiae, which mediates tRNA splicing, and Mov-10, which is a mouse protein of unknown function. Two additional factors in yeast, Upf2 and Upf3, also are essential for NMRD.
Several factors suggest that NMRD differs substantially between yeast and mammals. For example, while translation is thought to be involved in yeast, several observations suggest that translation does not play a similar role in mammalian cells (Peltz et al., 1994). First, for many genes and mutations, the reduction in the level of nonsense transcripts in the cytoplasm is coupled with a similar reduction in the level of nonsense transcripts in the nucleus of the cell. Examples of transcripts that are reduced in level in both the cytoplasm and nucleus, despite normal rates of transcription, include transcripts encoding .beta.-globin, DHFR, TPI, MUP, and avian sarcoma virus src. A second indication that mammalian NMRD may differ from yeast NMRD is the suggestion that NMRD occurs in the nucleus, rather than cytoplasm, of mammalian cells (Maquat, 1995). The factors that suggest that NMRD occurs in the nucleus of mammalian cells include the observations that: (i) NMRD is dependent upon intron sequences; (ii) most transcripts derived from intronless minigenes are immune to NMRD; (iii) once nonsense transcripts reach the cytoplasm and are bound by polysomes, they display a normal degree of stability; and (iv) nonsense codons influence pre-mRNA processing. A particularly compelling observation is that nonsense mutations can alter the ability of a cell's RNA splicing machinery to recognize exons; this process occurs within the nucleus, and is not dependent upon ribosomes (Dietz et al., 1993a; Dietz and Kendzior, 1994).
NMRD has a distinct physiologic role in intracellular processing, that is, to reduce the presence of abnormal proteins within cells. In the absence of NMRD, premature termination codons (PTCs) that result from nonsense mutations can lead to the production of proteins which are truncated versions of wild-type proteins. PTCs resulting from frameshifts, gene rearrangements, or the retention of introns can, in the absence of normal functioning NMRD, produce aberrant proteins which differ in sequence from the wild-type protein. Such deviant proteins are implicated in disease states. It is anticipated that mammalian organisms containing mutations in RENT1 are likely to suffer from syndromes associated with the excessive build up of these abnormal proteins such as Marfan Syndrome, accelerated aging or various cancers. Thus, RENT1 plays an important role in the control of NMRD and consequently for the prevention of disease states due to the expression of mutant proteins.
SUMMARY OF THE INVENTION
Applicant has isolated and characterized a human complementary DNA which encodes a protein designated RENT1, that regulates the stability of transcripts containing nonsense mutations. Applicant has shown that the expression of dominant negative forms of RENT1 (i.e., mutant proteins that interfere with the function of normal protein) produce stabilization and accumulation of nonsense transcripts. Applicant has also shown that expression of antisense regulatory molecules that inhibit expression of RENT1 result in the stabilization of nonsense transcripts. Applicant has demonstrated that RENT1 is expressed in all human tissues tested, as would be predicted for an essential component of the ubiquitous NMRD pathway.
In addition to cloning and sequencing the human RENT1 cDNA, Applicant has also cloned and sequenced in their entirety the murine RENT1 cDNA and genomic sequences. Applicant has shown that RENT1 is highly homologous to yeast Upf1, a known effector of nonsense transcript degradation. Applicant has shown that expression of a protein composed largely of the human protein sequence restores NMRD in yeast deficient for NMRD functions. Applicant has cloned the mouse gene encoding RENT1 and has shown that the human and mouse proteins are nearly identical. Applicant has concluded that RENT1 is the first mammalian regulator of nonsense transcript stability to be identified.
Applicant has shown that the NMRD pathway can influence the severity of diseases caused by premature termination codons in other genes. Modification of the efficiency of NMRD through manipulation of RENT1 or proteins of related function is proposed as a novel therapeutic strategy. Inhibition of RENT1 expression or function is used to stabilize nonsense transcripts that encode proteins that retain some of their intended function. Alternatively, augmentation of the level of expression of RENT1 or its function and increase in efficiency of NMRD is used to more efficiently and completely degrade nonsense transcripts that encode deleterious proteins such as those with harmful dominant negative or gain-of-function effects.
Modification of the efficiently of NMRD is also proposed as a means to identify new disease genes. If NMRD is experimentally impaired in a cell line harboring a premature termination codon in an unknown disease gene, then nonsense transcripts derived from that disease gene will be stabilized and accumulate within the cells. By identifying the transcript that is enriched upon inhibition of NMRD, the identification of the disease gene is greatly facilitated.
The invention provides substantially pure RENT1 polypeptides, fragments thereof, nucleic acid sequences encoding RENT1 or fragments thereof, methods of detecting modulators of RENT1 or NMRD, methods of administering formulations capable of gene delivery and gene expression of RENT1 nucleic acid, methods of hybridization for RENT1 nucleic acid, and transgenic animals created using RENT1 nucleic acid sequences.
The details of the preferred embodiment of the present invention are set forth in the accompanying drawings and the description below. Once the details of the invention are known, numerous additional innovations and changes will become obvious to one skilled in the art.

BRIEF DESCRIPTION OF THE DRAWINGS
FIGS. 1A-1C show the alignment of the amino acid sequence of RENT1 (SEQ ID NO:2) with homologous proteins.
FIG. 1A, Amino terminus aligned with the specified regions of yeast (y) heat shock protein Sis1 and B. napus (b) RNA-binding protein GRP10.
FIG. 1B, Body aligned with the specified region of S. cerevisiae Upf1p (amino acids 121-853 of SEQ ID NO:22).
FIG. 1C, Carboxy terminus aligned with the specified regions of human or mouse (h/m) RNA-binding protein Ews. Identical and conserved residues are separated by vertical lines (.vertline.) and dots (.multidot.), respectively. Underlined regions serve putative nucleotide-binding (segments 1 and 2) and NTP-hydrolysis (segments 3 through 5) functions. Bold and underlined regions are highly conserved among members of helicase superfamily I. Crosses (.dagger.) occur above sites of demonstrated dominant-negative mutations in Upf1p. Italicized symbols above the human sequence indicate differences in the characterized region of murine sequence, corresponding to amino acid 78 to 1118 in the human protein and flanked by .gtoreq. and.ltoreq. symbols in the figure.
FIG. 2 shows a Northern blot analysis of the expression of RENT1 in human tissues. Poly(A) RNA shows a predominant transcript size of approximately 5.4 kb in all of the indicated adult tissues. A less intense signal is seen at approximately 3.7 kb in all lanes, with an additional and significantly smaller hybridizing transcript unique to the pancreas. Additional tissues tested (spleen, thymus, prostate, testis, ovary, small intestine, colon, and peripheral blood leukocyte) all showed predominant .about.5.4 kb and less intense 3.7 kb bands, except in testes where equally intense signals were observed.
FIG. 3 shows an antisense targeting construct SEQ ID NO:26. The sequence (flanked by dashed lines) substituted for the Sm protein binding site (box SEQ ID NO:27) of native U1 snRNA is shown. This sequence is complementary to coding nucleotides 523-555 of RENT1 cDNA. The hammerhead ribozyme loop is aligned to a GUC triplet in the target, which serves as a consensus site for ribozyme cleavage (arrow). This construct will permit the process of transfecting and stably selecting cell lines which harbor known nonsense transcripts to test the efficiency of NMRD inhibition employing this strategy.
FIG. 4 shows the murine RENT1 complete genomic and amino acid sequence.
FIG. 5 shows the human RENT1 in a yeast recombinant expression vector construct MET25-RENT1.
FIG. 6 shows the human RENT1 in a yeast recombinant expression vector construct pAD54URA-RENT1.
FIG. 7 shows the human RENT1 in a mammalian recombinant expression vector construct CMV-RENT1.
FIG. 8 shows the human RENT1 in a mammalian recombinant expression vector construct BRENT1-neo.
FIG. 9 shows the human RENT1 in a mammalian recombinant expression vector construct RSVA.tangle-solidup.lac-RENT1.
FIG. 10 shows the targeting vector for murine RENT1 designated pBS.mRENT1.TK.genomic.Bam.TM.36.
FIG. 11 shows the murine RENT1 genomic clone designated pBS.mRENT1.genomic.Bam.
FIG. 12 shows the nucleic acid and deduced amino acid sequences of human RENT1 (SEQ ID NOS:1 and 2, respectively).

DETAILED DESCRIPTION OF THE INVENTION
Before the present nucleic and amino acid sequences, compositions, formulations and methods and uses thereof are described, it is to be understood that this invention is not limited to the particular compositions, formulations, sequences and methodologies described herein as such compositions, formulations, sequences and methodologies may vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and that the terminology used herein is not intended to limit the scope of the present invention which will be limited only by the appended claims.
DESCRIPTION OF THE PREFERRED EMBODIMENTS
The invention provides substantially pure polynucleotides encoding the RENT1 protein or fragments thereof. These polynucleotides include DNA, cDNA and RNA sequences which encode RENT1. All polynucleotides encoding all or a portion of RENT1 are also included herein, as long as they encode a polypeptide with RENT1 activity as described herein or a functional fragment of a RENT1 molecule. Such polynucleotides include naturally occurring, synthetic, and intentionally manipulated polynucleotides. For example, RENT1 polynucleotide may be subjected to site-directed mutagenesis. The polynucleotide sequence for RENT1 also includes antisense, nonsense, or missense sequences. The polynucleotides of the invention include sequences that are degenerate as a result of the genetic code. There are 20 natural amino acids, most of which are specified by more than one codon. Therefore, all degenerate nucleotide sequences are included in the invention as long as the amino acid sequence of RENT1 polypeptide or a part thereof encoded by the nucleotide sequence is functionally unchanged.
The invention also provides isolated nucleic acid molecules that encode the RENT1 polypeptides described above, as well as fragments thereof These nucleic acids can contain naturally occurring nucleotide sequences or sequences that differ from those of the naturally occurring nucleic acids that encode RENT1, but encode the same amino acids, due to the degeneracy of the genetic code. The nucleic acids of the invention can contain DNA or RNA nucleotides, or combinations or modifications thereof.
The term "isolated nucleic acid" as used herein means a nucleic acid, e.g., a DNA or RNA molecule, that is not immediately contiguous with the 5' and 3' flanking sequences with which it normally is immediately contiguous when present in the naturally occurring genome of the organism from which it is derived. The term thus describes, for example, a nucleic acid that is incorporated into a vector, such as a plasmid or viral vector; a nucleic acid that is incorporated into the genome of a heterologous cell (or the genome of a homologous cell, but at a site different from that at which it naturally occurs); and a nucleic acid that exists as a separate molecule, e.g., a DNA fragment produced by PCR amplification or restriction enzyme digestion, or an RNA molecule produced by in vitro transcription. The term also describes a recombinant nucleic acid that forms part of a hybrid gene encoding additional polypeptide sequences that can be used, for example, in the production of a fusion protein.
The nucleic acid molecules of the invention can be used as templates in standard methods for production of RENT1 gene products (e.g., RENT1 RNAs and RENT1 polypeptides; see below). In addition, the nucleic acid molecules that encode RENT1 polypeptides (and fragments thereof) and related nucleic acids, such as (1) nucleic acids containing sequences that are complementary to, or that hybridize to, nucleic acids encoding RENT1 polypeptides, or fragments thereof (e.g., fragments containing at least 9, 12, 15, 20, or 25 nucleotides); and (2) nucleic acids containing sequences that hybridize to sequences that are complementary to nucleic acids encoding RENT1 polypeptides, or fragments thereof (e.g., fragments containing at least 9, 12, 15, 20, or 25 nucleotides); can be used in methods focused on their hybridization properties. For example, as is described in further detail below, such nucleic acid molecules can be used in the following methods: PCR methods for synthesizing RENT1 nucleic acids, methods for detecting the presence of RENT1 nucleic acid in a sample, screening methods for identifying nucleic acids encoding new RENT1 family members, and therapeutic methods. The term sample, as used herein, comprises fluid, blood, serum, plasma, cells, tissue, swabs, or secretions or other clinical samples as are commonly familiar to those of ordinary skill in the clinical arts.
The term "substantially pure" is used herein to describe a molecule, such as a polypeptide (e.g., a RENT1 polypeptide, or a fragment thereof) that is substantially free of other proteins, lipids, carbohydrates, nucleic acids, and other biological materials with which it is naturally associated. For example, a substantially pure molecule, such as a polypeptide, can be at least 60%, by dry weight, the molecule of interest. One skilled in the art can purify RENT1 polypeptides using standard protein purification methods and the purity of the polypeptides can be determined using standard methods including, e.g., polyacrylamide gel electrophoresis (e.g., SDS-PAGE), column chromatography (e.g., high performance liquid chromatography (HPLC)), and amino-terminal amino acid sequence analysis.
Also included in the invention are polypeptides having sequences that are "conservative variations" of the sequence of a RENT1 polypeptide. A "conservative variation" amino acid sequence is a sequence that differs from a reference sequence only by conservative amino acid substitutions, for example, substitutions of one amino acid for another of the same class (e.g., substitution of one hydrophobic amino acid, such as isoleucine, valine, leucine, or methionine, for another, or substitution of one polar amino acid for another, such as substitution of arginine for lysine, glutamic acid for aspartic acid, or glutamine for asparagine), or by one or more nonconservative substitutions, deletions, or insertions, provided that the polypeptide retains at least one RENT1-specific activity or a RENT1-specific epitope. For example, one or more amino acids can be deleted from a RENT1 polypeptide, resulting in modification of the structure of the polypeptide, without significantly altering its biological activity. For example, amino- or carboxyl-terminal amino acids that are not required for RENT1 biological activity, can be removed. Such modifications can result in the development of smaller active RENT1 polypeptides.
The term "RENT1" (Regulator of Nonsense Transcripts) refers either to the gene or protein from either the murine or human species as in FIG. 1 (SEQ ID NOs:1, 2, 3 or 4).
A "rest composition," as used herein, is any composition such as a gene, a nucleic acid sequence, a polypeptide, peptide fragment or composition created through the use of a combinatorial library or other combinatorial process that can be assayed for its ability to function in a given capacity (e.g., as a RENT1 co-factor, or RENT1 interactor or RENT1 modulator of nonsense mediated RNA decay (NMRD) using the RENT1 pathway) or compound which mimics the activity of the RENT1 polypeptide (e.g., peptidominetics). Often, such a test composition, nucleic acid sequence or polypeptide is, because of its sequence or structure, suspected of being able to function in a given capacity. Nonetheless, randomly chosen "test" nucleic acid sequences, polypeptides or fragments thereof and compositions also can be used, and art-known techniques, such as expression of polypeptides from nucleic acid libraries, or PCR combinatorial generated polypeptides can be used to this end. A "co-factor" is any composition (e.g., a polypeptide, polypeptide derivative, or peptidominetics) that is capable of modulating RENT1 and influencing NMRD. Included are compositions that naturally induce NMRD via RENT1; also included are compositions that do not naturally induce NMRD (e.g., artificial compositions and natural compositions that serve other purposes). The term "agonist" as used herein means any composition that is capable of increasing RENT1 mediated NMRD. Such an agonist need not bind RENT1 to increase NMRD or to modulate NMRD via RENT1. The term "antagonist" as used herein means any composition that is capable of decreasing the ability of RENT1 or to induce NMRD via the RENT1 pathway. An antagonist need not directly bind, or compete with, RENT1 to modulate NMRD via the RENT1 pathway.
"Formulation" means a composition capable of gene delivery and gene expression, that is, capable of delivering a nucleotide sequence to, or directly into, a target cell whereupon the formulation containing the nucleotide sequence is incorporated on the cytoplasmic side of the outermost membrane of the target cell and capable of achieving gene expression so that detectable levels of gene expression of the delivered nucleotide sequence are expressed in the target cell. More preferably, after delivery into the cytoplasmic side of the cell membrane the composition is subsequently transported, without undergoing endosomal or lytic degradation, into the nucleus of the target cell in a functional state capable of achieving gene expression so that detectable levels of gene expression of the delivered nucleotide sequence are expressed in the target cell. Expression levels of the gene or nucleotide sequence inside the target cell are capable of providing gene expression for a duration of time and in an amount such that the nucleotide product therein is capable of providing a biologically beneficially effective amount of gene product or in such an amount as to provide a functionally beneficial biological effect on the target cell. As used herein, the term formulation can refer to, but is not limited by (either explicitly or implicitly) the following examples: (1) liposome or liposome formulations or liposomal compositions either cationic, anionic or neutral in net character and net charge; (2) DNA, nucleic acid or a nucleic acid expression vector ionically complexed with a polycation/s and a ligand/s such that after attachment of the [DNA+Polycation+Ligand] composition to a cell surface receptor on a target cell via the ligand, the [DNA+Polycation+Ligand] composition is capable of being endocytosed into the target cell and the DNA is subsequently decoupled from the ligand and polycation and delivered to the cell nucleus in a functional condition for subsequent expression. Various alterations in the composition can be envisioned by those of ordinary skill in the art such as including peptide sequences which (a) prevent the composition from endosomal lysis after incorporation into the target cell by allowing the composition to leave the lysosomal vesicle, or (b) which act as a nuclear targeting agent, chaperoning the nucleic acid through the pores of the nuclear envelope and into the nucleus of the cell. Similar formulations, which have been previously described, are the asialoglycoprotein-polylysine conjugation (Wu and Wu, J. Biol. Chem. 263:14621, 1988; Wu et al., J. Biol. Chem. 264:16985, 1989); (3) naked nucleic acid; (4) compacted nucleic acid or a compacted formulation; or (5) plasmid or naked DNA which can be microinjected (Wolff et al., Science 247:1465, 1990); (6) nucleic acid in a viral or retroviral vector compositions; and (7) colloidal dispersions (Felgner et al., Proc. Natl. Acad. Sci. USA84:7413, 1987; Ono et al., Neuroscience Lett 117:259, 1990; Brigham et al., Am. J. Med. Sci. 298:278, 1989; Staubinger and Papahadjopoulos, Meth. Enz. 101:512, 1983). One of ordinary skill in the art will recognize that other compositions for the delivery of nucleotide sequences to target cells may be envisioned.
"Gene delivery" means transportation or transfer of a composition or formulation inside of or into contact with a target cell so that the composition or formulation is capable of being taken up by means of a cytotic process (i.e., pinocytosis, endocytosis, NMRD, macrocytosis etc.) into the interior or cytoplasmic side of the outermost cell membrane of the target cell where it can subsequently be transported into the nucleus of the cell in such functional condition that it is capable of achieving detectable gene expression for a period of time and in such an amount to produce a detectable biologically beneficial effect.
"Gene expression" means the process, after delivery into a target cell, by which a nucleotide sequence undergoes successful transcription and translation such that detectable levels of the delivered nucleotide sequence are expressed in an amount and over a time period so that a functional biological effect is achieved. As used herein, gene expression can refer to, but is not restricted by (either explicitly or implicitly) the following examples. A RENT1 nucleic acid sequence is delivered and expressed in targeted cells such that the targeted cells increase, decrease, or are inhibited in the production of RENT1 protein or RENT1 RNA, thus: either enhancing NMRD, inhibiting NMRD, or modulating NMRD, and subsequently leading to a beneficially detectable biological effect or outcome. "Expressible genetic construct" means a construct which has the RENT1 gene positioned for expression. "Operably linked" means that a gene and a regulatory sequence(s) are connected to permit expression of the RENT1 gene when the appropriate molecules (e.g., transcriptional activator proteins) are bound to the regulatory sequence(s). "Transformed" means a cell into which (or into an ancestor of which) has been introduced, by means of recombinant nucleic acid techniques, a heterologous nucleic acid molecule. "Heterologous" refers to a nucleic acid sequence that either originates from another species or is modified from either its original form or the form primarily expressed in the cell.
"Transgene" means any piece of DNA which is inserted by artifice into a cell, and becomes part of the genome of the organism (i.e., either stably integrated or as a stable extrachromosomal element) which develops from that cell. Such a transgene may include a gene which is partly or entirely heterologous (i.e., foreign) to the transgenic organism, or may represent a gene homologous to an endogenous gene of the organism. Included within this definition is a transgene created by the providing of an RNA sequence which is transcribed into DNA and then incorporated into the genome. The term "trasgenic" as used herein additionally includes any organism whose genome has been altered by in vitro manipulation of the early embryo or fertilized egg or by any transgenic technology to induce a specific gene knockout. The term "gene knockout" as used herein, refers to the targeted disruption of a gene in vivo with complete loss of function that has been achieved by any transgenic technology familiar to those in the art. In one embodiment, transgenic animals having gene knockouts are those in which the target gene has been rendered nonfunctional by an insertion targeted to the gene to be rendered nonfunctional by homologous recombination. As used herein, the term "transgenic" includes any transgenic technology familiar to those in the art which can produce an organism carrying an introduced transgene or one in which an endogenous gene has been rendered nonfunctional or knocked out.
"Promoter" means the minimal nucleotide sequence sufficient to direct transcription. Also included in the invention are those promoter elements that are sufficient to render promoter-dependent gene expression controllable for cell-type specific, tissue specific, or inducible by external signals or agents; such elements may be located in the 5' or 3' regions of the native gene. "Detectably-labeled" means any means for marking and identifying the presence of a molecule, e.g., an oligonucleotide probe or primer, an antibody or fragment thereof, a protein or fragment thereof, a gene or fragment thereof, or a cDNA molecule. Methods for detectably-labeling are well known in the art and include, without limitation, radioactive labeling (e.g., with an isotope such as .sup.32 P or .sup.35 S) and nonradioactive labeling (e.g., chemiluminescent labeling, e.g., fluorescent labeling).
"Purified antibody" means antibody which is at least 60%, by weight, free from proteins and naturally-occurring organic molecules with which it is naturally associated. Preferably, the preparation is at least 75%, more preferably 90%, and most preferably at least 99%, by weight, antibody, e.g., a RENT1 specific antibody. A purified antibody may be obtained, for example, by affinity chromatography using recombinantly-produced protein or conserved motif peptides and standard techniques. The invention can employ not only intact monoclonal or polyclonal antibodies, but also an immunologically-active antibody fragment, such as a Fab' or (Fab')2 fragment, or a genetically engineered Fv fragment (Ladner et al., U.S. Pat. No. 4,946,788). "Specifically binds" means an antibody which recognizes and binds a specified protein but which does not substantially recognize and bind other molecules in a sample, e.g., a biological sample, which naturally includes protein.
"Therapeutically effective" as used herein, refers to an amount formulation that is of sufficient quantity to ameliorate the state of the patient so treated. "Ameliorate" refers to a lessening of the detrimental effect of the disease state or disorder in the patient receiving the therapy. The subject of the invention is preferably a human, however, it can be envisioned that any animal can be treated in the method of the instant invention. The term "modulate" means enhance, inhibit, alter, or modify the expression of RENT1 mRNA, nucleic acid, polypeptide or protein.
The invention also provides a method for determining whether a test agent or composition modulates NMRD in a cell. The method can be performed by (i) providing a cell that has RENT1; (ii) contacting the cell with a test agent or composition that, in the absence of the test agent or composition, activates the RENT1 in the cell; and (iii) detecting a change in the NMRD of the cell. In practicing the invention, the cell can be contacted with the test agent or composition either simultaneously or sequentially. An increase in NMRD indicates that the test agent or composition is an agonist of RENT1 while a decrease in NMRD indicates that the test agent or composition is an antagonist of RENT1. If desired, the above-described method for identifying modulators of NMRD can be used to identify compositions, co-factors or other compositions within the NMRD pathway comprising RENT1 for use in this aspect of the invention. Any agent or composition can be used as a test agent or composition in practicing the invention; a preferred test agent or compositions include polypeptides and small organic agent or compositions. Although sequence or structural homology can provide a basis for suspecting that a test agent or composition can modulate NMRD via RENT1 in a cell, randomly chosen test agent or compositions also are suitable for use in the invention. Art-known methods for randomly generating an agent or compositions (e.g., expression of polypeptides from nucleic acid libraries) can be used to produce suitable test agent or compositions. Those skilled in the art will recognize alternative techniques can be used in lieu of the particular techniques described herein.
The invention also provides a method for detecting novel co-factors or inhibitors which bind RENT1 which comprises contacting a sample comprising RENT1 with test compositions and measuring the change in NMRD after application of the test composition. The RENT1 protein of the instant invention is useful in a screening method for identifying novel test compounds or novel test compositions which affect NMRD via RENT1. Thus, in another embodiment, the invention provides a method for screening test compositions comprising incubating components, which include the test composition, and RENT1 under conditions sufficient to allow the components to interact, then subsequently measuring the effect the test composition has on NMRD in a test cell. The observed effect on NMRD between RENT1 and a composition may be either agonistic or antagonistic. Preferably, the polypeptide encoding the RENT1 is the polypeptide or functional fragment thereof of SEQ ID NO:2 or 4 or a synthetic peptide which has the biological activity of the RENT1 protein.
The invention also includes fragments of RENT1 polypeptides, that retain at least one RENT1-specific activity or epitope. For example, a RENT1 polypeptide fragment containing, e.g., at least 8-10 amino acids can be used as an immunogen in the production of RENT1-specific antibodies. Such fragments can easily be identified by comparing the sequence of RENT1 by reference to FIG. 1. In addition to their use as peptide immunogens, RENT1 fragments can be used in immunoassays, such as ELISAs, to detect the presence of RENT1-specific antibodies in samples.
The RENT1 polypeptides of the invention can be obtained using any of several standard methods. For example, RENT1 polypeptides can be produced in a standard recombinant expression systems (see below), chemically synthesized (this approach may be limited to small RENT1 peptide fragments), or purified from tissues in which they are naturally expressed (see, e.g., Ausubel, et al, supra).
The invention also provides isolated nucleic acid molecules that encode the RENT1 polypeptides described above, as well as fragments thereof These nucleic acids can contain naturally occurring nucleotide sequences, or sequences that differ from those of the naturally occurring nucleic acids that encode RENT1 s, but encode the same amino acids, due to the degeneracy of the genetic code or amino acids which are conservative variations. The nucleic acids of the invention can contain DNA or RNA nucleotides, or combinations or modifications thereof.
All organisms that have been studied to date possess the ability to detect and degrade RNA transcripts that contain a premature signal for the termination of translation. The process of nonsense-mediated RNA decay (NMRD) has been most comprehensively studied in the yeast Saccharomyces cerevisiae. Essential components of the yeast pathway include at least 3 trans-acting factors (Upf1-3). The human homologue of yeast Upf1, is RENT1 (regulator of nonsense transcripts). The invention includes methods for identifying nucleic acid molecules that encode members of mammalian RENT1 homologues. In these methods, a sample, e.g., a nucleic acid library, such as a cDNA library, that contains a nucleic acid encoding a RENT1 polypeptide is screened with a RENT1-specific probe, e.g., a RENT1-specific nucleic acid probe. RENT1-specific nucleic acid probes are nucleic acid molecules (e.g., molecules containing DNA or RNA nucleotides, or combinations or modifications thereof) that specifically hybridize to nucleic acids encoding RENT1 polypeptides, or to complementary sequences thereof.
Because RENT1 is closely related to the Upf family in yeast, the term "RENT1-specific probe," in the context of this invention, refers to probes that bind to nucleic acids encoding RENT1 polypeptides, or to complementary sequences thereof, to a detectably greater extent than to nucleic acids encoding Upf sequences, or to complementary sequences thereof. The term "RENT1-specific probe" thus includes probes that can bind to nucleic acids encoding RENT1 polypeptides (or to complementary sequences thereof), but not to nucleic acids encoding Upf sequences (or to complementary sequences thereof), to an appreciable extent.
The invention facilitates production of RENT1-specific nucleic acid probes. Methods for obtaining such probes can be designed based on the amino acid sequence alignments shown in FIG. 1. The probes, which can contain at least 9, e.g., at least 12, 15, 25, 35, 50, 100, or 150 nucleotides, can be produced using any of several standard methods (see, e.g., Ausubel, et al., supra). For example, preferably, the probes are generated using PCR amplification methods, such as those described below. In these methods, primers are designed that correspond to RENT1 sequences, which can include RENT1-specific amino acids, and the resulting PCR product is used as a probe to screen a nucleic acid library, such as a cDNA library.
As is known in the art, PCR primers are typically designed to contain at least 15 nucleotides, for example, 15-30 nucleotides. The design of RENT1-specific primers containing 21 nucleotides, which encode RENT1 peptides containing 7 amino acids, are described as follows. Preferably, most or all of the nucleotides in such a probe encode RENT1-conserved amino acids, including RENT1-specific amino acids. For example, primers containing sequences encoding peptides containing at least 40% RENT1-conserved amino acids can be used. Such a primer, containing 21 nucleotides, can include sequences encoding at least 3/7, 4/7, 5/7, 6/7, or 7/7 RENT1-conserved amino acids. As can be determined by analysis of FIG. 1, in the case of a 21 nucleotide primer, encoding 7 amino acids, up to 5 amino acids can be RENT1-specific. Thus, the primer can contain sequences encoding at least one RENT1-specific amino acid, for example, up to 5 RENT1-specific amino acids. Once RENT1-specific amino acid sequences are selected as templates against which primer sequences are to be designed, the primers can be synthesized using, e.g., standard chemical methods. As is described above, due to the degeneracy of the genetic code, such primers should be designed to include appropriate degenerate sequences, as can readily be determined by one skilled in the art.
Based on the guidelines presented above, examples of RENT1-conserved amino acid peptides that can be used as templates for the design of RENT1-specific primers are as follows. Additional examples can be found by analysis of sequence alignments of RENT1 polypeptides. Primers can be designed, for example, based on 5-10 amino acid regions of the RENT1 peptide, depending on the lengths of the primers desired. For example, primers can be designed to correspond to 7 consecutive amino acids of any of the segments shown below.
1. QVDFVQKSTSFDRMQSALKTFAV (SEQ ID NO:5) (corresponding to amino acids 411-434 of human RENT1)
2. LSLIOGPPGTGKTVTSATIVYHLARQDN (SEQ ID NO:6) (corresponding to amino acids 487-515 of human RENT1)
3. HIVNHLVRAKCKEVTLHKDGP(SEQ ID NO:7) (corresponding to amino acids 488-511 of human RENT1)
4. AGQLDAQVGPEGILQNGAVDDSVAKT (SEQ ID NO:8; corresponding to amino acids 72-97 of human RENT1 amino terminus)
5. ELIDESTQATEPECMVPVVLGAKQLLVGD (SEQ ID NO:9; corresponding to amino acids 634-663 of human RENT1)
6. SMSQPSQMSQPGLSQPELSQ (SEQ ID NO:10; corresponding to amino acids 1061-1075 of human RENT1-carboxy terminus)
As is described above, RENT1-specific primers, for example, primers based on the RENT1-specific peptides shown above, or portions thereof, can be used in PCR reactions to generate RENT1-specific probes, which can be used in standard screening methods to identify nucleic acids encoding RENT1 family members (see, e.g., Ausubel, et al., supra).
In addition to RENT1-specific nucleic acid probes, RENT1-specific polypeptide probes, such as RENT1-specific antibodies, can be used to screen samples, e.g., expression libraries, for nucleic acids encoding novel RENT1 polypeptides, or portions thereof For example, an antibody that specifically binds to a RENT1-specific peptide can be used in this method. Methods for carrying out such screening are well known in the art (see, e.g., Ausubel, et al., supra).
The sequences of a pair of nucleic acid molecules (or two regions within a single nucleic acid molecule) are said to be "complementary" to each other if base pairing interactions can occur between each nucleotide of one of the members of the pair and each nucleotide of the other member of the pair. A pair of nucleic acid molecules (or two regions within a single nucleic acid molecule) are said to "hybridize" to each other if they form a duplex by base pairing interactions between them. As is known in the art, hybridization between nucleic acid pairs does not require complete complementarity between the hybridizing regions, but only that there is a sufficient level of base pairing to maintain the duplex under the hybridization conditions used.
Hybridization reactions are typically carried out under low to moderate stringency conditions, in which specific and some nonspecific interactions can occur. After hybridization, washing can be carried out under moderate or high stringency conditions to eliminate nonspecific binding. As is known in the art, optimal washing conditions can be determined empirically, e.g., by gradually increasing the stringency. Condition parameters that can be changed to affect stringency include, e.g., temperature and salt concentration In general, the lower the salt concentration and the higher the temperature, the higher the stringency. For example, washing can be initiated at a low temperature (e.g., room temperature) using a solution containing an equivalent or lower salt concentration as the hybridization solution. Subsequent washing can be carried out using progressively warmer solutions having the same salt solution. Alternatively, the salt concentration can be lowered and the temperature maintained in the washing step, or the salt concentration can be lowered and the temperature increased. Additional parameters can be altered to affect stringency, including, e.g., the use of a destabilizing agent, such as formamide.
In nucleic acid hybridization reactions, the conditions used to achieve a particular level of stringency will vary, depending on the nature of the nucleic acids being hybridized. For example, the length, degree of complementarity, nucleotide sequence composition (e.g., GC v. AT content), and nucleic acid type (e.g., RNA v. DNA) of the hybridizing regions of the nucleic acids can be considered in selecting hybridization conditions. An additional consideration is whether one of the nucleic acids is immobilized, for example, on a filter.
An example of progressively higher stringency conditions is as follows: 2.times.SSC/0.1% SDS at about room temperature (hybridization conditions); 0.2.times.SSC/0.1% SDS at about room temperature (low stringency conditions); 0.2.times.SSC/0.1% SDS at about 42.degree. C. (moderate stringency conditions); and 0.1.times.SSC at about 68.degree. C. (high stringency conditions). Washing can be carried out using only one of these conditions, e.g., high stringency conditions, or each of the conditions can be used, e.g., for 10-15 minutes each, in the order listed above, repeating any or all of the steps listed. However, as mentioned above, optimal conditions will vary, depending on the particular hybridization reaction involved, and can be determined empirically.
The nucleic acid molecules of the invention can be obtained by any of several standard methods. For example, the molecules can be produced using standard recombinant, enzymatic (e.g., PCR or reverse transcription (RT)/PCR methods), and chemical (e.g., phosphoramidite-based synthesis) methods. In addition, they can be isolated from samples, such as nucleic acid libraries and tissue samples, using standard hybridization methods. For example, as described above, using standard methods, genomic or cDNA libraries can be hybridized with nucleic acid probes corresponding to RENT1 nucleic acid sequences to detect the presence of a homologous nucleotide sequence in the library (see, e.g., Ausubel, et al., supra). These methods are described in more detail above. Also as described above, nucleic acids encoding polypeptides containing at least one RENT1 epitope, such as a RENT1-specific epitope, can also be identified by screening a cDNA expression library, such as a library contained in lambda gt11, with a RENT1-specific antibody as a probe. Such antibodies can be either polyclonal or monoclonal and are produced using standard methods (see, e.g., Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1988).
RENT1-specific antibodies and nucleic acids can be used as probes in methods to detect the presence of a RENT1 polypeptide (using an antibody) or nucleic acid (using a nucleic acid probe) in a sample or specific cell type. In these methods, a RENT1-specific antibody or nucleic acid probe is contacted with a sample from a patient suspected of having a RENT1-associated disorder, and specific binding of the antibody or nucleic acid probe to the sample detected. The level of RENT1 polypeptide or nucleic acid present in the suspect sample can be compared with the level in a control sample, e.g., an equivalent sample from an unaffected individual, to determine whether the patient has a RENT1-associated disorder. RENT1 polypeptides, or fragments thereof, can also be used as probes in diagnostic methods, for example, to detect the presence of RENT1-specific antibodies in samples.
Additionally, RENT1-specific antibodies could be used to detect novel cofactors which have formed a complex with RENT1 or fragment thereof.
The RENT1-specific nucleic acid probes can be labeled with a compound that facilitates detection of binding to the RENT1 nucleic acid in the sample. For example, the probe can contain biotinylated nucleotides, to which detectably labeled avidin conjugates (e.g. horse-radish peroxidase-conjugated avidin) can bind. Radiolabeled nucleic acid probes can also be used. These probes can be used in nucleic acid hybridization assays to detect altered levels of RENT1 s in a sample. For example, in situ hybridization, RNASE protection, and Northern Blot methods can be used. Other standard nucleic acid detection methods that can be used in the invention are known to those of skill in the art (see, e.g., Ausubel, et al., supra). In addition, when the diagnostic molecule is a nucleic acid, it can be amplified prior to binding with a RENT1-specific probe. Preferably, PCR is used, but other nucleic acid amplification methods, such as the ligase chain reaction (LCR), ligated activated transcription (LAT), and nucleic acid sequence-based amplification (NASBA) methods can be used.
Additionally, RENT1-specific nucleic acid probes could be used to detect unique polypeptide expression clones from nucleic acid libraries such as expression libraries for fragments of the RENT1 nucleic acid sequence or homologues of the RENT1 nucleic acid sequence. RENT1-specific nucleic acid probes could be used to detect expression clones used to randomly generate compounds (e.g., expression of polypeptides from nucleic acid libraries) that can be used to produce suitable test compounds of the instant invention. A cDNA expression library can be screened indirectly for RENT1 peptides having at least one epitope, using antibodies specific for RENT1 as described herein. Such antibodies can be either polyclonally or monoclonally derived and used to detect expression product indicative of the presence of RENT1 cDNA.
Specifically disclosed herein is a complete cDNA sequence containing the entire human RENT1 coding sequence and a genomic DNA sequence containing murine RENT1.
Although divergence is seen at the extreme N- and C-termini, the large central regions of Upf1 and RENT1 (residues 60-853 and 121-917, respectively) show 58% identity and 80% conservation. Moreover, RENT1 is the first identified mammalian protein that contains all of the putative functional elements found in Upf1 including the cysteine-rich zinc finger-like domains that may participate in nucleotide binding, the domains with putative NTPase activity, and the motifs common to members of helicase superfamily I.
The N-terminus of RENT1 contains a region composed entirely of proline, glycine, and alanine (PGA) residues not found in Upf1. While the function of this region is unknown, PGA-rich stretches have been found to act as direct transcriptional repressors. Alternatively, the helix-disturbing properties imposed by the high PG content may confer a favorable conformation to the molecule. If one excludes the PGA-rich region, certain similarities are evident between the N-termini of RENT1 and Upf1. Both are relatively rich in serines and threonines (19 vs. 24%, respectively) and acidic residues (D or E; 22 vs. 18%, respectively), features commonly seen in nucleotide-binding proteins with transactivation or transcriptional regulation properties. Both C-termini are rich in serines and glutamines (21 vs. 18%, respectively) but the occurrence of the majority of these residues as SQ dipeptides (n=14) is unique to RENT1. Many RNA recognition motif (RRM)-containing proteins have glutamine rich regions that are postulated to regulate multiple aspects of RNA processing. BLAST analysis of the divergent N- and C-terminal sequences of RENT1 reveals homology to multiple proteins that interact with RNA and regulate its processing. These include the Sis1 heat shock protein of yeast (p=5.6e-07), the Gr10 RNA-binding protein of B. napus (p=1.2e-04), and the human or mouse EWS RNA-binding protein p=8.9e-03) (18-20).
The polynucleotide encoding RENT1 includes the nucleotide sequence in FIG. 1 (SEQ ID NO:1), as well as nucleic acid sequences complementary to that sequence. A complementary sequence may include an antisense nucleotide. When the sequence is RNA, the deoxynucleotides A, G, C, and T of FIG. 1 are replaced by ribonucleotides A, G, C, and U, respectively. Also included in the invention are fragments of the above-described nucleic acid sequences that are at least 9 bases in length, which is sufficient to permit the fragment to selectively hybridize to DNA that encodes the protein of FIG. 1 (SEQ ID NO:2) under physiological conditions.
DNA sequences of the invention can be obtained by several methods. For example, the DNA can be isolated using hybridization techniques which are well known in the art. These include, but are not limited to: 1) hybridization of genomic or cDNA libraries with probes to detect homologous nucleotide sequences, 2) polymerase chain reaction (PCR) on genomic DNA or cDNA using primers capable of annealing to the DNA sequence of interest, and 3) antibody screening of expression libraries to detect cloned DNA fragments with shared structural features. Therefore, given a partial DNA sequence of the gene of interest, one of skill in the art would be able to prepare probes for isolation of a full length cDNA clone, without undue experimentation (see for example, Ausubel, et al., Current Protocols in Molecular Biology, Units 6.3-6.4, Greene Publ., current edition; Maniatis, et al., Molecular Cloning, Cold Spring Harbor Laboratories, current edition).
The development of specific DNA sequences encoding RENT1 can also be obtained by: 1) isolation of double-stranded DNA sequences from the genomic DNA; 2) chemical manufacture of a DNA sequence to provide the necessary codons for the polypeptide of interest; and 3) in vitro synthesis of a double-stranded DNA sequence by reverse transcription of mRNA isolated from a eukaryotic donor cell. In the latter case, a double-stranded DNA complement of mRNA is eventually formed which is generally referred to as cDNA.
DNA sequences encoding RENT1 can be expressed in vitro, in vivo or ex vivo by DNA transfer into a suitable target cell. "Target cells" are cells in which a vector can be propagated and its DNA expressed or in which a formulation can be delivered into a cell for subsequent gene expression. The term also includes any progeny of the subject target cell. It is understood that all progeny may not be identical to the parental cell since there may be mutations that occur during replication. However, such progeny are understood to be included when the term "target cell" is used. Methods of stable transfer, meaning that the foreign DNA is continuously maintained in the host, are known in the art.
In the present invention, the RENT1 polynucleotide sequences may be inserted into a recombinant expression vector construct. The term "recombinant expression vector construct" refers to a plasmid, virus or other vehicle known in the art that has been manipulated by insertion or incorporation of RENT1 genetic sequences. Such expression vectors or constructs contain a promoter sequence which facilitates the efficient transcription of the inserted genetic sequence of the host. The expression vector or construct typically contains an origin of replication, a promoter, as well as specific genes which allow phenotypic selection of the transformed cells. Vectors or constructs suitable for use in the present invention include, but are not limited to the T7-based expression vector for expression in bacteria (Rosenberg, et al., Gene, 56:125, 1987), the pMSXND expression vector for expression in mammalian cells (Lee and Nathans, J. Biol. Chem., 263:3521, 1988) and baculovirus-derived vectors for expression in insect cells. The DNA segment can be present in the vector operably linked to regulatory elements, for example, a promoter (e.g., T7, metallothionein I, or polyhedrin promoters). The term "dominant negative" refers to the phenotypic effect of an expression vector or construct which expresses a nucleic acid sequence encoding a form of a RENT1 polypeptide which exerts a controlling or ruling influence that is deleterious compared to the normal form of the RENT1 polypeptide. In a preffered embodiment the dominant negative phenotype is conveyed by the expression of mutant RENT1 proteins that interfere with the function of the normal RENT1 protein. Such an effect is like the effect of dominance of one allele of a pair of alleles encoding the homologous genes on a pair of homologous chromosomes so that the phenotypic effect of the one allele exerts a deleterious controlling influence over the other allele.
Polynucleotide sequences encoding RENT1 can be expressed in either prokaryotes or eukaryotes. Hosts can include microbial, yeast, insect and mammalian organisms. Methods of expressing DNA sequences having eukaryotic or viral sequences in prokaryotes are well known in the art. Biologically functional viral and plasmid DNA vectors capable of expression and replication in a target cell are known in the art. Such vectors are used to incorporate DNA sequences of the invention.
Transformation of a target cell with recombinant DNA may be carried out by conventional techniques as are well known to those skilled in the art. Where the target is prokaryotic, such as E. coli, competent cells which are capable of DNA uptake can be prepared from cells harvested after their exponential growth phase and subsequently treated by the CaCl.sub.2 method using procedures well known in the art. Alternatively, MgCl.sub.2 or RbCl can be used. Transformation can also be performed after forming a protoplast of the target cell if desired.
When the target cell is a eukaryote, such methods of transfection of DNA as calcium phosphate co-precipitates, conventional mechanical procedures such as microinjection, electroporation, insertion of a plasmid encased in liposome or liposome formulations, or virus vectors may be used. Eukaryotic cells can also be co-transformed with DNA sequences encoding the RENT1 of the invention, and a second foreign DNA molecule encoding a selectable phenotype, such as the herpes simplex thymidine kinase gene. Another method of transformation is to use a eukaryotic viral vector, such as simian virus 40 (SV40) or bovine papilloma virus, to transiently infect or transform eukaryotic cells and express the protein. (see for example, Eukaryotic Viral Vectors, Cold Spring Harbor Laboratory, Gluzman ed., 1982).
As is demonstrated in Example 7 herein, RENT1 is expressed in all of the adult human tissues tested, but considerable variation in the tissue-specific level of expression exists. One of ordinary skill in the art can expand the survey of RENT1 expression by the addition of samples from more tissues and by the assessment of expression at various developmental stages in the mouse. One of ordinary skill in the art can also correlate the level of RENT1 expression with the deficiency of NMRD in various tissues and at various developmental stages. This can be accomplished by a combination of Northern blot and in situ hybridization analysis using a mouse strain (gus.sup.mps) that harbors a PTC in exon 10 (of 12) of the ubiquitously expressed gene encoding .beta.-glucuronidase (Sands & Birkenmeier, 1993).
.beta.-glucuronidase mRNA levels are decreased by -200 fold in gus.sup.mps /gus.sup.mps mice. In gus.sup.mps /+mice it is possible to determine the relative contribution of the wild-type and mutant alleles to the total pool of .beta.-glucuronidase mRNA using a quantitative RT-PCR/ASO hybridization protocol (Dietz, et al., 1993b). Five developmental stages can be targeted: day 10.5 pc [Witschi stage (WS) 25], day 16.5 pc (WS 35), birth (WS 36), day 7 (child), and day 30 (adult). Relative abundance of wild-type and mutant .beta.-glucuronidase mRNA (as a marker of NMRD efficiency) can be determined for entire early fetuses. The tissue-specific pattern can be assessed at all later developmental stages. These results can be correlated with the expression level of RENT1 using in situ hybridization (early fetus) or Northern analysis (late fetus and onward). Additionally, one of ordinary skill in the art can generate a monospecific antibody to N-terminal epitopes within RENT1 using the teachings herein. The skilled artisan can create fusion proteins in bacteria (with epitopes of RENT1 coupled with GST or MBP tags from Pharmacia or NEB vectors, respectively). The resulting peptides can be used in the generation of peptide antisera and affinity purification. Specific antibodies, can then be used for Western analysis and immunohistochemistry to determine if RENT1 protein expression parallels transcript expression.
It is hypothesized that mammalian NMRD has both a nuclear and cytoplasmic component. Using the teachings herein, determination of subcellular localization of RENT1 can be established. A pHA-RNT1 expression vector encoding a fusion protein between an HA-tag and RENT1 can be transiently transfected into Cos-7 cells using the DEAE-dextran method. Immunohistochemical analysis can be carried out 48 hours post-transfection. After fixation in 3.5% paraformaldehyde and permeablization in 0.1% Nonidet P40, cells can be incubated in a 1:100 dilution of primary antibody (anti-HA 12 CA5. Boehringer Mannheim) followed by incubation in a 1:200 dilution of secondary antibody (antimouse IgG fluorescein conjugate, BM), For the last 10 minutes of secondary incubation 1 .mu.l of DAPI (1 mg/ml) can be added to mark the nucleus. Staining can be visualized by fluorescence microscopy. Mock transfected (pHA without insert) and untransfected cells can be carried through all phases of experimentation as negative controls.
Isolation and purification of microbial expressed RENT1 polypeptide, or fragments, or conservative variants thereof, provided by the invention, may be carried out by conventional means including preparative chromatography and immunological separations involving monoclonal or polyclonal antibodies.
The RENT1 polypeptides of the invention can also be used to produce antibodies which are immunoreactive or bind to epitopes of RENT1 polypeptides. Antibody which consists essentially of pooled monoclonal antibodies with different epitopic specificities, as well as distinct monoclonal antibody preparations are provided Monoclonal antibodies are made from antigen containing fragments of the RENT1protein by methods well known in the art (Kohler, et al., Nature, 256:495, 1975; Current Protocols in Molecular Biology, Ausubel, et al., ed., 1989).
The term "antibody" as used in this invention includes intact molecules as well as fragments thereof, such as Fab, Fab', F(ab').sub.2, and Fv which are capable of binding the epitopic determinant. These antibody fragments retain some ability to selectively bind with its antigen or receptor and are defined as follows:
(1) Fab, the fragment which contains a monovalent antigen-binding fragment of an antibody molecule can be produced by digestion of whole antibody with the enzyme papain to yield an intact light chain and a portion of one heavy chain;
(2) Fab', the fragment of an antibody molecule can be obtained by treating whole antibody with pepsin, followed by reduction, to yield an intact light chain and a portion of the heavy chain; two Fab' fragments are obtained per antibody molecule;
(3) (Fab').sub.2, the fragment of the antibody that can be obtained by treating whole antibody with the enzyme pepsin without subsequent reduction; F(ab').sub.2 is a dimer of two Fab' fragments held together by two disulfide bonds;
(4) Fv, defined as a genetically engineered fragment containing the variable region of the light chain and the variable region of the heavy chain expressed as two chains; and
(5) Single chain antibody ("SCA"), defined as a genetically engineered molecule containing the variable region of the light chain, the variable region of the heavy chain, linked by a suitable polypeptide linker as a genetically fused single chain molecule.
Methods of making these fragments are known in the art. (See for example, Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, New York (current edition), incorporated herein by reference).
As used in this invention, the term "epitope" means any antigenic determinant on an antigen to which the paratope of an antibody binds. Epitopic determinants usually consist of chemically active surface groupings of molecules such as amino acids or sugar side chains and usually have specific three dimensional structural characteristics, as well as specific charge characteristics.
Antibodies which bind to the RENT1 polypeptide of the invention can be prepared using an intact polypeptide or fragments containing small peptides of interest as the immunizing antigen. The polypeptide or peptide used to immunize an animal can be derived from translated cDNA or chemical synthesis which can be conjugated to a carrier protein, if desired. Such commonly used carriers which are chemically coupled to the peptide include keyhole limpet hemocyanin (KLH), thyroglobulin, bovine serum albumin (BSA), and tetanus toxoid. The coupled peptide is then used to immnunize the animal (e.g., a mouse, a rat, goat, sheep or a rabbit).
If desired, polyclonal or monoclonal antibodies can be further purified, for example, by binding to and elution from a matrix to which the polypeptide or a peptide to which the antibodies were raised is bound. Those of skill in the art will know of various techniques common in the immunology arts for purification and/or concentration of polyclonal antibodies, as well as monoclonal antibodies (See for example, Coligan, et al., Unit 9, Current Protocols in Immunology, Wiley Interscience, current edition, incorporated by reference).
It is also possible to use the anti-idiotype technology to produce monoclonal antibodies which mimic an epitope. For example, an anti-idiotypic monoclonal antibody made to a first monoclonal antibody will have a binding domain in the hypervariable region which is the "image" of the epitope bound by the first monoclonal antibody.
The present invention identifies a nucleotide sequence that can be expressed in an altered manner as compared to expression in a normal cell, therefore it is possible to design appropriate therapeutic or diagnostic techniques directed to this sequence. Thus, where a disorder is associated with the altered expression of RENT1, nucleic acid sequences that modulate RENT1 expression at the transcriptional or translational level can be used. Such a modulation can be either inhibitory or stimulatory. This approach can utilize, for example, antisense, missense or nonsense, nucleic acid and ribozymes to block translation of a specific RENT1 mRNA, either by masking that mRNA with an antisense nucleic acid or by cleaving it with a ribozyme. Such RENT1 disorders may include diseases in which a deleterious excess of nonsense alleles are stabilized in a cell, for example, premature aging or various cancers.
The RENT1 gene can be used in human gene therapy. Cells harboring genes containing nonsense alleles that encode partially functional truncated proteins can be transfected with a construct that reduces or eliminates expression or function of RENT1. In the case of certain diseases such as cystic fibrosis, the resulting stabilization of the transcript, and increased expression of the truncated protein, may be sufficient to reduce symptoms of disease.
Conversely, a construct that substantially increases the expression or function of RENT1 in NMRD may further reduce the expression of partially functional truncated proteins. In the case of certain dominantly expressed disorders such as Marfan syndrome, the further reduction of these truncated protein may reduce or eliminate symptoms of disease.
The RENT1 gene and RENT1 protein can be used in discovery of unknown human genes, with apriori knowledge of the gene in question. In one manifestation of this invention, cells are isolated from an individual displaying a particular phenotype which is suspected of being caused by a gene or genes containing nonsense mutations. A subset of these cells is treated in a manner (such as transfecting the cells with a genetic construct) that reduces or eliminates the expression or function of RENT1 in the cells. Levels of mRNA containing nonsense mutations in these cells will thus be increased to higher levels. Using standard techniques of differential display of mRNA, or genetic subtraction techniques commonly applied to cDNAs, the mRNA containing nonsense mutations can be enriched and then isolated by comparing the mRNA populations of the original cells with the mRNA populations in cells treated to eliminate or reduce RENT1 activity.
Cells harboring nonsense alleles which encode partially functional truncated proteins can be transfected with constructs encoding dominant-negative forms of RENT1. If the mutant transcript were stabilized the cellular phenotype can be determined by RNA and protein quantification and biofunctional assays. In addition, subtractive hybridization methods can be used to enrich for transcripts that are unregulated after inhibition of NMRD without assuming any apriori knowledge regarding the disease gene in question since disruption of NMRD may rescue selected cellular phenotypes or manipulation of NMRD may identify novel disease genes. Furthermore, it may be possible to exploit the NMRD pathway for therapeutic purposes. Upon stabilization of nonsense transcripts by manipulation of NMRD, selected truncated protein products may retain enough of their intended function to rescue the disease phenotype. Alternatively, down regulation of NMRD in cultured patient cells that are expected to express some unknown disease gene can produce a dramatic increase in abundance of nonsense transcripts. If the phenotype is caused by a premature termination codon (PTC), then subtractive methods using RNA from unmanipulated and manipulated patient cells can greatly enrich transcripts thus permiting identification of a disease gene. By comparing the gene products of a cell line to itself, one of ordinary skill in the art can eliminate most of the "noise" from the cell (i.e., represented in nondisease mRNAs that occur when such techniques are used to compare a patient cell line to that from a control individual) thus permitting identification of specific genes and alleles. One of ordinary skill in the art can apply such a subtractive technique to identify genes and mutant alleles that are involved in complex multigenic disorders or rare phenotypes.
Antisense nucleic acids are DNA or RNA molecules that are complementary to at least a portion of a specific mRNA molecule (Weintraub, Scientific American, 262:40, 1990). In the cell, antisense nucleic acids hybridize to a corresponding mRNA, forming a double-stranded molecule. The antisense nucleic acids interfere with the translation of the mRNA, since the cell will not translate a mRNA that is double-stranded. Antisense oligomers of about 15 nucleotides are preferred, since they are easily synthesized and are less likely to cause problems than larger molecules when introduced into the target RENT1-producing cell. The use of antisense methods to inhibit the in vitro translation of genes is well known in the art (Marcus-Sakura, Anal.Biochem., 172:289, 1988).
Ribozymes are RNA molecules possessing the ability to specifically cleave other single-stranded RNA in a manner analogous to DNA restriction endonucleases. Through the modification of nucleotide sequences which encode these RNAs, it is possible to engineer molecules that recognize specific nucleotide sequences in an RNA molecule and cleave it (Cech, J. Amer. Med. Assn., 260:3030, 1988). A major advantage of this approach is that, because they are sequence-specific, only mRNAs with particular sequences are inactivated.
Specifically, in the instant application, applicants are utilizing selected features of naturally occurring regulatory complementary RNAs (cRNAs) that have been identified in prokaryotes. All have large stable stem-loop structures that flank the molecule, with a high G-C content of the 3' hairpin and all are expressed at high levels. The structural features are believed to confer extreme stability to the molecule. All of these features are also seen in the snRNAs, essential components of the mammalian spliceosome complex that are abundant and stable in the nucleus of all mammalian cells. U1 snRNA has been chosen as the framework for the construction of chimeric antisense cRNAs because U1 is enriched in the nucleus, is widely dispersed in the nucleoplasm, and is abundantly expressed. An antisense targeting core has been substituted for the Sm protein binding site between the two hairpins. This core contains a 30-35 basepair sequence that is directly complementary to the target message, interrupted in its center by an autocatalytic hammerhead ribozyme loop. Duplex formation is expected to align the ribozyme with the GUC or GUA consensus sites for ribozyme cleavage. When the core contained sequence complementary to fibriliin-1 mRNA, expression of the chimeric cRNA, under the transcriptional control of the potent and constitutively active U1 promoter, resulted in the complete absence of fibrillin-1 protein and message in stably transfected cells. No abnormalities were seen upon a survey of other proteins and transcripts, attesting to the specificity of antisense inhibition. An expression construct to target RENT1 transcripts, employing antisense is shown in FIG. 3.
The present invention also provides gene delivery and gene expression for disorders mediated by RENT1protein. Such gene delivery and gene expression achieves its beneficial effect by altering the levels of RENT1 mRNA in a cell. This may entail delivery and expression of RENT1 antisense to target cells or the delivery and expression of heterologous RENT1 nucleic acid to target cells to modulate the function of NMRD. Delivery and expression of RENT1 nucleic acid can be achieved by a variety of means known to those in the art. A preferred means is using a recombinant expression vector such as a chimeric virus or a colloidal dispersion system. Especially preferred for therapeutic delivery of antisense sequences is the use of formulations containing liposome or liposome formulations or liposomal-like agents capable of being targeted to particular cells or receptors. Various viral vectors which can be utilized for gene therapy as taught herein include adenovirus, herpes virus, vaccinia, or, preferably, an RNA virus such as a retrovirus.
Another targeted delivery system for RENT1 antisense polynucleotides is a colloidal dispersion system. Colloidal dispersion systems include macromolecule complexes, nanocapsules, microspheres, beads, and lipid-based systems including oil-in-water emulsions, micelles, mixed micelles, and liposome or liposome formulations. The preferred colloidal system of this invention is a liposome or liposomal formation. Liposome or liposome formulations are artificial membrane vesicles or formulations containing liposomal compositions that can be complexed with other compositions. These formulations may have net cationic, anionic or neutral charge characteristics are useful characteristics with in vitro, in vivo and ex vivo delivery methods.
It has been shown that large unilamellar vesicles (LUV), which range in size from 0.2-4.0 .mu.m, can encapsulate a substantial percentage of an aqueous buffer containing large macromolecules. RNA, DNA and intact virions can be encapsulated within the aqueous interior and be delivered to cells in a biologically active form (Fraley, et al., Trends Biochem. Sci., 6:77, 1981). Additionally, nonmembrane bound liposomal formulations can be used for delivery and expression of nucleic acids (Felgner et al., Proc. Natl. Acad. Sci. USA 84:7413, 1987). In addition to mammalian cells, liposome or liposome formulations have been used for delivery of polynucleotides in plant, yeast and bacterial cells. For a liposome or liposome formulation to be an efficient gene transfer vehicle, the following characteristics should be present: (1) encapsulation of the genes of interest at high efficiency while not compromising their biological activity; (2) preferential and substantial binding to a target cell in comparison to nontarget cells; (3) delivery of the aqueous contents of the vesicle or of the nucleic acid of the formulation to the target cell cytoplasm at high efficiency without degradation and in a functional state capable of permitting gene expression at such levels as to achieve a detectable biological effect; and (4) accurate and effective expression of genetic information which has been delivered (Mannino, et al., Biotechniques, 6:682, 1988).
A well-characterized "on/off" switch for use in a recombinant expression vector is the antibiotic (tetracycline) regulated promoter system. Means for construction of such a system are well-known in the art; for review in this regard, those of skill in the art may wish to consult Furth, et al., Proc. Natl. Acad. Sci. USA, 91:9302-9306, 1994 (tetracycline regulated control of gene expression in transgenic mice);
In addition, a transgenic animal model can be developed which is especially predictive of the impact on NMRD system in which RENT1 activity has been increased or decreased according to the method of the invention. Protocols useful in producing such RENT1 transgenic animals are described below. The protocol generally follows conventional techniques for introduction of expressible transgenes into mammals. Those of ordinary skill in the art will be familiar with these applications and will be able to apply the techniques in the context of the present invention without undue experimentation.
For example, embryonic target cells at various developmental stages can be used to introduce transgenes. Different methods are used depending on the stage of development of the embryonic target cell. The zygote is the best target for microinjection. In the mouse, the male pronucleus reaches the size of approximately 20 micrometers in diameter which allows reproducible injection of 1-2 pl of DNA solution. The use of zygotes as a target for gene transfer has a major advantage in that in most cases the injected DNA will be incorporated into the host gene before the first cleavage (Brinster, et al., Proc. Natl. Acad. Sci. USA82:4438-4442, 1985). As a consequence, all cells of the transgenic nonhuman animal will carry the incorporated transgene. In general, this will also be reflected in the efficient transmission of the transgene to offspring of the founder since 50% of the germ cells will harbor the transgene. Microinjection of zygotes is a preferred method for incorporating transgenes in practicing the invention.
Retroviral infection can also be used to introduce transgene into a nonhuman animal. The developing nonhuman embryo can be cultured in vitro to the blastocyst stage. During this time, the blastomeres can be targets for retroviral infection (Jaenisch, Proc. Natl. Acad. Sci. USA 73:1260-1264, 1976). Efficient infection of the blastomeres is obtained by enzymatic treatment to remove the zona pellucida (Hogan, et al., Manipulating the Mouse Embryo, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1986). The viral vector system used to introduce the transgene is typically a replication-defective retrovirus carrying the transgene (Jahner, et al., Proc. Natl. Acad. Sci. USA, 82:6927-6931, 1985; Van der Putten, et al., Proc. Natl. Acad. Sci. USA 82:6148-6152). Transfection is easily and efficiently obtained by culturing the blastomeres on a monolayer of virus-producing cells (Van der Putten, supra; Steward, et al., EMBO J., 6:383-388, 1987).
Alternatively, infection can be performed at a later stage. Virus or virus-producing cells can be injected into the blastocoele (Jahner, et al., Nature, 298:623-628, 1982). Most of the founders will be mosaic for the transgene since incorporation occurs only in a subset of the cells which formed the transgenic nonhuman animal. Further, the founder may contain various retroviral insertions of the transgene at different positions in the genome which generally will segregate in the offspring. In addition, it is also possible to introduce transgenes into the germ line, albeit with low efficiency, by intrauterine retroviral infection of the midgestation embryo (Jahner, et al., supra, 1982).
A third type of target cell for introduction of heterologous RENT1 nucleic acid sequences is the embryonal stem cell (ES). ES cells are obtained from pre-implantation embryos cultured in vitro and fused with embryos (Evans, et al., Nature, 292:154-156, 1981; Bradley, et al., Nature, 309:255-258, 1984; Gossler, et al., Proc. Natl. Acad Sci. USA, 83:9065-9069, 1986; and Robertson, et al., Nature, 322:445-448, 1986). Transgenes can be efficiently introduced into the ES cells by DNA transfection or by retrovirus-mediated transduction. These transformed ES cells can thereafter be combined with blastocysts from a nonhuman animal. The ES cells will thereafter colonize the embryo and contribute to the germ line of the resulting chimeric animal (see for review. Jaenisch, Science, 240:1468-1474, 1988).
Construction of RENT1 transgenes can be performed by those of ordinary skill in the art using the teachings concerning the RENT1 nucleotide sequences herein. One of ordinary skill in the art can "knock out" the NMRD pathway in mice by targeted disruption of the murine RENT1 gene. This can be accomplished by homologous recombination in murine embryonic stem (ES) cells using standard techniques. The clinical and cellular consequences of targeted disruption of RENT1 can be investigated in multiple genetic backgrounds including inbred strains, strains with many undefined nonsense alleles, and strains of known mutant genotype to determine if: (a) targeted disruption of RENT1 can effect a loss of NMRD function; (b) loss of NMRD function can have an phenotype consequences (i.e., the creation of knockout phenotypes), (c) loss of NMRD unmasks the effects of protein that can be expressed from "physiologic" somatically acquired or inherited nonsense alleles upon transcript stabilization.
Transgenic murine cells can be generated by using a vector for RENT1 gene targeting by homologous recombination. The vector contains a large genomic fragment of the murine RENT1 gene. Three exons can be deleted and substituted for by a Neomycin resistance expression cassette. A thymidine kinase gene can be inserted at the end of the long arm of homology to assist in the selection of bona fide-homologous recombinants. Transfection and stable selection of murine SV/129 cells will allow identification of a clonal colony of cells harboring one inactivated RENT1 allele. These cells can be injected into mouse blastocysts to create chimeras. Chimeras can be bred to yield animals heterozygous for the targeted allele. Finally, heterozygotes can be bred to create homozygotes. Mice with characterized phenotypes can be bred to mice deficient for NMRD. Differential display, SAGE, or other methods can allow identification of transcripts upregulated in the absence of NMRD. In this way, a mouse disease gene can be identified. It will then be possible to determine whether a human homologue of the mouse disease gene is responsible for similar human phenotypes. If necessary, the identical approach of homologous recombination-based targeting of endogenous genes can then be used in cultured human cells. This would require a second phase of transfection and selection, using a different selectable marker, to target both alleles. Only minor modifications in the methods used for murine cells, all previously employed for other purposes, will be necessary to permit one of ordinary skill in the art to completely inhibit RENT1 expression in cultured human cells. One example of such a method of transgenic construction is described below. However, this example is not meant to be limiting as other transgenic constructions can be used which are commonly known to those in the art.
Insertion of the 1.2 kb Pol II-neomycin resistance cassette into an early exon of the RENT1 gene will disrupt the translational reading frame for RENT1 with the creation of an in-frame premature termination codon (PTC). Insertion of the PTC in an early exon will prevent translation of the body and C-terminus of RENT1 will result in a complete loss of function. An alternate strategy is to target the very first exon eliminating the start-site for translation, however this might impair transcription, precluding the ability to assess the stability of targeted RENT1 transcripts as a potentially useful marker of the integrity of NMRD in lines of knockout mice. N-terminal epitopes can also be used to determine whether a truncated protein is expressed from stabilized transcripts from the knockout allele.
Construction of a targeting vector: A large fragment of murine RENT1 cDNA is cloned, (-20 kb) murine (129/Sv) genomic clone spanning from the second putative nucleotide binding motif to the first motif that confers NTPase activity, and characterized. A detailed restriction map of the clone and localizing intron-exon boundaries through a combination of the subcloning of relatively large (6-12 kb) restriction fragments into plasmid vector (pBlueprint II-SK) is determined, restriction analysis accompanied by Southern transfer and hybridization of radiolabeled oligonucleotide complementary to cDNA sequences, and direct sequencing of genomic subclones using cDNA primers can be done. Subsequently, a targeting vector is constructed using a (6-12 kb) genomic fragment which contains the exon of interest is subcloned into a suitable plasmid. Preferably, the exon is somewhat asymmetrically placed in the insert, with a minimum of -2 kb of sequence at either end (Deng & Capecchi, 1992). Genomic sequences that immediately flank the insert at the 5' and 3' ends are retained for use as probes in Southern analysis to confirm homologous recombination at a later time. The 1.2 kb Pol II-neomycin resistance expression cassette (Wang, et al., 1995) is inserted into the exon of interest using a suitable restriction site. The PGKtk expression cassette is added distal to the long arm of homology to enrich for homologous recombinants by FIAU selection (Li, et al., 1992: Andrikopoulos, et al., 1995).
The resultant construct is linearized and band-purified by CsCI.sub.2 ultracentrifugation (Wang, et al., 1995). A targeting vector using RENT1 sequence is illustrated in FIG. 10.
Additionally, recent advances in the efficiency of targeted gene delivery in cultured somatic cells can be used by one of ordinary skill in the art. Briefly, promoterless cDNAs that encode antibiotic resistance factors are used in targeting vectors such that expression can be driven by the promoter of the targeted allele upon homologous recombination. Enrichment ratios (homologous recombinants vs. random insertions) of up to 5,000 to 10,000-fold can be achieved compared to conventional methods (Hanson & Sedivy, 1995), thus efficiently inactivating both alleles by sequential gene targeting using two targeting vectors that contain different selectable genes.
Generation of targeted mice: Pluripotent J1 ES cells derived from the inner cell mass of 129/Sv blastocysts are cultured under standard conditions (Li, et al., 1992). Approximately 1.times.10.sup.7 cells are transfected with 10-20 .mu.g of linearized construct by electroporation at 230 m.sup.v, 500 .mu.F using a Bio-Rad Gene Pulser and are replated on a feeder layer of .gamma.-irradiated G418-resistant primary mouse embryonic fibroblasts in Delbecco's modified Eagle's media supplemented with 5% FBS, 0.1 mM nonessential aa, 0.1 mM .beta.ME and 1000 U/ml leukemia inhibitory factor (Li, et al., 1992). Selection with G418 and FIAU commences 24 hours after plating and is maintained for seven to ten days. An aliquot of each resistant colony (.about.90%) is frozen for later use and the remainder are replated and grown to confluence for DNA extraction. Identification of recombinant clones is accomplished by Southern analysis and facilitated by a single EcoR1 site in the Neo cassette and the probes that flank the homologous sequences are used for gene targeting as above. The 5'-flanking probe is used to detect a restriction fragment unique to the targeted allele. DNA from all positive clones are subsequently screened with the 3' probe to confirm bona fide homologous recombination (Wang, et al., 1995). Northern analysis are performed on RNA extracted from +/+ and +/- colonies. By observing the size and abundance of hybridizing species of RENT1 RNA one of ordinary skill in the art can learn early valuable information regarding the influence of the haplo-insufficiency state for RENT1 upon the efficiency of NMRD. The cDNA probe used in Northern analysis does not span the site of Neo insertion, and should hybridize equally well to the intact and targeted alleles. In addition, the transcription rate and transcript stability can be determined using nuclear run-on analysis and Northern or RNase-protection analysis of RNA extracted at various intervals after the addition of actinomycin D (5 .mu.g/ml) to inhibit new transcription (Urlaub, et al., 1989; Cheng & Maquat, 1993). These parameters can be determined on an allele-specific basis by observing differences in transcript size or by using fusion probes which contain both RENT1 and Neo sequences.
Approximately 15 cells from each targeted ES cell clone are microinjected into each C57B1/6J blastocysts (.about.15) collected at 3.5 days post coitus. Chimeric offspring are identified by agouti (ES-derived) coat color. Male chimeras are bred with C57B1/6J females. Homozygotes for the targeted allele are be generated by the breeding of heterozygotes. The genotype of all mice are determined by Southern analysis or a PCR-based assay.
Characterization of resultant mice: The genetic complement of all initial mice are composed solely of the genomes of two well characterized inbred stains. Therefore, the murine genomes carry no deleterious recessive nonsense alleles other than the targeted RENT1allele. Litter size, sex ratio, and genotyping of all newborn mice are used to monitor embryonic lethality. Mice of all 3 genotypes (+/+,+/-and-/-) are examined carefully over time for any phenotypic differences including birth weight, growth, activity, and congenital or acquired anomalies. Nonviable mice undergo autopsy.
Molecular analysis of mice of all three genotypes are performed. First, the character and steady state level of RENT1 transcripts are determined by Northern analysis and RNase protection. Second, the level and distribution of reactive protein are determined by Western analysis and immunohistochemistry. Experiments identical to can be performed to determine the allele-specific RENT1 transcription rates and transcript stabilities. A simultaneous analysis is performed on total, nuclear, and cytoplasmic RNAs (Daar & Maquat, 1988). Finally, nonsense-transcript stability is upregulated in RENT1-deficient mice, fetal fibroblast cultures are established and transfected with a construct expressing wild-type RENT1 to determine whether reconstitution with RENT1 can rescue an abnormal phenotype.
Outcrossing of homozygous null (-/-) mice and further experimentation: To determine the phenotypic consequence of loss of NMRD function in different genetic backgrounds, the following breeding experiments can be performed:
(1) Murine mucopolysaccharidosis type VII (analogous to human Sly syndrome) is an autosomal recessive disorder caused by spontaneous mutation (gus.sup.mps) in the .beta.-glucuronidase gene. Heterozygous mice are commercially available through the Jackson Laboratory. The gene product is required for the degradation of glycosarninoglyares in lysosomes and homozygous mutant mice display developmental, skeletal, and heart abnormalities that cause a shortened life-span. The gus.sup.mps mutation has recently been characterized as a 1 bp deletion in exon 10 (of 12) that causes a PTC in the same exon (Sands & Birkenmeier, 1993). .beta.-glucuronidase mRNA levels are decreased by .about.200-fold in gus.sup.mps /gus.sup.mps mice and no immunoreactive protein is detectable. In that .beta.-glucuronidase is expressed in all tissues and throughout development, one of ordinary skill in the art can determine the developmental-and tissue-specific relative stability of transcripts derived from the gus.sup.pms allele in (gus.sup.mps /+, RENT1 +/+) mice. The results can be compared to the tissue specific expression pattern of RENT1 to determine whether the level of RENT1 is a limiting factor in the determination of tissue-specific NMRD efficiency. In addition, gus.sup.mps /+ mice are crossed with either RENT1 +/- or RENT1 -/- mice (depending upon the viability and fertility of homozygotes). Resulting (gus.sup.mps /+, RENT1 +/-) mice are crossed to produce (gus.sup.mps /+, RENT1 -/-), (gus.sup.mps /gus.sup.mps, RENT1 -/-) and (gus.sup.mps /gus.sup.mps, RENT1 +/+) mice as determined by tail DNA genotyping. This permits one of ordinary skill in the art to examine the influence of RENT1-genotype upon the stability of transcripts derived from an unlinked nonsense allele. Molecular analyses are identical to those described above except that .beta.-glucuronidase gene-specific sequences and probes are utilized (Birkenmeier, et al., 1989). Mice of all genotypes are analyzed, and the genotype-specific results can be compared. If .beta.-glucuronidase transcripts are stabilized in the RENT1 -/-background, the phenotypic consequence to gus.sup.mps /gus.sup.mps mice can be determined. The encoded protein can contain a contiguous stretch of .about.190 wild-type amino acids (normally 648) and it is possible that the truncated protein can retain activity. This can be tested by Western analysis and histochemical stain for .beta.-glucuronidase activity (Sands & Birkenmeier, 1993).
(2) Strain III mice lack 4-hydroxyphenylpyruvic acid dioxygenase (HPD) activity and contain a nonsense mutation (R111X) in exon 7 (of 14) of the Hpd gene (Endo, et al., 1991, 1995). Homozygous mice develop normally but have elevated blood levels of tyrosine and show massive urinary secretion of metabolites, equatable with human type III tyrosinemia. R111X/R111X-homozygous mice have abundant amounts of Hpd transcript, albeit abnormally small in size. The vast majority of the message has been shown to lack exon 7 due to exon skipping during pre-mRNA processing (Endo, et al., 1995). All of the cis-acting elements known to regulate splicing are unaltered, suggesting that the abnormal splicing phenotype is caused by the nonsense mutation. By breeding strain III mice with RENT1 knockout mice, one of ordinary skill in the art can determine whether RENT1 and the NMRD pathway participate in abnormal splice-site selection in response to premature termination codons. This can be tested easily by Northern blot or RT-PCR analysis of Hpd mRNA extracted from the liver or kidneys of mice (Endo et aL, 1995) harboring various combinations of heterozygous and homozygous genotypes of the Hpd and RENT1 genes. The type III strain is available from the Central Institute for Experimental Animals in Kawasaki, Japan.
If homozygosity for the targeted allele is incompatible with embryonic development, but heterozygosity is not associated with a phenotype, it is possible to generate dominant negative or relative loss-of-function alleles. The size and character of such mutations would be influenced by expression studies using mammalian cells. The process of generating subtle (e.g., missense) mutations in the genome of ES-cells is well described and quite effective (Stacey et al, 1994). Briefly, a targeting vector is first used to replace a defined region of the target gene in HPRT-deficient ES cells with an HPRT minigene. After selection for the HPRT+phenotype, a second round of targeting is used to replace the HPRT minigene with a desired DNA fragment that harbors a site-specified mutation. Enrichment for homologous recombinants is achieved by selection for reversion to the HPRT phenotype. Mice heterozygous for a dominant-negative mutation or homozygous for a relative loss-of-function mutation may have sufficient impairment of NMRD to show a phenotype yet be viable. All potential mutations can be assessed in cultured cells for their relative impact on NMRD efficiency, and a select few can be used in transgenic experimentation.
Additionally, if homozygosity for the targeted RENT1 allele is incompatible with embryonic development, one of ordinary skill in the art can apply inducible gene targeting under the control of the CrelloxP recombination system of bacteriophage P1 (Sauer & Henderson, 1988). The Cre recombinase directs site-specific recombination between two short recognition sequences (loxP) without additional co-factors. Cre recognizes the loxP sites and nicks them on opposite strands, leaving behind a single loxP site after recombination. This process deletes or inverts the intervening ("floxed") DNA sequence when the loxP sites are placed in a head-to-tail or head-to-head orientation, respectively. In vivo gene inactivation can be restricted to a specific development stage or tissue by crossing a mouse strain harboring a floxed allele to a transgenic strain of activation (Gu et al., 1994; Kuhn et al., 1995). Alternatively, an inducible promoter can be used to drive Cre expression. First, an exon or region of RENT1 would be flanked by two loxP sites using gene targeting methods described above. A resistance-conferring gene is included between the loxP sites but outside of the coding region for RENT1 to allow for positive selection of recombinant clones. Resulting mice are bred to homozygosity for this targeted, albeit functionally intact, allele. Resulting homozygotes are bred to a transgenic strain that expresses Cre under the control of a promoter with desirable characteristics. By bypassing certain critical developmental stages or tissues, one of ordinary skill in the art can create a viable and useful model of NMRD deficiency despite the inherent essential nature of the gene product. The choice of the promoter for Cre expression can be an interferon-inducible promoter of the mouse Mx1 gene (Kuhn et al., 1995).
The present invention can also be used to for therapeutic purposes by modulating NMRD. Cells harboring stabilized nonsense alleles which encode partially functional truncated proteins can be transfected with constructs encoding dominant negative forms of RENT1. The cellular phenotype can be determined by RNA and protein quantification and biofunctional assays. In addition, subtractive methods can be used to enrich for transcripts that are upregulated after inhibition of NMRD without assuming any a priori knowledge regarding a possible disease gene in question. The use of RENT1 can allow disruption of NMRD and rescue of selected cellular phenotypes or manipulation of NMRD for the identification of new disease genes. One such nonlimiting example is described below, however, the skilled artisan using this example can create other such bioassays to explore disease genes using RENT1.
Two predominant pathogenetic mechanisms are generally inferred when an allele of a given disease gene is found to harbor a premature termination codon (PTC). Both relate to a presumed loss-of-function. Either the predicted truncated protein lacks C-terminal domains that are essential for intended function, or the NMRD pathway effectively eliminates expression from the mutant alleles by degrading much or all of the nonsense transcripts. These mechanisms are not mutually exclusive, and may act in combination. However, for certain proteins, selected C-terminally truncated forms retain sufficient activity to prevent or abrogate the disease phenotype. In such an instance, NMRD is the critical factor. This is probably the case for certain nonsense alleles of the cystic fibrosis transsmembrane conduction regulator (CFTR). As little as the amino-terminal half of CFTR can form a functional regulated chloride channel (Sheppard et al., 1994). Selected truncated proteins (e.g., corresponding to mutation D836X) had conductance properties indistinguishable from those of wild-type CFTR (Sheppard et al., 1994). However, in vivo, transcript levels are extremely low (e.g., for mutations W1282X and W1316X), generally less than 5% of that observed from the wild-type allele (Hamosh et al., 1991, 1992). Stabilization of selected CFTR nonsense transcripts, through manipulation of RENT1 and hence NMRD may effect emergence of significant chloride channel function in CTFR affected cells.
To test such a hypothesis one of ordinary skill in the art can stably transfectant the respiratory epithelial cell line IB3-1 with vectors encoding both wild-type and putative dominant-negative forms of rent1. IB3-1 harbors CFTR mutations .DELTA.F508 and W1282X and demonstrates normal chloride conductance parameters upon reconstitution with wild-type CFTR (Fulmer et al., 1995; incorporated herein in its entirety including all figures and drawings). Using dominant-negative forms of RENT1 one of ordinary skill in the art can determine if such a treatment stabilizes W1282 transcripts. If so, one of ordinary skill in the art can use a well described biofunctional assay to assess whether any change in cAMP-mediated chloride conductance is seen (Fulmer et al., 1995). Briefly, IB3-1 cells (untransfected, mock-transfected, expressing wild-type or dominant-negative RENT1) can be loaded with .sup.36 Cl- (Fulmer et al., 1995). Cells can be washed extensively in ice-cold Ringer's solution prior to the addition of warm solution. CPT-cAMP (to 200 mM; Boehringer Mannheim) can be added, and the incubating solution exchanged at various time points thereafter. After the final time point, cells can be lysed in 0.1N NaOH. Radioemissions from each time point of the retained samples counted and final values for each time point expressed as % total cellular counts at time 0 which were lost per minute. The efflux rates can be compared between experiments using the one-way analysis of variance (ANOVA) test and the Duncan multiple variable test (Fulmer et al., 1995). The results can be correlated with protein expression, assessed by Western analysis and immunohistochemistry. Product from the W1282X allele can be distinguished from that from .DELTA.F508 allele by virtue of its size and cell-surface localization.
If protein expression is upregulated, but chloride conductance does not change, then it is possible that the W1282X form of CFTR lacks critical domains needed for trafficking, processing, or chloride conductance. Other mutant cell lines can then be tested. If both protein expression and chloride conductance are upregulated by the expression of dominant-negative forms of RENT1, then it can be evident that transcripts stabilized by manipulation of NMRD can be translated and that the resulting protein products can show residual function. Such a result could be important for the development of novel therapeutic strategies. For example, it may be possible to manipulate the expression of RENT1 in vivo using genetic therapeutic or pharmacologic interventions. This would have a profound impact on the care of patients carrying W1282X (accounting for 60% of CF chromosomes in the Ashkenazi Jewish population; Shoshani et al., 1992), and perhaps for individuals harboring other nonsense mutations in CFTR or in other genes.
The present invention may ameliorate mutations in RENT1 genes. Because mutant RENT1 polypeptides can correlate with increased accumulation of nonsense mnRNAs, RENT1 nucleic acid can be useful in gene therapy. By using RENT1 constructs to enhance NMRD in cells afflicted with nonsense mutation accumulation, it is possible to treat disease states associated with stabilized transcripts of nonsense mutations. In preferred therapies, the RENT1 regulating gene product is preferentially expressed in those cells where enhanced NMRD is required. Alternatively, therapy is provided by administration of peptidornimetic or other compositions which mimic the biological activity of wild-type RENT1 polypeptides or which modify a NMRD defect, caused by a defect in a mutant RENT1 polypeptide thereby restoring wild-type biological activity to a mutant polypeptide.
The experimental manipulation of RENT1 can be used in the novel therapeutic strategies and the identification of unknown disease genes. Many strategies to identify new disease genes or to monitor the cellular response to environmental or physiologic stress rely upon the detection of differences in gene-specific transcript expression between control and experimental samples. These include differential cDNA screening, subtractive hybridization strategies, and multiple RT-PCR-based methods (reviewed in Maser & Calvert, 1995). RNA isolated from an "affected" cell line or tissue is compared to that from an "unaffected" control. Loss of NMRD function in both yeast and C. elegans has been shown to have negligible, if any, effect on the abundance of transcripts that do not contain PTCs therefore suggesting that cell viability remains unaffected (Leeds et al., 1991; Pulak & Anderson, 1993).
PTCs are caused by nonsense mutations and frameshifts (aberrant splicing, deletions, insertions, complex rearrangements), therefore, nonsense alleles account for a large proportion of all human disease (Cooper & Krawczak, 1993). This fact, in conjunction with experimental manipulation of NMRD, can permit identification of selected disease genes. One of ordinary skill in the art can be determine such disease genes using a patient cell line which harbors known nonsense alleles. If NMRD is downregulated in one aliquot of cells from such a cell line then the only difference between a cell line transfected with RENT1 constructs and a culture of the same line which has been unmanipulated should be a greatly increased abundance of nonsense transcripts in the RENT1 treated cells. This enrichment for nonsense transcripts of putative disease genes can then be detected by a number of methods including those described herein. One example of such a detection of disease alleles is described below. The example is meant to be illustrative and not restrictive in any manner either explicitly or implicitly. Other methods will be apparent to those of ordinary skill in the art.
A fibroblast cell line from a patient with gyrate atrophy who is homozygous for a 1 bp deletion at codon 318 in the OAT gene was obtained. This allele is associated with undetectable levels of OAT mRNA (Body et al., 1992). Cells from this line can be stably transfected with constructs expressing either wild-type or a dominant-negative form of RENT1. RNA can be extracted from both cell lines and compared by representational difference analysis (RDA)(Hubank & Schatz, 1994). RDA is a preferred method of comparative analysis using the instant technology because it efficiently detects quantitative as well as absolute differences, and eliminates cDNA fragments common to both cell populations, leaving behind only the differences (Hubank & Schatz, 1994). The identity of resultant cDNA fragments can be determined by a combination of subcloning, sequencing, and database analysis. The RDA method can also be applied to heterozygous nonsense alleles using identical methods and appropriate fibroblast cell lines from patients with other diseases such as Marfan syndrome (Dietz et al., 1993b).
Stabilization of inefficiently spliced pre-mRNAs from normal alleles will not be obstructive to this process because of their low abundance. Additionally, the RDA analysis method can enrich for transcripts derived from recessive nonsense alleles that are unrelated to the phenotype of interest. The number can be low and many can not be expressed in the tissue source for RNA isolation that was selected because of its relevance to the phenotype of interest (both OAT and fibrillin-1 are expressed abundantly in cultured fibroblasts). Such a method is preferred to define syndromes associated with mutations created by PTCs (e.g., the Stickler syndrome gene where all Stickler mutations create PTCs). This approach is preferred because of its unique applicability to detect rare sporadic or complex multigenic disorders. In complex multigenic disorders one of ordinary skill in the art can obtain a catalog of nonsense alleles in many patients with concordant phenotypes. Those nonsense alleles that are found to be common to multiple affected patients can be investigated further.
A preferred method of gene therapy is direct gene transfer, ie., local application of a formulation containing the RENT1 polypeptide-encoding nucleic acid into an afflicted site or other region. A variety of well known vectors are be used to deliver the RENT1 gene to targeted cells in a location like those cells affected in Stickler syndrome or Marfan syndrome, including but not limited to adenoviral vectors, adeno-associated vectors or formulations targeting endothelial cells. In addition, naked DNA, liposome formulations delivery methods, or other novel formulations developed to deliver the RENT1 gene to target cells are also preferred.
For any of the above approaches, the therapeutic RENT1 polynucleotide construct can be applied to a location where enhanced NMRD is desirable (e.g., by injection), but the RENT1 formulation may also be applied to tissue in the vicinity of the needed NMRD modulation, to a blood vessel supplying the cells where modulated of NMRD is desirable or even applied systemically.
In a RENT1 gene delivery formulation of the instant invention, polynucleotide expression is directed from any suitable promoter (e.g., the human cytomegalovirus, simian virus 40, actin or adenovirus constitutive promoters; or the cytokine or metalloprotease promoters for activated synoviocyte specific expression). Furthermore, RENT1 polynucleotide production can be regulated by any desired mammalian regulatory element. For example, if desired, enhancers known to direct preferential gene expression in cells known in the art to be associated with NMRD may be used to direct RENT1 gene expression. Such enhancers include, without limitation, those enhancers which are characterized as tissue or cell specific in their expression.
Alternatively, if a RENT1-gene regulating genomic clone is utilized as a therapeutic construct, expression is regulated by its cognate regulatory sequences or, if desired, by regulatory sequences derived from a heterologous source, e.g., any of the promoters or regulatory elements described above.
Gene therapy may also be accomplished by direct administration of the RENT1-regulating gene mRNA to a cell either in vitro, ex vivo, or in vivo. RENT1 mRNA may be produced and isolated by any standard technique, but is most readily produced by in vitro transcription using a cDNA under the control of a high efficiency promoter (e.g. the T7 promoter). Administration of RENT1 mRNA to accumulated cells is carried out by any of the methods for direct nucleic acid administration described herein.
In one embodiment, the production of the RENT1 protein by a gene therapy approach described herein results in a cellular level of the RENT1 polypeptide that is at least functionally equivalent to the normal, cellular level in a normal individual. Treatment by any gene therapy approach described herein may also be combined with more traditional therapies.
Another therapeutic approach included within the invention involves direct administration of recombinant RENT1 protein by any conventional recombinant protein administration techniques at the site where pathogenic cells accumulate (for example, by injection), or administered systemically. The RENT1 protein may also be targeted to specific cells or receptors by any of the methods described herein to target RENT1 nucleic acid formulations. The actual dosage of RENT1 protein depends on a number of factors, including the size and health of an organism, but, generally, between 0.1 mg and 100 mg inclusive are administered per day to an adult in any pharmaceutically-acceptable carrier.
In one embodiment, the invention provides a method of treating a patient having or at risk of having early stage as a result of genetic deficiency, disease or clinical treatment wherein the condition has an etiology associated with a defective NMRD-regulating gene or polypeptide, deficient RENT1 or level thereof, the method comprising administering to the patient a therapeutically effective amount of a formulation or composition which modulates the expression of the RENT1 gene or polypeptide such that the state of the patient is ameliorated.
Therapeutic applications also include utilizing a selective survival technique taking advantage of those cells specifically expressing the wild-type protein, e.g., RENT1. Such treatment kills or inactivates the cell that contains a defective RENT1 gene, while leaving cells containing the wild type or normal RENT1 gene/polypeptide unharmed. Several approaches for selective killing include but are not limited to: 1) infection with a viral vector to induce expression of the endogenous, normal RENT1 gene; 2) contact a cell having a mutant RENT1protein with an agent that specifically binds to the mutant and not the wild type protein; and 3) contact a cell having a mutant RENT1 protein with a first agent that protects the wild-type RENT1 and then a second agent that is toxic to a mutant RENT1.
EXAMPLES
The following examples are intended to illustrate but not admitted to limit the invention in any manner, shape, or form (either explicitly or implicitly). While they are typical of those that might be used, other procedures, methodologies, or techniques known to those skilled in the art may be used alternatively.
Example 1
Cloning Human Rent1 cDNA Using Degenerate Primers
Multiple primers were fashioned using degenerate sequences that encode short peptide fragments common to Upf1, Sen1, and Mov10 (Table 1).
TABLE 1______________________________________Peptides Encoded by Degenerate Sequences of Primers Used to Clone Human RENT1 Peptide Amino Acids SEQ ID NO______________________________________PGTGKT 432-437 of Upf1 23 CAPSN 458-462 of Upf1 24______________________________________
The primers were then used in multiple combinations for RT-PCR of RNA extracted from cultured human fibroblasts. RNA extraction and RT-PCR were performed according to conventional methods. RT-PCR using the primers PGTGKT (SEQ ID NO:23) and CAPSN (SEQ ID NO:24) together produced a product comparable in size to Upf1. The sense and antisense primers encode the peptide sequences PGTGKT (aa 432-437 in Upf1) and CAPSN (aa 458-462 in Upf1), respectively. Conceptual translation of the 30 codons contained within the RT-PCR product revealed that it shared 93% sequence conservation and 73% sequence identity with Upf1 of yeast, suggesting that the cloned gene encodes a mammalian regulator of NMRD.
Example 2
Cloning Human Rent1 cDNA Using Mamalian Expressed Sequence Tags (EST's)
The yeast Upf1 sequence was submitted to the X-REF database genome cross-referencing effort (Bassett, et al., 1995). This service compares the query sequence from a model organism protein (yeast, C. elegans, etc.) With the conceptual translation of mammalian expressed sequence tags (EST) using the BLAST local alignment search algorithm (Altschul, et al., 1994). Submission resulted in the identification of a human expressed sequence tag (EST, GenBank F06433), derived from a normal human infant brain cDNA library, that encodes a protein with significant similarity to Upf1 (p=2.8e-44). The cDNA clone obtained from the Human Genome Center of Lawrence Livermore National Laboratory, contained an insert of approximately 1.5 kb. DNA sequencing of this insert revealed a contiguous open reading frame of approximately 1.4 kb, with a poly(A) tail and a 3' UTR of 100 bp. Full-length RENT1 cDNA clones were isolated from an adult human heart cDNA library, contained within the cloning vector pCMV SPORT (BRL), using the GENE TRAPPER cDNA positive selection system (Life Technologies). Screening was carried out according to the manufacturer's instructions with oligonucleotide 23-5-2a (5'-CTTTGACAGGATGCAGAGCGC-3') (SEQ ID NO:11). Two independent clones, each having an insert of approximately 3.7 kb, were identified. DNA sequencing of the clones reveals an open reading from of 3,354 bp, flanked by a 5' UTR of 231 bp, a 3' UTR of 103 bp, and a poly(A) tail. The use of BLAST to compare the sequence of this clone with the sequence of yeast Upf1 suggested that the isolated clone, RENT1, encoded a polypeptide similar in sequence to Upf1 (p=0.00). Sequencing was performed using a Perkin Elmner Applied Biosystems Division (ABd) 373a automated DNA sequencer following manufacturer's protocols. Direct sequencing predicts an ORF of 3354bp with 231 bp of 5'UTR and 103bp of 3'UTR, excluding the poly(A) tail. The putative initiating methionine is encoded by an ATG codon that falls within context (GGCACCATGA) (SEQ ID NO:12) that closely matches the Kozak consensus sequence GCC(A/G)CCATGG(SEQ ID NO:13) including the highly conserved purine at position -3 (Kozak, 1991). Moreover, this is the first ATG3' of an in-frame amber codon (23 codons upstream). The mammalian polypeptide was designated RENT1.
Example 3
Cloning Murine Rent1 Genomic DNA and cDNA
A large (.about.15.5 kb) murine RENT1 genomic clone was identified after probing a 129/SV strain mouse genornic library (Stratagene) using a radiolabeled human cDNA fragment. An approximately 8.2 kb BamHI restriction fragment was subcloned into pBluescriptII/SK+ (Stratagene) and sequenced as described above. A 7 kb BamHI-NotI restriction fragment from the same genomic clone was subcloned and approximately 4.4 kb sequenced. Coding sequence was identified by aligning the conceptual translation of the human cDNA with that for the murine genomic clone using the MacVector 4.5.3 package of sequence analysis software (Kodak).
The RENT1 gene was also partially cloned from mouse liver. Degenerate PCR primers, encoding short peptide sequences which are identical between RENT1 and Upf1, were used for RT-PCR of mouse liver RNA. The primers LECYNCK (SEQ ID NO:28) and LEADYDK (SEQ ID NO:29) were used together, to retrieve an expected 414 bp RT-PCR product based on human and yeast sequences. Conceptual translation and homology analysis of 12.6 kb sequenced demonstrates that 1041 residues of the predicted murine protein, corresponding to residues 78 to 1118 in the human sequence, are encoded by 22 exons. Only 14 of 1041 residues differ between the characterized portions of the human and murine proteins suggesting that most residues in the mammalian RENT1 proteins have a high degree of functional significance and are conserved in other mammalian regulators of NMRD. Alignment of the seven regions common to members of helicase superfamily I (21) for Upf1, its homologues in human, mouse and S. pombe, along with Sen1 and Mov-10, reveal a conserved consensus that allows definition of this group of proteins as a distinct subset within the helicase superfamily. The entire genomic murine RENT1sequence is present in FIG. 4 including the amino acid sequence. A murine RENT1 genomic clone is incorporated in the vector shown in FIG. 11. Additionally, a targeting vector using the murine RENT1 sequence for the creation of a knockout phenotype is shown in FIG. 10.
Example 4
Mapping The Rent1 Human and Murine Chromosomal Location
The Jackson Laboratory BSS interspecific backcross DNA panel was used to map the murine RENT1 gene. This was accomplished by following the strain distribution pattern of a C57BL/6J-specific 1.6 kb Taq1 restriction fragment detected upon hybridization with a human RENT1 cDNA probe. The human probe detected a C57BL/6J-specific 1.6 kb TaqI restriction fragment, which was used to determine the map position of the murine gene. RENT1 was found to map murine chromosome 8 between the micro satellite markers D8Mit5 and D8Mit78, a region synthetic with human chromosome 19p13.2-p13.11, Neurocan (Ncan) was the closest mapped murine gene (Raunch, et al., 1995) with zero crossovers in 83 mice. Subsequent typing of the NIGMS human/rodent somatic cell hybrid mapping panel (version 2, Coriell Cell Repositories) for human-specific HindIII restriction fragments unambiguously confirmed the human chromosome 19 localization for RENT1. Relevant data may be viewed on the World Wide Web at URL http://www ncbi.nlm.nih.gov/XREFdb/. No apparent relevant mouse or human phenotypes are known to map to the specified regions of murine chromosome 8 or human chromosome 19, respectively. The murine hook (Hk) and quinky (Q) phenotypes map on mouse chromosome 8 with an offset from ten centromere of 26 and 38 cM, respectively. Both are characterized by tail deformities. Hook mice exhibit anal deformities while quinky mice show abnormal circling behavior.
Example 5
Sequence Analysis of Rent1
Direct sequencing predicted an ORF of 3,354 bp with 231 bp of 5' UTR and 103 bp of 3' UTR, excluding the poly(A) tail. The putative initiating methionine is encoded by an ATG that occurs within the context of a Kozak consensus sequence (12), 23 codons downstream of an in-frame translational terminator. Three tandem consensus polyadenylation signals (AATAAA) begin at positions 63, 70, and 76 of the 3' UTR, with initiation of the poly(A) tail at position 104. A comparison of the sequence of RENT1 with Upf1 indicates that, although the proteins differ at their amino and carboxyl termini, there is significant sequence homology within the central portions of the two proteins (amino acid 60-853 of Upf1 and amino acid 121-917 of RENT1). Throughout their central portions, RENT1 and Upf1 share 58% amino acid identity and 80% conservation. In addition, RENT1 and Upf1 share two zinc finger-like domains. These proteins also share motifs that a common to members of helicase superfamily I, including motifs that are thought to confer NTP-hydrolysis activity. Two of these motifs perfectly match the consensus sequences GXXXGK(S/T) (SEQ ID NO:14 and SEQ ID NO:25) and DXXG (SEQ ID NO:15) (Dever et al., 1987). In addition, the sequence of RENT1 is identical to the sequence of Upf1 at the residues that, when altered, confer dominant-negative activity to Upf1 (Leeds et al., 1992). These similarities in the central portions of RENT1 and Upf1 suggest that RENT1 regulates NMRD in mammals. Although the central portion of RENT1 is similar to the central portion of Upf1, these proteins differ at both their amino and carboxyl termini.
To facilitate understanding the similarities and differences between RENT1 and Upf1, it is best to divide the protein sequence into 3 regions, A) N-terminus, B) body, and C) C-terminus. The bodies of the two proteins (aa 60-853 and 121-917 in Upf1 and RENT1, respectively) show excellent alignment and a high degree of similarity. Throughout this region the two protein sequences show 58% residue identity and 80% conservation. Moreover, RENT1 is the first identified human protein sequence that contains all of the putative functional elements that are found in Upf1. These include the cysteine-rich zinc finger-like domains that serve a putative nucleotide-binding function and the motifs common to members of helicase superfamily 1 including those that are believed the confer NTP-hydrolysis activity. The first 2 NTP-hydrolysis motifs show a perfect match with the consensus GXXXXGK(S/T) (SEQ ID NO:14 and SEQ ID NO:25) and DXXG (SEQ ID NO:15) and are appropriately spaced (Dever, et al., 1987). The third sequence element, believed responsible for GTP-binding specificity, does not perfectly match the consensus NKXD. Although a consensus match is found in Upf1, the motif is not found at the predicted distance from the second NTP-hydrolysis element, leaving in doubt its functional significance (Leeds, et al., 1992). RENT1 is a strong structural homologue of Upf1, and contains all of the known or putative functional elements found in the yeast protein. Current theory holds that coordinated nucleotide-binding, helicase, and NTPase activated may be essential for the proper interaction between nonsense transcripts and the factors that scan for premature termination codons and other relevant cis-acting elements (Czapliniski, et al., 1995).
The N- and C-terminal of RENT1 do not align with the corresponding regions of Upf1. The first notable difference is that the N-terminus of RENT1 is longer than that found in Upf1 (120 vs. 59 aa, respectively) and it contains a long (26 aa) stretch composed entirely of proline, glycine, and alanine residues that is not found in the yeast protein. While the functional significance of this region is unknown, PGA-rich stretches have been found to act as a direct transcriptional repressor (Catron, et al., 1995). It is also possible that helix disturbing properties imposed by the high PG-content confers a favorable conformation to the molecule. If one excludes the PGA-rich region, certain similarities are evident between the N-terminal of RENT1 and Upf1. Both are relatively rich in serine and threonine (19 vs. 24% respectively) and acidic residues (D or E; 22 vs. 18% respectively). Such features are commonly seen in nucleotide-binding proteins with transactivation or transcriptional regulation properties (e.g., Calvert, et al., 1991; Seipel, et al., 1992). BLAST analysis of the isolated N-terminal sequence of RENT1 reveals homology to multiple homeobox/POU domain proteins that participate in transcriptional regulation. Homologous proteins that are known to interact with RNA include the Sis1 heat shock protein of yeast and the Gr10 RNA-binding protein of B. napus (p=5.6e-07 and 1.2e-04, respectively). Of particular interest, Sis1 has been shown to localize to both the nucleus and cytoplasm, associated with 40S ribosomal subunits and smaller polysome, is required for the initiation of translation, and may mediate the association of protein complexes within the translation machinery (Luke, et al., 1991; Hong & Arndt, 1993).
The C-terminus of RENT1 is longer than that found in Upf1 (203 vs. 118 aa, respectively). Of note, both C-termini are rich in serine and glutamines (21 vs. 18%, respectively). The occurrence of the majority of these residues as SQ dipeptides (n=14) is a feature unique to the human protein. Many RNA recognition motif (RRM)-containing proteins have glutamine rich regions that are postulated to regulate multiple aspects of RNA processing (DeAngelo, et al., 1991). BLAST analysis of the isolated C-terminus of RENT1 demonstrated significant homology with the human or mouse EWS RNA-binding protein (p=8.9e-3). Interestingly, the N-termini of RENT1 and EWS both show a high frequency (60 vs. 90%, respectively) of Y, Q, S, T, G, A, and P residues. EWS has been proposed to participate in RNA synthesis and processing (Delattre, et al., 1992).
Like the N-terminus, the C-terminus of RENT1 (203 amino acid) is longer than the corresponding region of Upf1 (116 amino acid). Although divergence is seen at the extreme N- and C-termini, the large central regions of Upf1 and RENT1 (residues 60-853 and 121-917, respectively) show 58% identity and 80% conservation. Moreover, RENT1 is the first identified mammalian protein that contains all of the putative functional elements found in Upf1 including the cysteine-rich zinc finger-like domains that may participate in nucleotide binding, the domains with putative NTPase activity, and the motifs common to members of helicase superfamily I.
Example 6
Production of Dominant-Negative Rent1
Dominant-negative versions of RENT1 were produced by site-directed mutagenesis performed according to previously described methods (Dietz and Kendzior, 1994). The mutations used to produce dominant-negative versions of RENT1 are similar to the mutations used to produce dominant-negative versions of Upf1 (Leeds et al., 1992).
Leeds et al. teaches:
Materials and Methods
Isolation of dominant mutations. Plasmid YepPL29 was mutagenized in vitro with hydroxylamine according to the method of Rose and Fink (1987, Cell 48:1047-1060) and used to transform strain PLY22. Cultures containing transformed cells were allowed to grow overnight in liquid synthetic medium lacking uracil prior to plating on solid medium.
Ura.sup.+ transformants capable of growth at 37.degree. C. on medium lacking both uracil and histidine were selected. In all cases, loss of the mutagenized plasmid resulted in reversion to a His.sup.- phenotype at 37.degree. C.
The mutations were localized within Upf1 by a gene conversion assay similar to that described by Sandbaken and Culbertson (1988, Genetics 120:923-934). Plasmids carrying the mutations were digested either with KpnI or BglII, and the digests were used to transform a yeast strain carrying the wild-type Upf1 gene. The frequency of conversion of the mutation on the plasmid to wild type was used as a measure of the distance of a mutation from a given restriction site. All of the dominant mutations resulted in a low frequency of conversion following KpnI digestion and a high frequency of conversion following BglII digestion, which indicated that the mutations were near the 3'-proximal BglII site. The DNA sequence of each plasmid was determined starting from the 3' end of the Upf1 ORF.
Seven of the plasmids contained a single base substitution in the region between the 3' end of the gene and the Bsu36I site at position+1191. Each of these plasmids was codigested with Bsu36I and BamHI, and the 2.4-kb fragment containing the mutation was used to replace the wild-type Bsu36I-BamH fragment in YepPL29. The resulting plasmids, which contain only one base change in the Upf1 coding region, were used to transform PLY22. All transformants were His.sup.+ at 37.degree. C., indicating that the single substitution was sufficient to confer a dominant phenotype.
The strains used to assay the strength of suppression of the dominant alleles were constructed as follows. PLY180 was transformed with YEp13 or YEpPL55 to produce strains carrying a single copy or multiple copies of Upf1.sup.+, respectively. Each of these strains was then transformed with plasmids carrying the UPF1-D allele in either YCp50 or EC402 to produce strains that carry either a single copy or multiple copies of the dominant allele.
The recessive upf1-2 mutation was cloned by the method of a gap repair (Orr-Weaver, T. L., et al., 1981, Proc. Natl. Acad. Sci. USA 78:6354-6358). Strain PLY36 was transformed with BamHI-digested YCpPL23 plasmid DNA. Temperature-independent transformants were identified and cloned in E. coli. The DNA sequence was determined starting at the 5' end of the Upf1 ORF.
Nucleotide sequence accession number. The GenBank accession number for the Upf1 sequence is M76659.
Results
Dominant-negative mutations map in region III of the Upf1 protein. The original Upf1 mutations isolated by in vivo selection were recessive (Culbertson, M. R, et al., 1980, Genetics 95:833-853). To continue the genetic analysis of Upf1, the dominant-negative alleles were sought (see Materials and Methods). By isolating and mapping such mutations, we reasoned that it might be possible to define a functional domain and correlate its location with the various motifs identified in the DNA sequence (Herskowitz, I., 1987, Nature (London) 329:219-222).
Fifteen independent dominant mutants were analyzed. DNA sequence analysis revealed that in seven of the mutants, a single base change was sufficient to confer the dominant phenotype. These changes cause amino acid substitutions at six positions clustered in region III. When the Upf1, SEN1, and Mov-10 sequences were simultaneously aligned, it was found that six of the seven mutations produced an amino acid substitution at a position that is conserved in all three proteins. The exceptional mutation, UPF1-D1, caused a substitution at Gly-556, which is conserved between Upf1 and SEN1 only. Even among alleles that contained multiple base changes, at least one change always produced a substitution in a conserved residue within region III. For comparison, we also determined the DNA sequence of one of the original recessive mutations, upf1-2 (Culbertson, M. R, et al., 1980, Genetics 95:833-853; Leeds, P., et al., 1991, Genes Dev. 5:2303-2314). Unlike the dominant mutations, upf1-2 resides outside of region III at nucleotide +615. The mutation changes the UGG Trp-205 codon to a UGA nonsense codon.
When Upf1 is deleted from strain PLY180, his4-38 mRNA is stabilized, leading to an increase in its steady-state level (Leeds, P., et al., 1991, Genes Dev. 5:2303-2314). Similarly, when plasmids carrying the dominant-negative alleles were introduced into PLY18 the steady-state level of his4-38 mRNA increased. Since the dominant mutations were phenotypically identical to recessive loss-of-function alleles, we inferred that the dominant mutations might act in a negative manner by interfering with wild-typ Upf1 function. To test this model, we estimated the extent of wild-type Upf1 function by assaying for suppression, using a in which the relative dosages of mutant and wild-type Upf1 genes were varied.
The mutations UPF1-D1 (Gly-556.fwdarw.Asp), UPF1-D2 (Ser-699.fwdarw.Phe), UPF1-D4 (Arg-779.fwdarw.Cys), UPF1-D6 (Arg-794.fwdarw.Cys), and UPF1-D7 (Gly-810.fwdarw.Arg) were placed on both single-copy and multicopy plasmids and analyzed in that carry a single copy of the wild-type Upf1 gene. In general, suppression conferred by each of these mutations was more efficient when the dominant allele was present in multiple gene copies. When the relative concentration of the wild-type gene product was increased by placing Upf1 on a 2 .mu.m plasmid, the efficiency of suppression was visibly diminished in strains carrying UPF1-D2, UPF1-D4, UPF1-D5, and UPF1-D6 but was not diminished in strains carrying UPF1-D1 or UPF1-D7. We infer from this analysis that at least some of the mutant proteins interfere with wild-type Upf1 function. Since the mutations causing the interference all map in region III, this region appears to contain an important functional domain.
The RENT1 mutation in mammals which confers a dominant-negative phenotype on the protein parallels dominant negative Upf1 mutations in yeast.
Example 7
Expression of Rent1
Conventional recombinant DNA techniques and gene expression methods can be used to express wild-type RENT1 or dominant-negative versions of RENT1 in a cell. A genetic construct for expressing the various versions of RENT1 is p.beta.RNT1-NEO produced by modifying the vector pH.beta.Apr-1 (Gunning et al., 1987). pH.beta.Apr-1 contains the human .beta.-actin promoter (.about.3 kb of 5' flanking sequence), 77 bp of .beta.-actin 5' UTR contained in exon 1, and the entire .beta.-actin intron 1 (including the splice donor and acceptor and the enhancer core sequence found therein), followed by a polylinker. To create p.beta.RNT1-NEO, pH.beta.Apr-1 was modified by the addition of a neomycin resistance cassette. In addition, the RENT1 open reading frame, including a short region of the 5'UTR and the entire 3' UTR was subdloned into the polylinker of pH.beta.Apr-1. Expression of RENT1 from p.beta.RNT1-NEO is driven by a cytomegalovirus (CMV) promoter. p.beta.RNT1-NEO transcripts have a portion of the 5' UTR of .beta.-actin at their 5' ends. This 5' tag is useful for distinguishing vector derived transcripts from transcripts which are endogenous to the transfected cell. Northern analysis and RT-PCR can be used to distinguish the transcripts. Another set of constructs have the RENT1 open reading frame cloned in-frame with a sequence that encodes a hemagglutinin (HA) tag at the N-terminus of RENT1. The resulting RENT1/HA fusion protein can be used in studies that employ in immunohistochemical analysis such as those that required determining whether subcellular compartmental localization occurs in RENT1 products.
Example 8
Analysis of Rent1 mRNA by Northern Blot
Prepared multiple human tissue Northern blots obtained from Clontech were probed with a 300 bp RENT1 cDNA fragment (encoding aa 644-745) or a b-actin cDNA probe (Clontech) according to manufacturer instructions. Northern blot analysis of poly(A) RNA shows a predominant transcript size of approximately 5.4 kb in all adult tissues tested. A less intense signal at approximately 3.7 kb is visible in all lanes, with an additional and significantly smaller hybridizing transcript unique to the pancreas. Additional tissues tested (spleen, thymus, prostate, testis, ovary, small intestine, colon, and peripheral blood leukocyte) all showed predominant 5.4 kb and less intense 3.7 kb bands, except in testes where equally intense signals were observed.
Example 9
Yeast Expression Vector Constructs for Rent1
Yeast constructs were prepared that express human RENT1 protein. By modifying the allo suppression assay used to identify and clone the Upf genes (Leed, et al., 1991), one of ordinary skill in the art can determine whether expression of RENT1 can complement the Upf1-deficient phenotype using a PLY38 yeast strain (MATa, ura3-52, his-38, SUF1-1, Upf1-2). This strain harbors a +1 frameshift mutation (his4-38) near the 5' end of the HIS4 transcript and also a SUF1-1 allele which encodes a glycine tRNA frameshift suppressor and allows low-level read through of the frameshift mutation. At both 30.degree. C. and 37.degree. C. PLY38 has a His+ phenotype, but upon reconstitution with wild-type Upf1 the cells are His-at 37.degree. C. and fail to grow. Using a basic assay one of ordinary skill in the art can determine whether expression of RENT1 in this genetic background can inhibit growth at 37.degree. C. To optimize expression, the Upf1 and RENT1 ORFs were both subdloned into a 2-micron vector containing the MET25 promoter. MET25 promoter shows excellent performance in the expression of heterologous proteins in yeast, is not overly influenced by the respiratory status of the cell, and is inducible in the absence of methionine (Mumberg, et al., 1994). Expressing wild-type Upf1 in PLY38 at 37.degree. C. using MET25 promoter, the growth phenotype was easily distinguishable from untransformed cells or transformed cells grown for 2 days in the presence of methionine.
Expression of heterologous genes in yeast is sensitive to the length and origin of the UTR sequences (reviewed in Romanos, et al., 1992). Yeast UTRs tend to be extremely short and RNA conformation in these regions, as dictated by the primary nucleotide sequence, may influence the trafficking and translation of transcripts. To address this issue, two additional yeast expression constructs were prepared. The first is a modification of pAD54LEu2 which drives expression of HA-tagged fusion proteins using the yeast alcohol dehydrogenase (ADH1) promoter and includes the yeast ADH 5' UTR, terminator, 3' UTR, and poly (A) signal. The URA3 was switched for the LEU2 selectable marker (enabling the vector for use in PLY38), and subcloned in the yeast and human ORFs for Upf1 and RENT1, respectively, downstream of and in-frame with the HA tag-encoding region. The RENT1 and Upf1 UTRs were not included in the constructs. These constructs are preferred because inhibition of expression by heterologous UTRs has been obviated, and one of ordinary skill in the art can directly assay for expression of the fusion protein using anti-HA antibodies (Boehringer Mannheim). This vector can be used successfully for the expression of heterologous proteins in yeast. Additionally, the addition of an N-terminal epitope does not to inhibit the function of wild-type Upf1 (Cui, et al., 1995). These construct are designated pAD54-RNT1 or pAD54-UPF1.
A second set of constructs designated pMET25-RNT1 or Upf make use of a vector that expresses wild-type Upf1. To prevent possible interference by heterologous UTRs we substituted the ORF of RENT1 for that of Upf1, leaving in place the 5'UTR, initiating methionine, terminator, and 3'UTR of the Upf1 gene. A PLY38 stain (MATa, ura3-52, his4-38, SUF1-1, Upf1-2) harboring a+1 frameshift mutation (his4-38) near the 5' end of the HIS4 transcript was used to construct the RENT1 yeast expression vector. The strain also contains the SUF1-1 allele which encodes a glycine tRNA frameshift suppressor and allows low-level read through of the frameshift mutation. At both 30.degree. C. and 37.degree. C. this strain has a His+phenotype, but upon reconstitution with wild-type Upf1 the cells are His-at 37.degree. C. and fail to grow. A test to determine whether RENT1 can substitute for Upf1 in this capacity can be established using a previously described allosuppression assay (Leeds, et al., 1991: 1992). Briefly, PLY38 transformants containing pmt.-UPF1, pmt.-RNT1, or pmt. (without insert) can be selected on uracil-deficient media. Three independent transformants for each can be grown in liquid culture to OD600 between 0.4-0.6. Four .mu.l aliquot of serial diluted cultures (undiluted, 1:100, 1:100, and 1:1000) can be plated on solid media lacking methane (for promoter induction), uracil, and histidine. Growth can be monitored at both 30 and 37.degree. C. If pmt.-RNT1 fails to complement the Upf1-phenotype, then PLY38 transformants containing pAD54-UPF1, pAD54-RNT1, and pAD54 (under the control of the constitutive ADHI promoter) can be created and assayed as above. The advantage to this second set of vectors is that they encode an N-terminal HA tag. Additional yeast recombinant expression vector contstructs are shown in FIGS. 5 and 6 and are presented for illustrative purposes for one of ordinary skill in the art to demonstrate other vector constructs can be created using the teachings supplied herein.
If complementation in yeast is seen, this can allow us to interrogate the functional significance of specific residues of RENT1 in an efficient and powerful yeast system. For example, yeast strains PLY154 (MAT.alpha., ura3-52, his4-38, upf1-.DELTA.1, leu2-1, rpb1-1) is particularly useful to measure the decay rates of HIS4 transcripts. The temperature-sensitive rbp1-1 polymerase II allele allows rapid cessation of new transcription after a shift from 25 to 36.degree. C. Quantitative Northern blotting can be performed on RNA isolated from aliqouts of cells that are removed at specified time intervals after the temperature shift (Parker, et al., 1991). This assay can be used to compare the relative strength of various putative dominant negative and loss-of-function mutations in RENT1. First, PLY154 can be complemented with wild-type RENT1. The resulting strain (PLY154R) can be transformed with constructs expressing putative dominant-negative forms of RENT1. The decay rate of His4 transcripts can then be determined can be assayed in PLY154 without prior reconstitution of NMRD function with wild-type RENT1. Alleles showing the most desirable functional characteristics can be targeted for use in mammalian cell culture experimentation. Also, if none of the mutations in Upf1 have similar effects upon the function of RENT1, it can be necessary to screen for dominant-negative forms of RENT1 and then transforming with a RENT1 expression construct that has undergone random mutagenesis (Leeds, et al., 1992). Transformants that are able to grow at 37.degree. C. can harbor dominant-negative RENT1 alleles which can then be characterized and used in further experimentation.
Example 10
Human Rent1 Protein (AA 121-917) Restores NMRD in Yeast Deficient for Upf1 Activity
To explore the functional properties of RENT1, we determined whether its expression in yeast deficient for Upf1 activity could restore NMRD using a modification of the allosupression assay originally used to identify Upf1. We utilized the PLY38 strain (MATa ura3-52 his4-38 SUF1-1 upf1-2) that harbors a+1 frameshift mutation in the HIS4 transcript and a tRNA frameshift suppressor with decreased efficiency at elevated temperatures. This strain grows in histidine-deficient media due to the combination of tRNA suppressor activity and the stability of his4-38 mRNA in the absence of Upf1. Reconstitution with Upf1 activity decreases his4-38 message abundance and causes growth failure at high culture temperatures which are less permissive for suppressor tRNA function.
Transformation of yeast strain PLY38 with a RENT1 expression construct failed to complement the yeast Upf1-deficient phenotype. The same result was obtained when the yeast ADH1 UTRs were placed flanking the entire RENT1 coding sequence (data not shown). To test whether the divergence at the extreme N- and C-termini conferred species-specific functional constraints, we prepared a construct (pMET-Chimera) encoding the Upf1 5' UTR and N-terminus (aa 1-59), the body of the human protein (aa 121-917), and the Upf1 C-terminus (aa 854-971) and 3' UTR. A dramatic inhibition of growth was seen in pMET25-Chimera transformants at elevated temperatures indicating that the central portion of the human RENT1 protein is capable of functioning in yeast and rescuing a mutant yeast phenotype that has a deficient Upf1 protein.
Example 11
Mammalian Expression Vector Constructs for Rent1
To express RENT1 in mammalian cells, mammalian expression constructs were created. Each construct was made in multiple forms, either expressing wild-type RENT1 or one of two putative dominant-negate forms. The dominant-negative mutations were created by oligonucleotide-mediated site-directed mutagenesis (Dietz & Kendzior, 1994). The site and character of the mutations were chosen based upon previous work with Upf1 (Leeds, et al., 1992). Two mutations in Upf1, G556D, and R779C, conferred the strongest dominant negative phenotype. Corresponding mutations were made in the ORF of human RENT1 (G619D and R843C).
The mammalian expression constructs designated p.beta.RNT1-NEO is based upon a modification of the vector pH.beta.Apr-1 (Gunning, et al., 1987). The vector contains the human .beta.-actin promoter (-3 kb of 5' flanking sequence), the 77 bp of .beta.-actin 5' UTR contained in exon 1, and the entire .beta.-actin intron 1 including the splice donor and acceptor and the enhancer core sequence found therein, followed by a polylinker. This vector supports extremely high expression levels in a large variety of mammalian cells (Gunning, et al., 1987). The vector was modified by the addition of a neomycin resistance cassette and subcloned with the RENT1 ORF, including a short region of 5'UTR and the entire 3' UTR, into the polylinker. Resultant transcripts are 5'-tagged with the .beta.-actin 5' UTR enabling the discrimination of endogenous transcripts from vector-derived transcripts using either Northern analysis or RT-PCR-based methods. The pCMV-RNT1 constructs contain the RENT1 ORF (wild-type and multiple putative dominant-negative forms) driven by the CMV promoter. Immunohistochemical analysis of the fusion protein permits determination of subcellular compartmental localization of RENT1. The final set of constructs, termed pHA-RNT1, have the RENT1 ORF cloned in-frame with a sequence that encodes an N-terminal HA tag which are useful for transient transfection studies.
To construct pMET25-RENT, an XhoI fragment containing the entire RENT1 coding region was inserted into the SmaI site of p426MET25. The BamHI fragment from pBM272UPF1 was inserted into the BamHI site of p426MET25 to create pMET25-UPF1. pMET25-CHMERA was constructed using high fidelity Taq polymerase (Pfu, Stratagene) with the addition of restriction sites for cloning as follows: The 5' region (5' UTR and sequence encoding aa 1-59) of Upf1 was amplified by PCR with UPF-Bam-S(5'-GGATCCCATCAGGAAAGAAG-3') (SEQ ID NO:16) and UPF-Sal-AS (5'-GTCGACTGAAGCTGAAGGCGAACGG-3') (SEQ ID NO:17). The 3' region of Upf1 (encoding aa 854-971 and 3' UTR) was amplified by UPF-Not-S (5'-GCGGCCGCGAAAGACTGAACGGCCAAT-3') (SEQ ID NO:18) and UPF-Hind-AS (5'-AAGCTTAT-CCAAAGTATATTGGACCGG-3') (SEQ ID NO:19). The central region of RENT1 (encoding aa 121-917) was amplified with RNT-SalS-1 (5'-ACGCGTCGACCACGCCTGCAGTACTGTGGAATAC-3') (SEQ ID NO:20) and RNT-NotAS-1
(5'-ATAAGAATGCGGCCGCGGCTGCTGAACGCATGAGGCTCTCACG-3') (SEQ ID NO:21). Each PCR product was subcloned into the SmaI site of pBluescriptII/SK+ (Stratagene) and excised with the appropriate restriction enzymes and ligated into p426MET25 digested with BamHI and HindHIII. pMET25-y5' was constructed by inserting the 5' Upf1 BamHI/SalI fragment into BamHI/SalI digested p426MET25. Transformants were grown in liquid culture to a similar OD600 and 4ml aliquots of serially diluted cultures were plated on solid media lacking methionine (for promoter induction), uracil (for selection of transformants), and histidine (as a marker for the stability of his4-38 transcripts). Additional mammalian recombinant expression vector constructs are shown in FIGS. 7, 8, and 9 and are presented for illustrative purposes for one of ordinary skill in the art to demonstrate other vector constructs can be created using the teachings supplied herein.
Example 12
Disease Diagnosis Using NMRD and Rent1 Expression
The FBNI genotype-specific efficiency of NMRD modulates phenotypic severity in the Marfan syndrome: A 4 bp tandem insertion was identified at nucleotide 5138 in one allele in the gene (FBN1) encoding fibrillin-1 of a patient with extremely mild Marfan syndrome (MFS) disease (Dietz, et al., 1993b). The transcript level from the mutant allele was 6% of the fraction produced by the wild-type allele. While mutations associated with equal levels of mRNA from the wild-type and mutant alleles cause classic and severe MFS disease, the phenotype in this patient is restricted to mitral valve prolapse, long-bone overgrowth, and striae distinae. This clinical presentation fails to meet the diagnosis criteria for MFS and would be more accurately characterized as the MASS phenotype. One hypothesis for the pathogenic basis for this mild phenotype suggests that a low-level of mutant transcript and protein, relative to that from the wild-type allele, results in a favorable stoichiometry for the formation of structurally normal multimers, albeit in reduced amounts, and hence mild disease. Experience with additional nonsense alleles causing MFS allowed us to test this hypothesis. It was observed that mutant alleles associated with levels of -15% or greater of mutant transcript, relative to that from the wild-type allele, were associated with severe MSF disease, while those associated with <6% were associated with distinctly milder phenotypes of MSF. As observed in the disease osteogenesis imperfecta, perhaps some critical threshold of mutant transcript and monomer, possibly between 6 and 16% of wild-type levels, is necessary for the expression of classic MFS.
Fibrillin-1 metabolism was examined in cell lines harboring nonsense alleles (Aoyama, et al., 1993; 1994). Fibroblasts from patients with defined FBNI mutations were grown in the presence of radiolabeled cysteine. The cultures were then "chased" with unlabeled media for specific time intervals prior to the determination of radiolabeled fibrillin content in the cellular compartment and in the extracellular matrix. Interestingly, all mutations associated with .gtoreq.15% mutant transcript levels showed 50% fibrillin-1 synthesis, relative to control lines, but severely impaired matrix utilization of synthesized protein, presumed to be product from the wild-type allele. In contrast, the mutation associated with a 6% mutant transcript level also showed approximately 50% synthesis, but all of this protein was effectively incorporated into the matrix.
A number of embodiments of the present invention have been described. Nevertheless, it will be understood that various modifications may be made without departing from the spirit and scope of the invention. Accordingly, it is to be understood that the invention is not to be limited by the specific illustrated embodiment, but only by the scope of the appended claims.
__________________________________________________________________________# SEQUENCE LISTING - - - - (1) GENERAL INFORMATION: - - (iii) NUMBER OF SEQUENCES: 29 - - - - (2) INFORMATION FOR SEQ ID NO:1: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 3760 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: genomic DNA - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:1: - - GAATTCCCGG GTCGACCCAC GCGTCCGAGC GGCTGGCGGC TTCGAGGGGA - #GCTGAGGCGC 60 - - GGAGGGGCTC GGCGGCAGCG GCGGCGGCTC GGCACTGTTA CCTCTCGGTC - #CGGCTGGCGC 120 - - CGGGGCGGGC GGTTTGGTCC TTTCCGGGCG CGCGGGGGCG ACAGCGGCAG - #CGACCCGAGG 180 - - CCTGCGGCCT AGGCCTCAGC GCGGCGGCGG GCTCGAGTGC AGCGCGGAAC - #CGGCCCGAGG 240 - - GCCCTACCCG GAGGCACCAT GAGCGTGGAG GCGTACGGGC CCAGCTCGCA - #GACTCTCACT 300 - - TTCCTGGACA CGGAGGAGGC CGAGCTGCTT GGCGCCGACA CACAGGGCTC - #CGAGTTCGAG 360 - - TTCACCGACT TTACTCTTCC TAGCCAGACG CAGACGCCCC CCGGCGGCCC - #CGGCGGCCCG 420 - - GGCGGTGGCG GCGCGGGAGG CCCGGGCGGC GCGGGCGCGG GCGCTGCGGC - #GGGACAGCTC 480 - - GACGCGCAGG TTGGGCCCGA AGGCATCCTG CAGAACGGGG CTGTGGACGA - #CAGTGTAGCC 540 - - AAGACCAGCC AGTTGTTGGC TGAGTTGAAC TTCGAGGAAG ATGAAGAAGA - #CACCTATTAC 600 - - ACGAAGGACC TCCCCATACA CGCCTGCAGT TACTGTGGAA TACACGATCC - #TGCCTGCGTG 660 - - GTTTACTGTA ATACCAGCAA GAAGTGGTTC TGCAACGGAC GTGGAAATAC - #TTCTGGCAGC 720 - - CACATTGTAA ATCACCTTGT GAGGGCAAAA TGCAAAGAGG TGACCCTGCA - #CAAGGACGGG 780 - - CCCCTGGGGG AGACAGTCCT GGAGTGCTAC AACTGCGGCT GTCGCAACGT - #CTTCCTCCTC 840 - - GGCTTCATCC CGGCCAAAGC TGACTCAGTG GTGGTGCTGC TGTGCAGGCA - #GCCCTGTGCC 900 - - AGCCAGAGCA GCCTCAAGGA CATCAACTGG GACAGCTCGC AGTGGCAGCC - #GCTGATCCAG 960 - - GACCGCTGCT TCCTGTCCTG GCTGGTCAAG ATCCCCTCCG AGCAGGAGCA - #GCTGCGGGCA 1020 - - CGCCAGATCA CGGCACAGCA GATCAACAAG CTGGAGGAGC TGTGGAAGGA - #AAACCCTTCT 1080 - - GCCACGCTGG AGGACCTGGA GAAGCCGGGG GTGGACGAGG AGCCGCAGCA - #TGTCCTCCTG 1140 - - CGGTACGAGG ACGCCTACCA GTACCAGAAC ATATTCGGGC CCCTGGTCAA - #GCTGGAGGCC 1200 - - GACTACGACA AGAAGCTGAA GGAGTCCCAG ACTCAAGATA ACATCACTGT - #CAGGTGGGAC 1260 - - CTGGGCCTTA ACAAGAAGAG AATCGCCTAC TTCACTTTGC CCAAGACTGA - #CTCTGACATG 1320 - - CGGCTCATGC AGGGGGATGA GATATGCCTG CGGTACAAAG GGGACCTTGC - #GCCCCTGTGG 1380 - - AAAGGGATCG GCCACGTCAT CAAGGTCCCT GATAATTATG GCGATGAGAT - #CGCCATTGAG 1440 - - CTGCGGAGCA GCGTGGGTGC ACCTGTGGAG GTGACTCACA ACTTCCAGGT - #GGATTTTGTG 1500 - - TGGAAGTCGA CCTCCTTTGA CAGGATGCAG AGCGCATTGA AAACGTTTGC - #CGTGGATGAG 1560 - - ACCTCGGTGT CTGGCTACAT CTACCACAAG CTGTTGGGCC ACGAGGTGGA - #GGACGTAATC 1620 - - ATCAAGTGCC AGCTGCCCAA GCGCTTCACG GCGCAGGCCC TCCCCGACCT - #CAACCACTCC 1680 - - CAGGTTTATG CCGTGAAGAC TGTGCTGCAA AGACCACTGA GCCTGATCCA - #GGGCCCGCCA 1740 - - GGCACGGGGA AGACGGTGAC GTCGGCCACC ATCGTCTACC ACCTGGCCCG - #GCAAGACAAC 1800 - - GGGCCGGTGC TGGTGTGTGC TCCGAGCAAC ATCGCCGTGG ACCAGCTAAC - #GGAGAAGATC 1860 - - CACCAGACGG GGCTAAAGGT CGTGCGCCTC TGCCCCAAGA GCCGTGAGGC - #CATCGACTCC 1920 - - CCGGTGTCTT TTCTGGCCCT GCACAACCAG ATCAGGAACA TGGACAGCAT - #GCCTGAGCTG 1980 - - CAGAAGCTGC AGCAGCTGAA AGACGAGACT GGGGAGCTGT CGTCTGCCGA - #CGAGAAGCGG 2040 - - TACCGGGCCT TGAAGCGCAC CGCAGAGAGA GAGCTGCTGA TGAACGCAGA - #TGTCATCTGC 2100 - - TGCACATGTG TGGGCGCCGG TGACCCGAGG CTGGCCAAGA TGCAGTTCCG - #CTCCATTTTA 2160 - - ATCGACGAAA GCACCCAGGC CACCGAGCCG GAGTGCATGG TTCCCGTGGT - #CCTCGGGGCC 2220 - - AAGCAGCTGA TCCTTGTAGG CGACCACTGC CAGCTGGGCC CAGTGGTGAT - #GTGCAAGAAG 2280 - - GCGGCCAAGG CCGGGCTGTC ACAGTCGCTC TTCGAGCGCC TGGTGGTGCT - #GGGCATCCGG 2340 - - CCCATCCGCC TGCAGGTCCA GTACCGGATG CACCCTGCAC TCAGCGCCTT - #CCCATCCAAC 2400 - - ATCTTCTACG AGGGCTCCCT CCAGAATGGT GTCACTGCAG CGGATCGTGT - #GAAGAAGGGA 2460 - - TTTGACTTCC AGTGGCCCCA ACCCGATAAA CCGATGTTCT TCTACGTGAC - #CCAGGGCCAA 2520 - - GAGGAGATTG CCAGCTCGGG CACCTCCTAC CTGAACAGGA CCGAGGCTGC - #GAACGTGGAG 2580 - - AAGATCACCA CGAAGTTGCT GAAGGCAGGC GCCAAGCCGG ACCAGATTGG - #CATCATCACG 2640 - - CCCTACGAGG GCCAGCGCTC CTACCTGGTG CAGTACATGC AGTTCAGCGG - #CTCCCTGCAC 2700 - - ACCAAGCTCT ACCAGGAGGT GGAGATCGCC AGTGTGGACG CCTTTCAGGG - #ACGCGAGAAG 2760 - - GACTTCATCA TCCTGTCCTG TGTGCGGGCC AACGAGCACC AAGGCATTGG - #CTTTTTAAAT 2820 - - GACCCCAGGC GTCTGAACGT GGCCCTGACC AGAGCAAGGT ATGGCGTCAT - #CATTGTGGGC 2880 - - AACCCGAAGG CACTATCAAA GCAGCCGCTC TGGAACCACC TGCTGATCTT - #CTATAAGGAG 2940 - - CAGAAGGTGC TGGTGGAGGG GCCGCTCAAC AACCTGCGTG AGAGCCTCAT - #GCAGTTCAGC 3000 - - AAGCCACGGA AGCTGGTCAA CACTATCAAC CCGGGAGCCC GCTTCATGAC - #CACAGCCATG 3060 - - TATGATGCCC GGGAGGCCAT CATCCCAGGC TCCGTCTATG ATCGGAGCAG - #CCAGGGCCGG 3120 - - CCTTCCAGCA TGTACTTCCA GACCCATGAC CAGATTGGCA TGATCAGTGC - #CGGCCCTAGC 3180 - - CACGTGGCTG CCATGAACAT TCCCATCCCC TTCAACCTGG TCATGCCACC - #CATGCCACCG 3240 - - CCTGGCTATT TTGGACAAGC CAACGGGCCT GCTGCAGGGC GAGGCACCCC - #GAAAGGCAAG 3300 - - ACTGGTCGTG GGGGACGCCA GAAGAACCGC TTTGGGCTTC CTGGACCCAG - #CCAGACTAAC 3360 - - CTCCCCAACA GCCAAGCCAG CCAGGATGTG GCGTCACAGC CCTTCTCTCA - #GGGCGCCCTG 3420 - - ACGCAGGGCT ACATCTCCAT GAGCCAGCCT TCCCAGATGA GCCAGCCCGG - #CCTCTCCCAG 3480 - - CCGGAGCTGT CCCAGGACAG TTACCTTGGT GACGAGTTTA AATCACAAAT - #CGACGTGGCG 3540 - - CTCTCACAGG ACTCCACGTA CCAGGGAGAG CGGGCTTACC AGCATGGCGG - #GGTGACGGGG 3600 - - CTGTCCCAGT ATTAAAAGGT GGCGGCGGAA GAGCTAAGCA ACGTGGCTTA - #GTCCATCAGC 3660 - - ATCTTATTCT GGGTAATAAA AAATAAAAAT AAACGGATAC CTGTTTTCCA - #CTGCTAAAAA 3720 - - AAAAAAAAAA AAAGAATTCC CGGGTCGACC CACGCGTCCG - # - # 3760 - - - - (2) INFORMATION FOR SEQ ID NO:2: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 1118 amino - #acids (B) TYPE: amino acid (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: protein - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:2: - - Met Ser Val Glu Ala Tyr Gly Pro Ser Ser - #Gln Thr Leu Thr Phe Leu 1 - #5 - #10 - #15 - - Asp Thr Glu Glu Ala Glu Leu Leu Gly Ala - #Asp Thr Gln Gly Ser Glu 20 - # 25 - # 30 - - Phe Glu Phe Thr Asp Phe Thr Leu Pro Ser - #Gln Thr Gln Thr Pro Pro 35 - # 40 - # 45 - - Gly Gly Pro Gly Gly Pro Gly Gly Gly Gly - #Ala Gly Gly Pro Gly Gly 50 - # 55 - # 60 - - Ala Gly Ala Gly Ala Ala Ala Gly Gln Leu - #Asp Ala Gln Val Gly Pro 65 - # 70 - # 75 - #80 - - Glu Gly Ile Leu Gln Asn Gly Ala Val Asp - #Asp Ser Val Ala LysThr - #85 - #90 - #95 - - Ser Gln Leu Leu Ala Glu Leu Asn Phe Glu - #Glu Asp Glu Glu Asp Thr 100 - # 105 - # 110 - - Tyr Tyr Thr Lys Asp Leu Pro Ile His Ala - #Cys Ser Tyr Cys Gly Ile 115 - # 120 - # 125 - - His Asp Pro Ala Cys Val Val Tyr Cys Asn - #Thr Ser Lys Lys Trp Phe 130 - # 135 - # 140 - - Cys Asn Gly Arg Gly Asn Thr Ser Gly Ser - #His Ile Val Asn His Leu 145 - #150 - #155 -#160 - - Val Arg Ala Lys Cys Lys Glu Val Thr Leu - #His Lys Asp Gly ProLeu 165 - # 170 - # 175 - - Gly Glu Thr Val Leu Glu Cys Tyr Asn Cys - #Gly Cys Arg Asn Val Phe 180 - # 185 - # 190 - - Leu Leu Gly Phe Ile Pro Ala Lys Ala Asp - #Ser Val Val Val Leu Leu 195 - # 200 - # 205 - - Cys Arg Gln Pro Cys Ala Ser Gln Ser Ser - #Leu Lys Asp Ile Asn Trp 210 - # 215 - # 220 - - Asp Ser Ser Gln Trp Gln Pro Leu Ile Gln - #Asp Arg Cys Phe Leu Ser 225 - #230 - #235 -#240 - - Trp Leu Val Lys Ile Pro Ser Glu Gln Glu - #Gln Leu Arg Ala ArgGln 245 - # 250 - # 255 - - Ile Thr Ala Gln Gln Ile Asn Lys Leu Glu - #Glu Leu Trp Lys Glu Asn 260 - # 265 - # 270 - - Pro Ser Ala Thr Leu Glu Asp Leu Glu Lys - #Pro Gly Val Asp Glu Glu 275 - # 280 - # 285 - - Pro Gln His Val Leu Leu Arg Tyr Glu Asp - #Ala Tyr Gln Tyr Gln Asn 290 - # 295 - # 300 - - Ile Phe Gly Pro Leu Val Lys Leu Glu Ala - #Asp Tyr Asp Lys Lys Leu 305 - #310 - #315 -#320 - - Lys Glu Ser Gln Thr Gln Asp Asn Ile Thr - #Val Arg Trp Asp LeuGly 325 - # 330 - # 335 - - Leu Asn Lys Lys Arg Ile Ala Tyr Phe Thr - #Leu Pro Lys Thr Asp Ser 340 - # 345 - # 350 - - Asp Met Arg Leu Met Gln Gly Asp Glu Ile - #Cys Leu Arg Tyr Lys Gly 355 - # 360 - # 365 - - Asp Leu Ala Pro Leu Trp Lys Gly Ile Gly - #His Val Ile Lys Val Pro 370 - # 375 - # 380 - - Asp Asn Tyr Gly Asp Glu Ile Ala Ile Glu - #Leu Arg Ser Ser Val Gly 385 - #390 - #395 -#400 - - Ala Pro Val Glu Val Thr His Asn Phe Gln - #Val Asp Phe Val TrpLys 405 - # 410 - # 415 - - Ser Thr Ser Phe Asp Arg Met Gln Ser Ala - #Leu Lys Thr Phe Ala Val 420 - # 425 - # 430 - - Asp Glu Thr Ser Val Ser Gly Tyr Ile Tyr - #His Lys Leu Leu Gly His 435 - # 440 - # 445 - - Glu Val Glu Asp Val Ile Ile Lys Cys Gln - #Leu Pro Lys Arg Phe Thr 450 - # 455 - # 460 - - Ala Gln Ala Leu Pro Asp Leu Asn His Ser - #Gln Val Tyr Ala Val Lys 465 - #470 - #475 -#480 - - Thr Val Leu Gln Arg Pro Leu Ser Leu Ile - #Gln Gly Pro Pro GlyThr 485 - # 490 - # 495 - - Gly Lys Thr Val Thr Ser Ala Thr Ile Val - #Tyr His Leu Ala Arg Gln 500 - # 505 - # 510 - - Asp Asn Gly Pro Val Leu Val Cys Ala Pro - #Ser Asn Ile Ala Val Asp 515 - # 520 - # 525 - - Gln Leu Thr Glu Lys Ile His Gln Thr Gly - #Leu Lys Val Val Arg Leu 530 - # 535 - # 540 - - Cys Pro Lys Ser Arg Glu Ala Ile Asp Ser - #Pro Val Ser Phe Leu Ala 545 - #550 - #555 -#560 - - Leu His Asn Gln Ile Arg Asn Met Asp Ser - #Met Pro Glu Leu GlnLys 565 - # 570 - # 575 - - Leu Gln Gln Leu Lys Asp Glu Thr Gly Glu - #Leu Ser Ser Ala Asp Glu 580 - # 585 - # 590 - - Lys Arg Tyr Arg Ala Leu Lys Arg Thr Ala - #Glu Arg Glu Leu Leu Met 595 - # 600 - # 605 - - Asn Ala Asp Val Ile Cys Cys Thr Cys Val - #Gly Ala Gly Asp Pro Arg 610 - # 615 - # 620 - - Leu Ala Lys Met Gln Phe Arg Ser Ile Leu - #Ile Asp Glu Ser Thr Gln 625 - #630 - #635 -#640 - - Ala Thr Glu Pro Glu Cys Met Val Pro Val - #Val Leu Gly Ala LysGln 645 - # 650 - # 655 - - Leu Ile Leu Val Gly Asp His Cys Gln Leu - #Gly Pro Val Val Met Cys 660 - # 665 - # 670 - - Lys Lys Ala Ala Lys Ala Gly Leu Ser Gln - #Ser Leu Phe Glu Arg Leu 675 - # 680 - # 685 - - Val Val Leu Gly Ile Arg Pro Ile Arg Leu - #Gln Val Gln Tyr Arg Met 690 - # 695 - # 700 - - His Pro Ala Leu Ser Ala Phe Pro Ser Asn - #Ile Phe Tyr Glu Gly Ser 705 - #710 - #715 -#720 - - Leu Gln Asn Gly Val Thr Ala Ala Asp Arg - #Val Lys Lys Gly PheAsp 725 - # 730 - # 735 - - Phe Gln Trp Pro Gln Pro Asp Lys Pro Met - #Phe Phe Tyr Val Thr Gln 740 - # 745 - # 750 - - Gly Gln Glu Glu Ile Ala Ser Ser Gly Thr - #Ser Tyr Leu Asn Arg Thr 755 - # 760 - # 765 - - Glu Ala Ala Asn Val Glu Lys Ile Thr Thr - #Lys Leu Leu Lys Ala Gly 770 - # 775 - # 780 - - Ala Lys Pro Asp Gln Ile Gly Ile Ile Thr - #Pro Tyr Glu Gly Gln Arg 785 - #790 - #795 -#800 - - Ser Tyr Leu Val Gln Tyr Met Gln Phe Ser - #Gly Ser Leu His ThrLys 805 - # 810 - # 815 - - Leu Tyr Gln Glu Val Glu Ile Ala Ser Val - #Asp Ala Phe Gln Gly Arg 820 - # 825 - # 830 - - Glu Lys Asp Phe Ile Ile Leu Ser Cys Val - #Arg Ala Asn Glu His Gln 835 - # 840 - # 845 - - Gly Ile Gly Phe Leu Asn Asp Pro Arg Arg - #Leu Asn Val Ala Leu Thr 850 - # 855 - # 860 - - Arg Ala Arg Tyr Gly Val Ile Ile Val Gly - #Asn Pro Lys Ala Leu Ser 865 - #870 - #875 -#880 - - Lys Gln Pro Leu Trp Asn His Leu Leu Ile - #Phe Tyr Lys Glu GlnLys 885 - # 890 - # 895 - - Val Leu Val Glu Gly Pro Leu Asn Asn Leu - #Arg Glu Ser Leu Met Gln 900 - # 905 - # 910 - - Phe Ser Lys Pro Arg Lys Leu Val Asn Thr - #Ile Asn Pro Gly Ala Arg 915 - # 920 - # 925 - - Phe Met Thr Thr Ala Met Tyr Asp Ala Arg - #Glu Ala Ile Ile Pro Gly 930 - # 935 - # 940 - - Ser Val Tyr Asp Arg Ser Ser Gln Gly Arg - #Pro Ser Ser Met Tyr Phe 945 - #950 - #955 -#960 - - Gln Thr His Asp Gln Ile Gly Met Ile Ser - #Ala Gly Pro Ser HisVal 965 - # 970 - # 975 - - Ala Ala Met Asn Ile Pro Ile Pro Phe Asn - #Leu Val Met Pro Pro Met 980 - # 985 - # 990 - - Pro Pro Pro Gly Tyr Phe Gly Gln Ala Asn - #Gly Pro Ala Ala Gly Arg 995 - # 1000 - # 1005 - - Gly Thr Pro Lys Gly Lys Thr Gly Arg Gly - #Gly Arg Gln Lys Asn Arg 1010 - # 1015 - # 1020 - - Phe Gly Leu Pro Gly Pro Ser Gln Thr Asn - #Leu Pro Asn Ser Gln Ala 1025 - #1030 103 - #5 104 - - Ser Gln Asp Val Ala Ser Gln Pro Phe Ser - #Gln Gly Ala Leu Thr Gln 1045 - # 1050 - # 1055 - - Gly Tyr Ile Ser Met Ser Gln Pro Ser Gln - #Met Ser Gln Pro Gly Leu 1060 - # 1065 - # 1070 - - Ser Gln Pro Glu Leu Ser Gln Asp Ser Tyr - #Leu Gly Asp Glu Phe Lys 1075 - # 1080 - # 1085 - - Ser Gln Ile Asp Val Ala Leu Ser Gln Asp - #Ser Thr Tyr Gln Gly Glu 1090 - # 1095 - # 1100 - - Arg Ala Tyr Gln His Gly Gly Val Thr Gly - #Leu Ser Gln Tyr 1105 - #1110 111 - #5 - - - - (2) INFORMATION FOR SEQ ID NO:3: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 13146 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: genomic DNA - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:3: - - ATGGCATACT GAGTGGCCCT TGTTGCCAGC CAGCATTGAC TCTTTAATCC - #TTTTGCTCAG 60 - - TAGAGGAGCA CGGGATTCAG TAGCATAGAC CTCAGGAGTG GGGCCTCTGG - #GTGCCCTTGG 120 - - TGGCCTGCAC TGGTGATACT GTGTTCTCTC TAGGTTGGAC CAGAGGGCAT - #CTTGCAAAAT 180 - - GGGGCTGTGG ATGACAGTGT GGCCAAGACC AGCCAGCTGC TAGCTGAGCT - #GAACTTCGAG 240 - - GAAGATGAAG AGGACACATA CTACACTAAG GACCTCCCAG TCCACGCCTG - #CAGGTATGCT 300 - - GCAGGGCTCC AGGACCAAGA GGTGGCCTGC TTCAGAGTAC CGGTTCCTTG - #TTCAGAACCC 360 - - AGAGCACAGT ACCTAACACC CCAGATTCAT AGGGTTCTTG TGGGTCCCCT - #GCCATAGCCA 420 - - CTCAAGCAAG GACCCCTGAA GGAGCCAAGG CAGGGCATGG ATCCTGACTA - #AATCAGCTCC 480 - - ATCAGGGCCA CATGAGGGCA CTGGAGGCTT AAAGAGTTGG AATGTCCTTG - #TTGTGGAATA 540 - - CCCAGCTCAG CTAACTTCAC ACCCACCCAC CCACACACAC ACCCAGCAAG - #GCCAGAGCTT 600 - - GTCTTTACTA GGGTTTTGTA GCCATCTGCC GCCCTCTACA GGGCTGTTTT - #GGCCTCTCCT 660 - - CTCCACACCT ATTGCTTTCC GTTATAATGG CTCTCTCCTG GTTGACAAGT - #GTTTTCTTTT 720 - - TCTTTTTTTT TTTTTTTTAA AGATTTATTT ATTTATTATA TGTAAGTACA - #CTGTAGCTGT 780 - - CTTCAGACAC ACCAGAAGAG GGAGTCAGAT CTCGTGATCA GATGGTTGTG - #AGCCACCATG 840 - - TGGTTGCTGG GATTTGAACT CCTGACCTTC GGAAGAGCAG TTGGGTGCTC - #TTACCCACTG 900 - - AGCCATCTCA CCAGCCCGAC AAGTGTTTTC GAGGATAAAA CCAGAGCTAC - #AGGCAGGCTG 960 - - ATCTGGGAGC CCTAGTCGTC CTTTCCACCA GGAATAGACG AGAGAGCCCA - #GTGAGAGCGT 1020 - - TTTCTGGTTT GACACCTCAT GGCCCCAGCC TGCCGGTGCA CAACAGAGCT - #ATGGAGACCC 1080 - - AGTGATTCAG GGGCCTCCCT TAGCCTGGGT TGGGCCTGAG CATTCTCTGG - #TTGCAGAGTA 1140 - - CCTGCCTTCT GGAGTCAGGT GCTCCCACAA CCTTGTTAGA AACTTGCAGG - #CTGAAGGGAA 1200 - - GGGGCCAGGA TTGCCTTGGG CCTGTGCCAC TCAGGCATCT GTGTTGCCCT - #CACACTAACC 1260 - - AAACCTGAAA GCTGCAGGCC AGTACTGACT GTTGATGTTT GGGCTTTTCC - #AGTTACTGTG 1320 - - GAATCCATGA TCCTGCCTGC GTGGTTTACT GTAATACCAG CAAGAAGTGG - #TTCTGCAATG 1380 - - GCCGAGGAAA TACTTCTGGC AGGTAGCTGA CAGCCATGCA TGTGTGTTTA - #ATCAGCAACA 1440 - - CTAGGGCTGC TGTGAGTTAC GGTGTTGTTG GAGCAAAGCT GGAATGAGAT - #GGTGCTGGTG 1500 - - AACCTGGGCT CCCCCTTTGA CTGGTGTAAC TTGAAACAGA TGGTGGCGTG - #TGAACGCTTC 1560 - - GACATGTTTA TCCTTGATTG ATTCTCTGCC TCGCTCATTA TGTGAGGAGT - #TTGGCTTAAT 1620 - - TCTGTTCTCA GGCTGTGCCT GCCTCTCATG AAATGAGGCT GGCATGGCCT - #GCCTGTCCTT 1680 - - GTTCCTGGGA GGTTGAGGGC ATCCAGCTGA GCCAGTTGAC TTGATTGTCT - #CTGGAACCAA 1740 - - TGGTTCAAGA TCCTAAGTCA TTAGGAACAA CTAGACTCAT CCCTATATCA - #TGCTGGCTCT 1800 - - CCATGCAAGT GTCAGGAAAC ACTGTTGGAG AGAAACAACT GAGCCAGGTG - #TGCCTGTTTC 1860 - - CCACTGCCAC CAGGGGTGTG GCTTGTTTCT GAGGACATTC TGTAAAAAGA - #ATGCCACAGA 1920 - - AGGTTGTAGG TACCAGGTCT ACAGTGAGGC AGGGATTATC ATCTTTAAAA - #GATCTTAAAG 1980 - - TCACTTTCAG GGACCAAGAC ATCCCATTCT CAGAAGGAGG AGTAAGACCT - #ACAAAGCTAA 2040 - - GAATGGCTGG ATGGTCACTA CAGTGGGGGT TTCATGGGAT CATACAGAAA - #GACAACTAAG 2100 - - ACAGTCAGGA AGAACTGGCA GAGCCTGTGG GCCCTGAGGT GGCCAGCCAA - #TGTGGGCCAC 2160 - - TATTGGGGTA GGCCATGTCC TCATATGTGA CGGGGAAGGG ATGGGAGCTA - #TGGTCCTTAG 2220 - - GGCAGCTCCT TGCTATAGAG ACCAGGAGGT GACCTGTTTG TTTAAATAGG - #CATGGAAAAA 2280 - - GAGGACCTGG AAGGAGCCAT TTTTTGCTGA GCATGGCTGC CAGAGGTTAA - #GTTAGCACCA 2340 - - TGTGCTGGGG CTAGAGAAAG AGGAAATGGA GGGGTTGTGT GAGTCAGTGA - #ACAAGCGAGC 2400 - - GGGGCTGAGG CTCCCTGGGC ACCTGTGCCC CTGAGGTGTG ACCATCTGGT - #CTGTGCTGAC 2460 - - AGACCATGAG CAGTACTGGA CATTTTGCAT GGGGTAGCCG ACCTGGAGGT - #GCCGAGAAGC 2520 - - CAAGCTTGGG GTGTTAACTG CGATGGTTTC CTGGTCTCAG CCACATTGTG - #AATCACCTCG 2580 - - TGAGGGCAAA ATGCAAGGAA GTGACGCTGC ACAAGGACGG GCCTCTGGGC - #GAGACCGTGC 2640 - - TGGAGTGCTA CAACTGTGGC TGCCGCAACG TCTTCCTGCT GGGCTTCATC - #CCTGCGAAGG 2700 - - CCGACTCTGT GGTGGTGCTG TTGTGCAGGT GAGCTGCCTG CAGCAGGGCT - #GGACTGGAGA 2760 - - GGACAATGTC TGCTGGGACC AAGTTCTGTG TGTATTCTGG TCAAATTAGA - #AAATGAAGTC 2820 - - TGGCCTGATG TGGTAGTGTA CACTTTTAAC TTCAGCCCTG GGGAGGCAAA - #GGCAGAAGTT 2880 - - TCTCTGAGTT CAAGGCCAGC CTGGTCTACA AAGAGAGGCC AAGGCCAGCC - #AGGGCTACCC 2940 - - AGTTAGAACC TGTCTGAAAA ACTGAAAGAA GGAAAGTGAC AGGTCTGCTG - #TGAACTGAGG 3000 - - CCAGAGCTGG GCGTGCAGAT GCTGCTGCTG CCTTCTGGCT AGTTTGAGGC - #CTCCTGGGCC 3060 - - AGGTCCCAAC CCTCTCTCCT GCCCCACACC TGCACAGGCA GCCCTGTGCC - #AGCCAGAGCA 3120 - - GCCTGAAGGA CATCAACTGG GACAGCTCAC AGTGGCAGCC CCTAATCCAG - #GACCGGTGCT 3180 - - TTCTGTCATG GCTGGTCAAG ATTCCCTCTG AGCAGGAGCA GCTGCGAGCA - #CGGCAGATCA 3240 - - CGGCACAGCA GATCAACAAG CTGGAAGAGC TCTGGAAGGT GAGCCACTCA - #TAGACAAAAG 3300 - - AAAAGTAACG TGGCAAGCCT CACACTGGGC AGGAGATATT GGGGGTGGGG - #GTGGGGACAT 3360 - - GACCTAGGGC TCTGCAGGGG ACATAGTGGA TGGTCTGAGT AATTGGGTTA - #GGCTGTTATG 3420 - - AGATTCCTAC TCCAAGGAGC ACCTGTCCTT ATCCCTAATG ACAAGTCAGG - #GTTCCAGATT 3480 - - AGGTTGGAGT TCTGTTCTGG CTAGCTTTAG ACTCTGACCT TGTTTTCCAA - #ATGTGACTAG 3540 - - GGGTGTCAGT TGAGCACCCT CTAACCAGGA ATCCCAAGTA GTATTGGATA - #GAAACCTTCT 3600 - - AAGCTTGTCC AGCTTAGTCT CTTTGCACTT GGGTGGTCAA GTTCCAGTTA - #TCTCAGTATG 3660 - - CCCAGGTTCT CTGTTCTCTG TCTCAGTGAG GCTCACAGAG GGCAGTTGGT - #CCCAGAGGAG 3720 - - GCATGTTGCT ACAGGATATG AGAGAGGGAC TTGGCTCACT GGGAGAATCA - #TGAGACTCTG 3780 - - ACAGCCGAAT CTGGGGCTCC AGATGGGCCT GAGTATTGTG CTGGGCCGTG - #GGGGTGCTGT 3840 - - TGCCAGGTTT ATTGGGGTTA GAATGGTGTT GAGTATGCCA GGGCCATCAG - #AACAGTAGGC 3900 - - TCAGCGCAGG CCCCGGCACA GTGGCCACTC TCCACCTACG AGGGTTTGTG - #CTGAGAGGCC 3960 - - TTGGCTTGCT TCTGAGCTCT TGATCACTGG CTGCCAGGAC GAACACAGCA - #CTATTCTTGG 4020 - - CCATAGGAAA ATCCTTCAGC CACTCTGGAG GACCTGGAGA AGCCAGGCGT - #AGACGAGGAG 4080 - - CCACAGCACG TGCTCCTGCG TTACGAGGAT GCTTACCAGT ACCAGAACAT - #CTTCGGGCCA 4140 - - CTGGTCAAGC TGGAGGCTGA CTATGACAAG AAGTTGAAGG AGTCACAGGT - #GATGTGGCAC 4200 - - AACAGACCAG GCCTCTAGCA AAACATCTCC CGAGTCAGGG GCTCTTCCTG - #GCCTTGAGCC 4260 - - TGGATGAAAC CAGGCATGCA GATGAGAAAA CCCTTGTGTC TGGTTCACAG - #CTTTGTCTGC 4320 - - AGCTCCAAGA ACATTTCTGG GATATGGGAC CCATGCCACC AATTCCCCAA - #AGTGCCTTCC 4380 - - CTCCCTACAG AGCCTGGCGT GTGGGGTCTC CTGAGGCTCT CTACAAAGCT - #TGCTGCTGGG 4440 - - ACTGGCTTAG GCAGTGGGTG TTGGGGGGTC CTGGTTGCTT CTTTCCCAGA - #TGCTGGAGTT 4500 - - CCTGGCCGTG GATGCTGTGC TCTGCACCCC AAAGGCAGCA CAGCACAGAC - #ATGGCCTTCC 4560 - - TAGAGGCTCT GACCTGTGGG AAGCCCAGCC CGTGAATGAG TGTGGGGCTA - #ACCCGGCCCA 4620 - - TGTTTCTCAT GTGTTCAGAC TCAAGATAAC ATCACGGTCA GGTGGGACCT - #GGGCCTTAAC 4680 - - AAGAAGAGAA TCGCCTTCTT CACTTTGCCC AAGACTGACT CTGGTAATGA - #GGATTTAGTC 4740 - - ATAATTTGGT TAAGAGGTGA TTTTAAGTTT TAAAATATTT GTGACCATAA - #GTAGAATAAA 4800 - - ATTCCTAGTC CCCCATATCA TGTCCCTTAT GTGAACTCTG CATGGTGGAG - #GCCACGCCCT 4860 - - CTTGAAAGTG CTAACTCTGC TACTCCTTCC TGCAAGACAT GCGGCTCATG - #CAGGGTGATG 4920 - - AGATCTGTCT GCGGTACAAA GGGGATCTGG CGCCCCTGTG GAAGGGGATT - #GGCCACGTCA 4980 - - TCAAGGTTCC TGATAGTATC CTTTGTCATA TCTGCTAGGA GGATGGGTTC - #TGTAACAGGA 5040 - - CCCCTGGCTG TCCCCAGGGC TTTAATATGT ACAACTTCTT CCTCTTAATA - #TACAATTTCT 5100 - - TCTCTCTTTC CACTTTGTGA GACATACACA CCGTGACATG GTAGTGAGTG - #CGCGTGCGAG 5160 - - CATGCACATG TGTGAGTGAA ACAGCCTGGA ATCTGTCTGC AGCAGTTCCT - #TTGCCTGATA 5220 - - GGCAAGGAGA GCTGGTCTAG TGATGAAGTC AGGGGCTCTG TAGAAGGTGA - #CTTTGAACAG 5280 - - GAAACTGACT TAACTCAGTT GCCAGATTAT GGTGATGAGA TTGCTATTGA - #GCTCCGCAGC 5340 - - AGCGTGGGTG CCCCTGTGGA AGTGACCCAC AACTTCCAAG TGGATTTTGT - #GTGGAAGTCA 5400 - - ACCTCTTTTG ATAGGTTTGT GAGGGCCATA CCCTTGGGGG CCACCTCCAC - #CTTTGGTACC 5460 - - TGTGGCTCGT GTGGGTTTTA CACTGGCTGT TTTTATAGGA TGCAGAGTGC - #ACTGAAGACC 5520 - - TTCGCTGTGG ACGAGACCTC TGTGTCAGGG TATATTTACC ACAAGCTGCT - #GGGCCACGAG 5580 - - GTGGAGGATG TGGTCATCAA GTGCCAGCTG CCAAAGCGCT TCACAGCTCA - #GGGGCTCCCT 5640 - - GACCTCAACC ACTCTCAGGT GCCATTAGGC CCCTAGGGCC AGGGTCTGTA - #GGGGCTGTGC 5700 - - CTTTGCAGCT TTGCTGATGC TCCGTCCTTG CAGGTGTATG CTGTGAAGAC - #CGTGCTGCAG 5760 - - AGACCACTCA GCCTCATCCA GGGCCCTCCA GGCACAGGCA AGACTGTGAC - #ATCAGCCACT 5820 - - ATTGTCTACC ACCTTGCTCG GCAGGGCAAT GGGTAGGTAG TAGCAAGAGC - #CTTGTGGGTG 5880 - - GGAGGTAGTA ATGTCTTGTG TGGCCTTGTG GTCTGTTATA GCTCTGCCGG - #GGCCACACAG 5940 - - AAAATATATA CAGCGTTACA ATACAGGCAC CTTTTGTGTT CTACAACCCT - #CTGGCCTGCC 6000 - - TCATGTGGAT GACAGGGTGA GGTCACCGTT GAGCTGATGG TGGCTAGGCA - #GGTGACAGGA 6060 - - GGCTTTGCTT GTTTTGCCTT GGCTGTGCAG CTTTTCCCTG GGCCTTGCTG - #AGCTGCTCTG 6120 - - GGTGATGCTG ACAGCCTATT CCACTCTCTG CAGGCCTGTA CTGGTTTGTG - #CTCCAAGTAA 6180 - - CATCGCTGTG GACCAGCTCA CAGAGAAGAT CCACCAGACA GGACTGAAGG - #TCGTACGCCT 6240 - - CTGTGCCAAG AGCCGTGAGG CCATTGACTC CCCAGTGTCC TTCCTGGCTT - #TGCACAACCA 6300 - - GATCAGGAAC ATGGACAGGT GAGTATCTCC AGCTTCGGGC TCAGTACAGG - #CTGCGCCCTG 6360 - - CTGCTGGCGC TGACTCCCAC CACATTTTCT GTAGCATGCC TGAGCTGCAG - #AAGCTGCAGC 6420 - - AGCTAAAGGA TGAGACAGGC GAGCTGTCAT CTGCAGATGA GAAGCGGTAC - #CGGGCGCTTA 6480 - - AGCGCACAGC TGAGAGAGAA CTTCTCATGG TGAGCTCAGT GCCAGCCCAG - #GAGCCTTTGG 6540 - - GCTGTTCCTT GTGGGCAGAG GATCTGGAGA GACTTGTCTG TTCGAGTCAG - #AAGCCTGGTA 6600 - - GCATGTCTGT ACCTTTGCTT TTGAAGACTT GGAGGGACCT CATCTTCCTG - #ATCTGTGCCA 6660 - - TAGTCAGGAA CATAGCTGCC ACTCCTGTCA GTCTCCAGTC TAACAAACCA - #GTCCATCAAA 6720 - - GCTGGAGTCT CAGCCTTGGG GTAGTACCAC CAGCTCAGTA CTGTCCCAGA - #GATTATTGGC 6780 - - AGACACAGCT GTGTCAATGC TGGGGAGTGT GCTCCAGAAG GCTGTACCAT - #TTGAAAGTTG 6840 - - ACGCTCATGG TCCCTGGGAT GTTCACACTT GGGCTGCAGG AGAAGTGGCT - #AGTTTACTTG 6900 - - TTGGGGAATT GTCTGTGGAG AGCCAGTCTG GGGCAACACA GTAAGACCCT - #GTCAGAACAA 6960 - - CTTGTGCGGG CGCACTTCAA GAGTGCTGGG TGGGTGTAGA ACAGGGTATT - #CCAGGTCCCA 7020 - - CCCTAAGCCA TCTAGCTGTG GTGAGGTAGG CACATGTGCC CTGATGTCTG - #TGCCTTCCCC 7080 - - AGAATGCAGA TGTCATATGC TGCACATGTG TGGGTGCTGG TGACCCGAGG - #CTGGCCAAGA 7140 - - TGCAGTTCCG TTCCATCCTC ATTGACGAGA GCACCCAGGC CACTGAGCCT - #GAGTGCATGG 7200 - - TGCCTGTAGT CCTTGGGGCC AAGCAGGTGG GTACCTGTCA CTCATGTGGC - #CCTTGATAGT 7260 - - GGTGCTGGGT GACACAAGAC CTGCTAGAGG TCTTTGAAGG GGGCTGAGTC - #CCATGTGTTC 7320 - - CACAGGCCCG CGCCTCCTGG GGTGTTGGCA GCCTGTACTG AGCAGCTCCC - #CCTACCCCCC 7380 - - TGGGGTACTC GTTCTGTTGC TTTTAGATGG TGGAGGTGAC CCCTGTCCCT - #GTGGTAGGCA 7440 - - CTTAGGAACA TGGAGGGGTT AACTTGAGGG ACTTCTTGCT GCAGCTAATC - #CTCGTCGGTG 7500 - - ACCACTGCCA GCTGGGCCCA GTGGTGATGT GCAAGAAGGC AGCCAAGGCC - #GGACTGTCAC 7560 - - AATCGCTCTT CGAGCGCTTG GTGGTGCTGG GCATCCGGCC CATCCGCCTG - #CAGGTGCAAT 7620 - - ACCGCATGCA CCCTGCACTC AGCGCCTTTC CGTCCAACAT CTTCTACGAG - #GGCTCATTGC 7680 - - AGAATGGCGT CACTGCAGGT AACAGTTGCA GCACTGTGAA GGGCATAGGG - #AAGGGCCATG 7740 - - AGGACGCAAC CCAACTGTTA TACCCTATGC CCTTCATGGT GCTGCTCACC - #CCAGCTTCTC 7800 - - AGACACAGTG CTGCTGGAGT GTGTGGTGGC TCCACAGTGG TCGTCATACC - #TTTCACCATG 7860 - - GCCAGGTCAT GCACTGGCTC TGCTCCCATG GCTGTTGCTT TATGCTGAAC - #AGTCCCAGGC 7920 - - TAGGCACCCC ATGCTTAGAA ATGAACCAAC CACCCCGACA ACAGGAATTC - #CCAGCCTTTT 7980 - - CCTTGTGATG GTGGTTGGCT GAGATGTCAC CCTATCACAA GTTTAAGTGA - #GACCAGGCAG 8040 - - GTAGATTATG AGAGCTTGTC TTCTGAGGTC AGCAGCTGAT GACACCTCTT - #ACCTGCAGCA 8100 - - ATTTGAGGCT CTGTGAACAG GGAATTTAAG GACACTAGGG TCACCTTTGA - #ATGTAGTTCT 8160 - - GGCCCTGTCC TAAGAGTATT TATGGCAGTG ACCTCTTCAG GGTCTTTGCA - #CTGTATCTGT 8220 - - TGGTACAACC TAGAGGATCT GGAGCAGTAG ACAGAGTGAC ACTGTGGTGT - #CAAGTGAGCC 8280 - - ATAAGTATAC TGTCACACAC CCTTGAAAGC TATTTGCTTT CATGGGAGGT - #TGGTACAGAA 8340 - - ACCAACTGGG CCTTACTGTC CTCCACGAAG CCTGAGTGAA GTGGAATGAA - #AGGTTGCTAT 8400 - - CTGACTTGCT TTGCAACATA AATGTGTTTT TCACCAAACT GTTAAAACAT - #CTAGGCATGG 8460 - - CTCTCAGCTT TAATCCCAGG ACTTGTGAAG CAGACAGGCA GGCTCTCTGG - #GAGGTCAGGG 8520 - - CCATAGTGAA ACCCTCTCTC AAACACACAA ACACGGCTTC AGCACAGTGG - #CTTAGGCATG 8580 - - GATTTGAATG TCTGCCTTTG ATGAGCTGTG ACGGGGAAGG AGCCTGCTCA - #GAGCTGCTGT 8640 - - GTCTATGTGG CCTCCCATGT GGATCCAGGC AGCCATATTT GGGGACACCA - #CCTCTCTGCT 8700 - - GGCTAGGTCC TGCCATGATC TTCTCTTCCC TATGTGATTG TCCGAGTGTG - #GGAGGCTCTT 8760 - - GGGTGTTTCC TGGGCTCTGC TGCACTTGGT CACCACTCAG CACAGGAAGT - #GTCCTCGTGT 8820 - - ACTCAGTAGG CAGCCATGTC TTGAATAGTG TTGACCCAGG CCCTTGGCTG - #CCCACAGTGT 8880 - - GGTTGTACTT GATTGAGCCC CTGAGCTTCT CAGTGGGTGA CACCTTCTGT - #CTTTCCTTAT 8940 - - CAGCGGATCG TGTCAAAAAA GGCTTTGACT TCCAGTGGCC ACAACCTGAC - #AAGCCTATGT 9000 - - TCTTCTACGT GACGCAGGGC CAGGAGGAGA TTGCCAGCTC TGGCACATCC - #TACCTCAACA 9060 - - GGTGTGCAGC TGCGTCTCTG GTATGGAGCC ATTCTCACTC ACCCTCGGCT - #CCAACCCGAG 9120 - - ACCCACAGCA TCTTACTCCT TGGGTTGCTC TGCTTGTTAA CAGCATGTGA - #GGGAAGACGC 9180 - - AAACAGGCTC TTGTTTCTCC TGGGGCCTCA AAATGACAGG GGCGGGCAAC - #TATCATGTGG 9240 - - CCTCCTGTAA CCCCTTTGGT TACTGGAGGT CTGCCAGGCT GGGGAACCTG - #TGAGGAGCCT 9300 - - TTTCACTGAC AGCCAGATGT TCTCAGGACG GAGGCAGCCA ATGTGGAGAA - #GATAACTACG 9360 - - AAGCTGTTGA AGGCAGGTGC AAAGCCTGAC CAGATCGGCA TCATCACCCC - #CTACGAGGGC 9420 - - CAGCGCTCTT ACTTGGTGCA GTACATGCAG TTCAGCGGCT CCCTGCACAC - #AAAGCTCTAC 9480 - - CAGGTACCCC ATACCCAGCA GTTAGGAGAG AGCGCATGAG CACACGTCAT - #GACACACAGG 9540 - - TCAGCCTTGG GCTACTGACC TGGCTGGAGG CAAAAGTAGA AAGAGTGTGG - #TGCTGTGTCA 9600 - - GCACTTCAGT GACATGACCA GGTGGGTCTT CATGAATTTG AGGTGGTCAG - #CCTTGATTGA 9660 - - GAGCTTCAAG GCAGCCAGGG CTGTTCAGTA AGGCTTTGTC TCAAAGAAAG - #AGCAGCCCAC 9720 - - GGCTAGACAG GAAGGGGCAG GACAGCTGGG CCCACCTGAG GGGCATGGTA - #CTTGTGACAG 9780 - - ATGCAGAGCT GTGGTTGGTT ATACCATGGA GCCTACTCAG CATTTGCTTC - #ATTGGGCCTG 9840 - - TGGTATCTCT ATTATTGGGG ACTCTTGTAG CATCTGGCTA TAATGATGCA - #GCTAAAGGAA 9900 - - GAGACAGGAG AACGAGGGGC CGGGATATGG CTGACAGGAC ACTTGTCTCA - #TTCAGGAAGT 9960 - - GGAGATTGCC AGTGTGGACG CCTTCCAGGG CCGGGAGAAG GACTTCATCA - #TTCTGTCCTG 10020 - - CGTGCGCGCC AATGAACATC AGGGCATTGG GTTCCTAAAC GACCCCCGGC - #GTCTGAATGT 10080 - - GGCTCTCACC AGAGCAAGGT AGGCCGCTGC CCATCACTAC CATCCACCCT - #CCAGCCAAAA 10140 - - CAAGAAGCCC CCCCCCCTGT GATTCATTTT ACTCATATCT GTCCTGGGAG - #TACATGTGCA 10200 - - TGCTGGCACC CCATCTTGAG AACTGGGCAC TATGGCCTAC CTGCTGCCTT - #ACTGCTTCAA 10260 - - GAACTCAACT ACAAGATCCT ATAGGACACA GATTTAGCTC ATGATCAAGA - #GAGGCATTTA 10320 - - GAGAGCTGCG AATCACACCC AGAGCTCTCA CTGCTGCTTA AGTGCTACCT - #CATGTCTTAG 10380 - - CATCCTGCTC TTCACATTCA AGGTGCTAAC CCTAGACAGT GGAGTTCAGT - #AGGTGTGGCC 10440 - - ATGGGCTCAG CATTTTGATT GCCCTGCAGA TATGGCGTGA TCATTGTGGG - #TAACCCAAAG 10500 - - GCCCTGTCGA AGCAGCCCCT GTGGAATCAC CTGCTGAGCT ACTACAAGGA - #ACAGAAGGCG 10560 - - CTAGTGGAAG GGCCGCTCAA CAACCTACGT GAGAGCCTCA TGCAGTTCAG - #CAAGCCTCGC 10620 - - AAACTTGTCA ACACTGTCAA CCCGGTGGGC CTAGGGGCTG GCCTGGGACC - #TGGGAAAGCT 10680 - - GGGAGCTCTT AGCCTCTGCT GCTGTTGACT GACACATTCC TCACTCTTAT - #GCCACCCTGC 10740 - - AGGGTGCCCG CTTCATGACT ACTGCCATGT ACGATGCCCG TGAGGCCATC - #ATCCCCGGGT 10800 - - CTGTCTATGA CCGCAGCAGC CAGGGTGAGT CTTCCTGGCC AGAACCCATG - #TGTTTATCTT 10860 - - CCCACGTCCC ACTCCGAACC TGTTGCCCCA TGGGTGGCCT CCGTCTGGAA - #CTTGTCCAGT 10920 - - AGCTTCTGTA GCTTCTCCAA CCAGGTCCCC AAGAGCTGTT CTGGCCTCAG - #CTAGTGGTTT 10980 - - GGGCCATGAT CCCTTTAGAA CTGCTAAGGC CACCTGTCTG CCTGAGTGCT - #GCTGCCCTTG 11040 - - TATCCTGCAA CAAACCCGTG TCTACCTCAG CTAGGCTGGC CTCTGCTTTC - #TGGAAGCTTC 11100 - - CAAGTTTGTC TAGAAAGTTC CATCGTGGCC AGATCTCACC AACCCTTCTG - #CCATTTCTTA 11160 - - CCCTCTACCA GCACTCTGCA TGTCAAGACA CACTCGACCT CCCGACTTGT - #CTGGCTGGCC 11220 - - CAGCAGCTAG TTCATGGCAG CCAGTGTCCA CTGGAGCCCT GCATCTGACT - #CAAATGTTTT 11280 - - GCAGGCCGGC CCTCGAACAT GTACTTCCAG ACCCATGACC AGATCAGTAT - #GATCAGCGCA 11340 - - GGCCCCAGCC ACGTGGCTGC CATGAACATC CCTATTCCCT TCAACTTGGT - #CATGCCTCCC 11400 - - ATGCCGCCAC CTGGCTACTT CGGACAGGCC AACGGGCCGG CAGCTGGTAA - #GCGGTTTTAT 11460 - - CTCTACTGCC CAGGCTCTCC TCCTAGCTTT AGGTAGACCT TGCCATATTT - #CACTGCTGTC 11520 - - TTTCAGGTCG GGGCACCCCA AAAACCAAGA CTGGCCGTGG GGGCCGCCAG - #AAGAACCGCT 11580 - - TTGGGCTTCC TGGGCCCAGC CAGACCACCC TTCCCAACAG CCAGGCCAGC - #CAGGACGTGG 11640 - - CCTCCCAGCC CTTTTCACAG GGTGCCCTCA CACAGGGTTA CGTGTCCATG - #AGCCAGCCCT 11700 - - CTCAGATGAG CCAGCCTGGC CTCTCCCAGC CAGAACTGTC CCAGGTGGGC - #TGCATCCTAC 11760 - - AGCAGAGAAA AGGGGGTGGA GGGGTGAGGG GACACATGAG ACCATGATGC - #TGCCTTTCTG 11820 - - AAGGGTGAAT GAACTCTACT GCTATGGATC TGAACCTGTC ACCCTGCTAC - #TCTGGCTGCA 11880 - - GTATGGGGTT TCTTCCCATC CTCGGGTCTG CGGACTGGGT GGCTGTGGGC - #TACTAGCTTT 11940 - - CCTGGCCATG TTCACACTAC TTTTGCCTTT CAGGACAGCT ACCTCGGTGA - #TGAGTTTAAA 12000 - - TCACAGATTG ACGTGGCACT CTCACAAGAC TCCACATACC AGGGAGAGCG - #GGCATACCAG 12060 - - CACGGCGGGG TCACCGGGCT GTCCCAGTAC TAGAAGGCAA GTGCCCTGGT - #GGGTTCAGCT 12120 - - CTCTGCACAC GTGTGCAAAC AGGGTCTTCC CAGACAGACT GGGCAAGTAG - #ATATGGTGTG 12180 - - TTGGCAGGTC CTGCCTCTAC TGGCCCTGAC ACCTCTAACC CTGTCCCTGA - #TCACAGGTAG 12240 - - CGGAGGAAGA GCTAAGCTAT GTGGCTTAGT CTATCAGCAT CTTATTCTGG - #GTAATAAAAA 12300 - - ATAAAAATAA ATGGATACCT GTTTTCCACT GCTAAAACTG AAGCACCACT - #GTGTGAGCAG 12360 - - CCGAGGAGAG GAGAGGAAAG AGGAGCGAGA GCGAGCAGAG AGCGGCCAGG - #GAGGACGACA 12420 - - GAGCGGAGCG CCGAGGAGCG GGCGCCCCCT GTGGGCGGCG AGAGGAGAGA - #GGCCCGCACC 12480 - - GCTGCGAGGC CGGCCCAGCG CCGTGCCCGC CAGAGGGAGA GGCCTCGCCA - #GGACCGGCCC 12540 - - CGCTGGTCTT TTTCTTTGTT TCTCGTGATT GAGGGGCTAC GTTTTAGCAG - #GACGAACTTC 12600 - - GCGTTTCTGT GCCCAAGCGG GCGGCCAGGA GCATCAGTGC GCGGTCCCAG - #CGCTAAGGGG 12660 - - TTTCATTTAA AGAAAATACG GTGTTTGGGG TTTTTCTGGT TTTCCTTTTT - #TTTTTCTTTT 12720 - - TTTTGGTTTT TTTTTTGTTT GTTTGGTTTT TTTTTTTTTT TTTTTTTTTC - #TTTTTGGTTT 12780 - - TCCTTTCCTC CCCCCTACCC CCTTCAAAGA TTCTTTCAAA GGAGTATGGG - #AAGTACTTGG 12840 - - ATCGGTTTGT CTCTAGAGAC CTGACTGTTA AACCTGAGAG ATGCGAGAAG - #CTTCCGGGAA 12900 - - AGGCAGCGCT GAGAAGCCTG AGCCCCGCAG CCTGGGATCA CCGCCTGCAC - #CACAGCCGGA 12960 - - GGATTTGTTT TGGAGTTTGA GCTTCAGAGG CCACAGGCGA ATCGTGAGCA - #CGGCCTGCGG 13020 - - GTTCTTCCCC ATCGAGGGGT GGAGGCCTCA TTGTTTGGGC GCCCTGCCCC - #GGACCCCACC 13080 - - TCCCCGCGGA GCCACCCAAC CCTACCCAGG AAACCTGGCC AACGAAATGG - #AATTTAATTT 13140 - - TAGCAA - # - # -# 13146 - - - - (2) INFORMATION FOR SEQ ID NO:4: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 1043 amino - #acids (B) TYPE: amino acid (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: protein - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:4: - - Val Gly Pro Glu Gly Ile Leu Gln Asn Gly - #Ala Val Asp Asp SerVal 1 - #5 - #10 - #15 - - Ala Lys Thr Ser Gln Leu Leu Ala Glu Leu - #Asn Phe Glu Glu Asp Glu 20 - # 25 - # 30 - - Glu Asp Thr Tyr Tyr Thr Lys Asp Leu Pro - #Val His Ala Cys Ser Tyr 35 - # 40 - # 45 - - Cys Gly Ile His Asp Pro Ala Cys Val Val - #Tyr Cys Asn Thr Ser Lys 50 - # 55 - # 60 - - Lys Trp Phe Cys Asn Gly Arg Gly Asn Thr - #Ser Gly Ser His Ile Val 65 - # 70 - # 75 - #80 - - Asn His Leu Val Arg Ala Lys Cys Lys Glu - #Val Thr Leu His LysAsp - #85 - #90 - #95 - - Gly Pro Leu Gly Glu Thr Val Leu Glu Cys - #Tyr Asn Cys Gly Cys Arg 100 - # 105 - # 110 - - Asn Val Phe Leu Leu Gly Phe Ile Pro Ala - #Lys Ala Asp Ser Val Val 115 - # 120 - # 125 - - Val Leu Leu Cys Arg Gln Pro Cys Ala Ser - #Gln Ser Ser Leu Lys Asp 130 - # 135 - # 140 - - Ile Asn Trp Asp Ser Ser Gln Trp Gln Pro - #Leu Ile Gln Asp Arg Cys 145 - #150 - #155 -#160 - - Phe Leu Ser Trp Leu Val Lys Ile Pro Ser - #Glu Gln Glu Gln LeuArg 165 - # 170 - # 175 - - Ala Arg Gln Ile Thr Ala Gln Gln Ile Asn - #Lys Leu Glu Glu Leu Trp 180 - # 185 - # 190 - - Lys Glu Asn Pro Ser Ala Thr Leu Glu Asp - #Leu Glu Lys Pro Gly Val 195 - # 200 - # 205 - - Asp Glu Glu Pro Gln His Val Leu Leu Arg - #Tyr Glu Asp Ala Tyr Gln 210 - # 215 - # 220 - - Tyr Gln Asn Ile Phe Gly Pro Leu Val Lys - #Leu Glu Ala Asp Tyr Asp 225 - #230 - #235 -#240 - - Lys Lys Leu Lys Glu Ser Gln Thr Gln Asp - #Asn Ile Thr Val ArgTrp 245 - # 250 - # 255 - - Asp Leu Gly Leu Asn Lys Lys Arg Ile Ala - #Phe Phe Thr Leu Pro Lys 260 - # 265 - # 270 - - Thr Asp Ser Asp Met Arg Leu Met Gln Gly - #Asp Glu Ile Cys Leu Arg 275 - # 280 - # 285 - - Tyr Lys Gly Asp Leu Ala Pro Leu Trp Lys - #Gly Ile Gly His Val Ile 290 - # 295 - # 300 - - Lys Val Pro Asp Asn Tyr Gly Asp Glu Ile - #Ala Ile Glu Leu Arg Ser 305 - #310 - #315 -#320 - - Ser Val Gly Ala Pro Val Glu Val Thr His - #Asn Phe Gln Val AspPhe 325 - # 330 - # 335 - - Val Trp Lys Ser Thr Ser Phe Asp Arg Met - #Gln Ser Ala Leu Lys Thr 340 - # 345 - # 350 - - Phe Ala Val Asp Glu Thr Ser Val Ser Gly - #Tyr Ile Tyr His Lys Leu 355 - # 360 - # 365 - - Leu Gly His Glu Val Glu Asp Val Val Ile - #Lys Cys Gln Leu Pro Lys 370 - # 375 - # 380 - - Arg Phe Thr Ala Gln Gly Leu Pro Asp Leu - #Asn His Ser Gln Val Tyr 385 - #390 - #395 -#400 - - Ala Val Lys Thr Val Leu Gln Arg Pro Leu - #Ser Leu Ile Gln GlyPro 405 - # 410 - # 415 - - Pro Gly Thr Gly Lys Thr Val Thr Ser Ala - #Thr Ile Val Tyr His Leu 420 - # 425 - # 430 - - Ala Arg Gln Gly Asn Gly Pro Val Leu Val - #Cys Ala Pro Ser Asn Ile 435 - # 440 - # 445 - - Ala Val Asp Gln Leu Thr Glu Lys Ile His - #Gln Thr Gly Leu Lys Val 450 - # 455 - # 460 - - Val Arg Leu Cys Ala Lys Ser Arg Glu Ala - #Ile Asp Ser Pro Val Ser 465 - #470 - #475 -#480 - - Phe Leu Ala Leu His Asn Gln Ile Arg Asn - #Met Asp Ser Met ProGlu 485 - # 490 - # 495 - - Leu Gln Lys Leu Gln Gln Leu Lys Asp Glu - #Thr Gly Glu Leu Ser Ser 500 - # 505 - # 510 - - Ala Asp Glu Lys Arg Tyr Arg Ala Leu Lys - #Arg Thr Ala Glu Arg Glu 515 - # 520 - # 525 - - Leu Leu Met Asn Ala Asp Val Ile Cys Cys - #Thr Cys Val Gly Ala Gly 530 - # 535 - # 540 - - Asp Pro Arg Leu Ala Lys Met Gln Phe Arg - #Ser Ile Leu Ile Asp Glu 545 - #550 - #555 -#560 - - Ser Thr Gln Ala Thr Glu Pro Glu Cys Met - #Val Pro Val Val LeuGly 565 - # 570 - # 575 - - Ala Lys Gln Leu Ile Leu Val Gly Asp His - #Cys Gln Leu Gly Pro Val 580 - # 585 - # 590 - - Val Met Cys Lys Lys Ala Ala Lys Ala Gly - #Leu Ser Gln Ser Leu Phe 595 - # 600 - # 605 - - Glu Arg Leu Val Val Leu Gly Ile Arg Pro - #Ile Arg Leu Gln Val Gln 610 - # 615 - # 620 - - Tyr Arg Met His Pro Ala Leu Ser Ala Phe - #Pro Ser Asn Ile Phe Tyr 625 - #630 - #635 -#640 - - Glu Gly Ser Leu Gln Asn Gly Val Thr Ala - #Ala Asp Arg Val LysLys 645 - # 650 - # 655 - - Gly Phe Asp Phe Gln Trp Pro Gln Pro Asp - #Lys Pro Met Phe Phe Tyr 660 - # 665 - # 670 - - Val Thr Gln Gly Gln Glu Glu Ile Ala Ser - #Ser Gly Thr Ser Tyr Leu 675 - # 680 - # 685 - - Asn Arg Thr Glu Ala Ala Asn Val Glu Lys - #Ile Thr Thr Lys Leu Leu 690 - # 695 - # 700 - - Lys Ala Gly Ala Lys Pro Asp Gln Ile Gly - #Ile Ile Thr Pro Tyr Glu 705 - #710 - #715 -#720 - - Gly Gln Arg Ser Tyr Leu Val Gln Tyr Met - #Gln Phe Ser Gly SerLeu 725 - # 730 - # 735 - - His Thr Lys Leu Tyr Gln Glu Val Glu Ile - #Ala Ser Val Asp Ala Phe 740 - # 745 - # 750 - - Gln Gly Arg Glu Lys Asp Phe Ile Ile Leu - #Ser Cys Val Arg Ala Asn 755 - # 760 - # 765 - - Glu His Gln Gly Ile Gly Phe Leu Asn Asp - #Pro Arg Arg Leu Asn Val 770 - # 775 - # 780 - - Ala Leu Thr Arg Ala Arg Tyr Gly Val Ile - #Ile Val Gly Asn Pro Lys 785 - #790 - #795 -#800 - - Ala Leu Ser Lys Gln Pro Leu Trp Asn His - #Leu Leu Ser Tyr TyrLys 805 - # 810 - # 815 - - Glu Gln Lys Ala Leu Val Glu Gly Pro Leu - #Asn Asn Leu Arg Glu Ser 820 - # 825 - # 830 - - Leu Met Gln Phe Ser Lys Pro Arg Lys Leu - #Val Asn Thr Val Asn Pro 835 - # 840 - # 845 - - Val Gly Gly Ala Arg Phe Met Thr Thr Ala - #Met Tyr Asp Ala Arg Glu 850 - # 855 - # 860 - - Ala Ile Ile Pro Gly Ser Val Tyr Asp Arg - #Ser Ser Gln Gly Arg Pro 865 - #870 - #875 -#880 - - Ser Asn Met Tyr Phe Gln Thr His Asp Gln - #Ile Ser Met Ile SerAla 885 - # 890 - # 895 - - Gly Pro Ser His Val Ala Ala Met Asn Ile - #Pro Ile Pro Phe Asn Leu 900 - # 905 - # 910 - - Val Met Pro Pro Met Pro Pro Pro Gly Tyr - #Phe Gly Gln Ala Asn Gly 915 - # 920 - # 925 - - Pro Ala Ala Gly Arg Gly Thr Pro Lys Thr - #Lys Thr Gly Arg Gly Gly 930 - # 935 - # 940 - - Arg Gln Lys Asn Arg Phe Gly Leu Pro Gly - #Pro Ser Gln Thr Thr Leu 945 - #950 - #955 -#960 - - Pro Asn Ser Gln Ala Ser Gln Asp Val Ala - #Ser Gln Pro Phe SerGln 965 - # 970 - # 975 - - Gly Ala Leu Thr Gln Gly Tyr Val Ser Met - #Ser Gln Pro Ser Gln Met 980 - # 985 - # 990 - - Ser Gln Pro Gly Leu Ser Gln Pro Glu Leu - #Ser Gln Asp Ser Tyr Leu 995 - # 1000 - # 1005 - - Gly Asp Glu Phe Lys Ser Gln Ile Asp Val - #Ala Leu Ser Gln Asp Ser 1010 - # 1015 - # 1020 - - Thr Tyr Gln Gly Glu Arg Ala Tyr Gln His - #Gly Gly Val Thr Gly Leu 1025 1030 - # 1035 - # 1040 - - Ser Gln Tyr - - - - (2) INFORMATION FOR SEQ ID NO:5: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 23 amino - #acids (B) TYPE: amino acid (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: peptide - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:5: - - Gln Val Asp Phe Val Gln Lys Ser Thr Ser - #Phe Asp Arg Met Gln Ser 1 - #5 - #10 - #15 - - Ala Leu Lys Thr Phe Ala Val 20 - - - - (2) INFORMATION FOR SEQ ID NO:6: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 28 amino - #acids (B) TYPE: amino acid (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: peptide - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:6: - - Leu Ser Leu Ile Gln Gly Pro Pro Gly Thr - #Gly Lys Thr Val Thr Ser 1 - #5 - #10 - #15 - - Ala Thr Ile Val Tyr His Leu Ala Arg Gln - #Asp Asn 20 - # 25 - - - - (2) INFORMATION FOR SEQ ID NO:7: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 21 amino - #acids (B) TYPE: amino acid (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: peptide - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:7: - - His Ile Val Asn His Leu Val Arg Ala Lys - #Cys Lys Glu Val Thr Leu 1 - #5 - #10 - #15 - - His Lys Asp Gly Pro 20 - - - - (2) INFORMATION FOR SEQ ID NO:8: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 27 amino - #acids (B) TYPE: amino acid (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: peptide - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:8: - - Ala Gly Gln Leu Asp Ala Gln Val Gly Pro - #Glu Gly Ile Leu Gln Asn 1 - #5 - #10 - #15 - - Gly Ala Val Asp Phe Asp Ser Val Ala Lys - #Thr 20 - # 25 - - - - (2) INFORMATION FOR SEQ ID NO:9: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 30 amino - #acids (B) TYPE: amino acid (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: peptide - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:9: - - Ile Leu Ile Asp Glu Ser Thr Gln Ala Thr - #Glu Pro Glu Cys Met Val 1 - #5 - #10 - #15 - - Pro Val Val Leu Gly Ala Lys Gln Leu Ile - #Leu Val Gly Asp 20 - # 25 - # 30 - - - - (2) INFORMATION FOR SEQ ID NO:10: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 20 amino - #acids (B) TYPE: amino acid (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: peptide - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:10: - - Ser Met Ser Gln Pro Ser Gln Met Ser Gln - #Pro Gly Leu Ser Gln Pro 1 - #5 - #10 - #15 - - Glu Leu Ser Gln 20 - - - - (2) INFORMATION FOR SEQ ID NO:11: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 21 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:11: - - CTTTGACAGG ATGCAGAGCG C - # - # - #21 - - - - (2) INFORMATION FOR SEQ ID NO:12: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 10 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:12: - - GGCACCATGA - # - #- # 10 - - - - (2) INFORMATION FOR SEQ ID NO:13: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 10 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:13: - - GCCRCCATGG - # - #- # 10 - - - - (2) INFORMATION FOR SEQ ID NO:14: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 8 amino - #acids (B) TYPE: amino acid (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: peptide - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:14: - - Gly Xaa Xaa Xaa Xaa Gly Lys Ser 1 - #5 - - - - (2) INFORMATION FOR SEQ ID NO:15: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 4 amino - #acids (B) TYPE: amino acid (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: peptide - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:15: - - Asp Xaa Xaa Gly 1 - - - - (2) INFORMATION FOR SEQ ID NO:16: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 20 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:16: - - GGATCCCATC AGGAAAGAAG - # - # - # 20 - - - - (2) INFORMATION FOR SEQ ID NO:17: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 25 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:17: - - GTCGACTGAA GCTGAAGGCG AACGG - # - # 25 - - - - (2) INFORMATION FOR SEQ ID NO:18: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 27 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:18: - - GCGGCCGCGA AAGACTGAAC GGCCAAT - # - # 27 - - - - (2) INFORMATION FOR SEQ ID NO:19: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 27 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:19: - - AAGCTTATCC AAAGTATATT GGACCGG - # - # 27 - - - - (2) INFORMATION FOR SEQ ID NO:20: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 34 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:20: - - ACGCGTCGAC CACGCCTGCA GTACTGTGGA ATAC - # -# 34 - - - - (2) INFORMATION FOR SEQ ID NO:21: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 43 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:21: - - ATAAGAATGC GGCCGCGGCT GCTGAACGCA TGAGGCTCTC ACG - # - # 43 - - - - (2) INFORMATION FOR SEQ ID NO:22: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 971 amino - #acids (B) TYPE: amino acid (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: protein - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:22: - - Met Val Gly Ser Gly Ser His Thr Pro Tyr - #Asp Ile Ser Asn Ser Pro 1 - #5 - #10 - #15 - - Ser Asp Val Asn Val Gln Pro Ala Thr Gln - #Leu Asn Ser Thr Leu Val 20 - # 25 - # 30 - - Glu Asp Asp Asp Val Asp Asn Gln Leu Phe - #Glu Glu Ala Gln Val Thr 35 - # 40 - # 45 - - Glu Thr Gly Phe Arg Ser Pro Ser Ala Ser - #Asp Asn Ser Cys Ala Tyr 50 - # 55 - # 60 - - Cys Gly Ile Asp Ser Ala Lys Cys Val Ile - #Lys Cys Asn Ser Cys Lys 65 - # 70 - # 75 - #80 - - Lys Trp Phe Cys Asn Thr Lys Asn Gly Thr - #Ser Ser Ser His IleVal - #85 - #90 - #95 - - Asn His Leu Val Leu Ser His His Asn Val - #Val Ser Leu His Pro Asp 100 - # 105 - # 110 - - Ser Asp Leu Gly Asp Thr Val Leu Glu Cys - #Tyr Asn Cys Gly Arg Lys 115 - # 120 - # 125 - - Asn Val Phe Leu Leu Gly Phe Val Ser Ala - #Lys Ser Glu Ala Val Val 130 - # 135 - # 140 - - Val Leu Leu Cys Arg Ile Pro Cys Ala Gln - #Thr Lys Asn Ala Asn Trp 145 - #150 - #155 -#160 - - Asp Thr Asp Gln Trp Gln Pro Leu Ile Glu - #Asp Arg Gln Leu LeuSer 165 - # 170 - # 175 - - Trp Val Ala Glu Gln Pro Thr Glu Glu Glu - #Lys Leu Lys Ala Arg Leu 180 - # 185 - # 190 - - Ile Thr Pro Ser Gln Ile Ser Lys Leu Glu - #Ala Lys Trp Arg Ser Asn 195 - # 200 - # 205 - - Lys Asp Ala Thr Ile Asn Asp Ile Asp Ala - #Pro Glu Glu Gln Glu Ala 210 - # 215 - # 220 - - Ile Pro Pro Leu Leu Leu Arg Tyr Gln Asp - #Ala Tyr Glu Tyr Gln Arg 225 - #230 - #235 -#240 - - Ser Tyr Gly Pro Leu Ile Lys Leu Glu Ala - #Asp Tyr Asp Lys GlnLeu 245 - # 250 - # 255 - - Lys Glu Ser Gln Ala Leu Glu His Ile Ser - #Val Ser Trp Ser Leu Ala 260 - # 265 - # 270 - - Leu Asn Asn Arg His Leu Ala Ser Phe Thr - #Leu Ser Thr Phe Glu Ser 275 - # 280 - # 285 - - Asn Glu Leu Lys Val Ala Ile Gly Asp Glu - #Met Ile Leu Trp Tyr Ser 290 - # 295 - # 300 - - Gly Met Gln His Pro Asp Trp Glu Gly Arg - #Gly Tyr Ile Val Arg Leu 305 - #310 - #315 -#320 - - Pro Asn Ser Phe Gln Asp Thr Phe Thr Leu - #Glu Leu Lys Pro SerLys 325 - # 330 - # 335 - - Thr Pro Pro Pro Thr His Leu Thr Thr Gly - #Phe Thr Ala Glu Phe Ile 340 - # 345 - # 350 - - Trp Lys Gly Thr Ser Tyr Asp Arg Met Gln - #Asp Ala Leu Lys Lys Phe 355 - # 360 - # 365 - - Ala Ile Asp Lys Lys Ser Ile Ser Gly Tyr - #Leu Tyr Tyr Lys Ile Leu 370 - # 375 - # 380 - - Gly His Gln Val Val Asp Ile Ser Phe Asp - #Val Pro Leu Pro Lys Glu 385 - #390 - #395 -#400 - - Phe Ser Ile Pro Asn Phe Ala Gln Leu Asn - #Ser Ser Gln Ser AsnAla 405 - # 410 - # 415 - - Val Ser His Val Leu Gln Arg Pro Leu Ser - #Leu Ile Gln Gly Pro Pro 420 - # 425 - # 430 - - Gly Thr Gly Lys Thr Val Thr Ser Ala Thr - #Ile Val Tyr His Leu Ser 435 - # 440 - # 445 - - Lys Ile His Lys Asp Arg Ile Leu Val Cys - #Ala Pro Ser Asn Val Ala 450 - # 455 - # 460 - - Val Asp His Leu Ala Ala Lys Leu Arg Asp - #Leu Gly Leu Lys Val Val 465 - #470 - #475 -#480 - - Arg Leu Thr Ala Lys Ser Arg Glu Asp Val - #Glu Ser Ser Val SerAsn 485 - # 490 - # 495 - - Leu Ala Leu His Asn Leu Val Gly Arg Gly - #Ala Lys Gly Glu Leu Lys 500 - # 505 - # 510 - - Asn Leu Leu Lys Leu Lys Asp Glu Val Gly - #Glu Leu Ser Ala Ser Asp 515 - # 520 - # 525 - - Thr Lys Arg Phe Val Lys Leu Val Arg Lys - #Thr Glu Ala Glu Ile Leu 530 - # 535 - # 540 - - Asn Lys Ala Asp Val Val Cys Cys Thr Cys - #Val Gly Ala Gly Asp Lys 545 - #550 - #555 -#560 - - Arg Leu Asp Thr Lys Phe Arg Thr Val Leu - #Ile Asp Glu Ser ThrGln 565 - # 570 - # 575 - - Ala Ser Glu Pro Glu Cys Leu Ile Pro Ile - #Val Lys Gly Ala Lys Gln 580 - # 585 - # 590 - - Val Ile Leu Val Gly Asp His Gln Gln Leu - #Gly Pro Val Ile Leu Glu 595 - # 600 - # 605 - - Arg Lys Ala Ala Asp Ala Gly Leu Lys Gln - #Ser Leu Phe Glu Arg Leu 610 - # 615 - # 620 - - Ile Ser Leu Gly His Val Pro Ile Arg Leu - #Glu Val Gln Tyr Arg Met 625 - #630 - #635 -#640 - - Asn Pro Tyr Leu Ser Glu Phe Pro Ser Asn - #Met Phe Tyr Glu GlySer 645 - # 650 - # 655 - - Leu Gln Asn Gly Val Thr Ile Glu Gln Arg - #Thr Val Pro Asn Ser Lys 660 - # 665 - # 670 - - Phe Pro Trp Pro Ile Arg Gly Ile Pro Met - #Met Phe Trp Ala Asn Tyr 675 - # 680 - # 685 - - Gly Arg Glu Glu Ile Ser Ala Asn Gly Thr - #Ser Phe Leu Asn Arg Ile 690 - # 695 - # 700 - - Glu Ala Met Asn Cys Glu Arg Ile Ile Thr - #Lys Leu Phe Arg Asp Gly 705 - #710 - #715 -#720 - - Val Lys Pro Glu Gln Ile Gly Val Ile Thr - #Pro Tyr Glu Gly GlnArg 725 - # 730 - # 735 - - Ala Tyr Ile Leu Gln Tyr Met Gln Met Asn - #Gly Ser Leu Asp Lys Asp 740 - # 745 - # 750 - - Leu Tyr Ile Lys Val Glu Val Ala Ser Val - #Asp Ala Phe Gln Gly Arg 755 - # 760 - # 765 - - Glu Lys Asp Tyr Ile Ile Leu Ser Cys Val - #Arg Ala Asn Glu Gln Gln 770 - # 775 - # 780 - - Ala Ile Gly Phe Leu Arg Asp Pro Arg Arg - #Leu Asn Val Gly Leu Thr 785 - #790 - #795 -#800 - - Arg Ala Lys Tyr Gly Leu Val Ile Leu Gly - #Asn Pro Arg Ser LeuAla 805 - # 810 - # 815 - - Arg Asn Thr Leu Trp Asn His Leu Leu Ile - #His Phe Arg Glu Lys Gly 820 - # 825 - # 830 - - Cys Leu Val Glu Gly Thr Leu Asp Asn Leu - #Gln Leu Cys Thr Val Gln 835 - # 840 - # 845 - - Leu Val Arg Pro Gln Pro Arg Lys Thr Glu - #Arg Pro Met Asn Ala Gln 850 - # 855 - # 860 - - Phe Asn Val Glu Ser Glu Met Gly Asp Phe - #Pro Lys Phe Gln Asp Phe 865 - #870 - #875 -#880 - - Asp Ala Gln Ser Met Val Ser Phe Ser Gly - #Gln Ile Gly Asp PheGly 885 - # 890 - # 895 - - Asn Ala Phe Val Asp Asn Thr Glu Leu Ser - #Ser Tyr Ile Asn Asn Glu 900 - # 905 - # 910 - - Tyr Trp Asn Phe Glu Asn Phe Lys Ser Ala - #Phe Ser Gln Lys Gln Asn 915 - # 920 - # 925 - - Arg Asn Glu Ile Asp Asp Arg Asn Leu Tyr - #Gln Glu Glu Ala Ser His 930 - # 935 - # 940 - - Leu Asn Ser Asn Phe Ala Arg Glu Leu Gln - #Arg Glu Glu Gln Lys His 945 - #950 - #955 -#960 - - Glu Leu Ser Lys Asp Phe Ser Asn Leu Gly - #Ile 965 - # 970 - - - - (2) INFORMATION FOR SEQ ID NO:23: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 6 amino - #acids (B) TYPE: amino acid (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: peptide - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:23: - - Pro Gly Thr Gly Lys Thr 1 - #5 - - - - (2) INFORMATION FOR SEQ ID NO:24: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 5 amino - #acids (B) TYPE: amino acid (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: peptide - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:24: - - Cys Ala Pro Ser Asn 1 - #5 - - - - (2) INFORMATION FOR SEQ ID NO:25: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 8 amino - #acids (B) TYPE: amino acid (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: peptide - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:25: - - Gly Xaa Xaa Xaa Xaa Gly Lys Thr 1 - #5 - - - - (2) INFORMATION FOR SEQ ID NO:26: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 215 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: genomic RNA - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:26: - - GAUACUUACC UGGCAGGGGA GAUACCAUGA UCACGAAGGU GGUUUUCCCA - #GGGCGAGGCU 60 - - UAUCCAUUGC ACUCCGGAUG UGCUGACCCC UGCGAUUUCC CCAAAUGUGG - #GAAACUCGAC 120 - - UGCAGAAUUG UUGUAGCACU CCAGCUGAUG AGUCCGUGAG GACGAAACUG - #UCUCCCCCAG 180 - - GGGCUAGUGG GGGACUGCGU UCGCGCUUUC CCCUG - # -# 215 - - - - (2) INFORMATION FOR SEQ ID NO:27: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 10 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: genomic RNA - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:27: - - UAAUUUGUGG - # - #- # 10 - - - - (2) INFORMATION FOR SEQ ID NO:28: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 7 amino - #acids (B) TYPE: amino acid (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: peptide - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:28: - - Leu Glu Cys Tyr Asn Cys Lys 1 - #5 - - - - (2) INFORMATION FOR SEQ ID NO:29: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 7 amino - #acids (B) TYPE: amino acid (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: peptide - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:29: - - Leu Glu Asn Asp Tyr Asp Lys 1 - #5__________________________________________________________________________

Mammalian regulator of nonsense-mediated RNA decay

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Non-Patent Literature Citations (9)

Entry
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Perlick, et al., American Society of Human Genetic Meeting, San Francisco, Nov. 1, 1996.
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Leeds, et al., Gene products that promote mRNA turnover in saccharomyces, Molec. Cell. Biol., vol. 12, No. 5, pp. 2165-2177, May, 1992.
Czaplinski, et al., Purification and characterization of the Upf1 protein: A factor involved in translation and mRNA degradation, RNA, Oct. 1995, vol. 1, pp. 610-633.
He et al., Identification of a novel component of the nonsense-mediated mRNA decay pathway by use of an interacting protein screen, Genes and Development, Feb. 1995, vol. 9, pp. 437-454.
Adams et al. (1995) Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequences. Nature 377 (suppl.) 3-17, Sep. 1995.
Khan et al. (1992) Single pass sequencing and physical and genetic mapping of human brain cDNAs. Nature Genetics 2:180-185, Nov. 1992.