Megabase transcript map: novel sequences and antibodies thereto

BACKGROUND OF THE INVENTION
Hemochromatosis is an autosomal disorder of iron metabolism wherein the body accumulates excess iron. The hemochromatosis (HH) gene was originally shown to be linked to the MHC on chromosome 6p21 (Simon et al. Gut 17:332-334 (1976)). The HH gene was recently cloned by Feder et al. (Nature Genetics 13:399-408 (1996)).
Fine structure mapping of the region to which the HH gene was mapped makes possible the identification of candidate sequences comprising the HH genes, along with structural elements for regulation and expression and neighboring genes.
A variety of techniques is available for fine structure mapping, including direct cDNA selection, exon-trapping, and genomic sample sequencing. The direct selection approach (Lovett et al. Proc. Natl. Acad. Sci. U.S.A. 88:9628-9623 (1991)) involves the hybridization of cDNA fragments to genomic DNA. This technique is extremely sensitive and capable of isolating portions of rare transcripts. Exon-trapping (Church et al. Nature Genetics 6:98-105 (1994)) recovers spliced introns from in vivo expressed genomic DNA clones and produces candidate exons without requiring any prior knowledge of the target's gene expression. High-through-put genomic DNA sequencing with comparison of the sequence data to databases of expressed sequences has also been used, such as in the positional cloning of the Werner syndrome gene (Yu et al. Science 277:258-262 (1996)) and in cloning by homology of the second Alzheimer's disease gene on chromosome 1 (Levy-Lahad et al. Science 269:973-977 (1995)).
Thus, a need exists for both methods for fine structure mapping and a fine structure map of the region of the chromosome to which the HH locus maps. This and other needs are addressed by the present invention.
SUMMARY OF THE INVENTION
One aspect of the invention is an isolated nucleic acid sequence comprising a nucleic acid sequence substantially identical to BTF1.
A further aspect of the invention is an isolated nucleic acid sequence comprising a nucleic acid sequence substantially identical to BTF2.
A further aspect of the invention is an isolated nucleic acid sequence comprising a nucleic acid sequence substantially identical to BTF3.
A further aspect of the invention is an isolated nucleic acid sequence comprising a nucleic acid sequence substantially identical to BTF4.
A further aspect of the invention is an isolated nucleic acid sequence comprising a nucleic acid sequence substantially identical to BTF5.
A further aspect of the invention is an isolated nucleic acid sequence comprising a nucleic acid sequence substantially identical to NPT3.
A further aspect of the invention is an isolated nucleic acid sequence comprising a nucleic acid sequence substantially identical to NPT4.
A further aspect of the invention is an isolated nucleic acid sequence comprising a nucleic acid sequence substantially identical to RoRet.
Additional aspects of the invention include nucleic acid sequences that are cDNAs, polypeptides encoded by the nucleic acids of the invention and antibodies specifically immunoreactive thereto, vectors comprising the nucleic acid sequences of the invention, and host cells stably transfected with the nucleic acids of the invention.
A further aspect of the invention is a 250 KB sequence of the HH subregion shown in FIG. 8.
A further aspect of the invention is an isolated nucleic acid sequence comprising at least 18 contiguous nucleotides substantially identical to at least 18 contiguous nucleotides of BTF1.
A further aspect of the invention is an isolated nucleic acid sequence comprising at least 18 contiguous nucleotides substantially identical to at least 18 contiguous nucleotides of BTF2.
A further aspect of the invention is an isolated nucleic acid sequence comprising at least 18 contiguous nucleotides substantially identical to at least 18 contiguous nucleotides of BTF3.
A further aspect of the invention is an isolated nucleic acid sequence comprising at least 18 contiguous nucleotides substantially identical to at least 18 contiguous nucleotides of BTF4.
A further aspect of the invention is an isolated nucleic acid sequence comprising at least 18 contiguous nucleotides substantially identical to at least 18 contiguous nucleotides of BTF5.
A further aspect of the invention is an isolated nucleic acid sequence comprising at least 18 contiguous nucleotides substantially identical to at least 18 contiguous nucleotides of NPT3.
A further aspect of the invention is an isolated nucleic acid sequence comprising at least 18 contiguous nucleotides substantially identical to at least 18 contiguous nucleotides of NPT4.
A further aspect of the invention is an isolated nucleic acid sequence comprising at least 18 contiguous nucleotides substantially identical to at least 18 contiguous nucleotides of RoRet.
Additional aspects of the invention include isolated nucleic acids of about 18 to 100 nucleotides substantially identical to about 18 to 100 contiguous nucleotides of the nucleic acids of the invention, and the use of these isolated nucleic acids as PCR probes.
BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 depicts a combination genetic, physical and transcription map of the HH candidate gene region. The first line shows the relative positions of selected genetic markers that define the HH region. The heavy bar below represents the YAC clone used in the direct selection experiment. The order and positions of the bacterial clones employed in the exon-trapping and sample sequencing is indicated under the YAC. The thin bar under the bacterial clones represents the approximate locations of a subset of the expressed sequence fragments mapped to the contig. The thicker bars show the location of the cDNAs cloned. Two regions are bracketed; the butyrophilin family of genes (BTF), and the region where complete genomic sequencing was carried out.
FIG. 2 is a schematic of the 250 kb of genomic sequence including the HH candidate gene, HLA-H. Both the structure of the overall cDNA (top) and that corresponding to the coding regions (bottom), as well as the direction of transcription are shown. The positions of the histone genes, the zinc a-2 glycoprotein pseudogene, and the ESTs are also shown.
FIG. 3 (SEQ ID NOS:1-6) depicts an alignment of the predicted amino acid sequence of the BTF proteins. Sequences were aligned in a pair-wise fashion using CLUSTAL W (Thompson et al. Nucl. Acids Res. 22:4673-4680) to deduce the most parsimonious arrangement. The asterisks under the alignment represent amino acids conserved in all 6 proteins; the "dots" represent conserved amino acids substitutions. Boxed are the regions within the proteins which correspond to three conserved motifs: 1) the B-G domain, 2) the transmembrane domain (TM), and 3) the B30-2 exon domain.
FIG. 4, panel (A) depicts a Northern blot analysis of representative members of the two groups of BTF proteins, BTF1 and BTF5. BTF1 hybridized to all tissues on the blot as a major transcript at 2.9 kb and a minor one at 5.0 kb. BTF5 hybridized to several transcripts ranging between 4.0 and 3.1 kb and as a similar expression profile to BTF1. Autoradiography was for 24 hours. The b-actin hybridization demonstrated the variation in ploy (A)+ RNA between the lanes. Autoradiography was for 1 hour. In panel (B), RT-PCR analysis demonstrated that the expression of both genes was widespread. Included in the (+) lane are cDNA 21 and 44 as positive controls; the (-) lane represents the no-DNA control. Amplification using primers for the RFP gene (Isomura et al. Nucleic Acid Res. 20:5305-5310 (1992)) controlled for the integrity of the cDNA. All first strand cDNAs were checked for contaminating genomic DNA amplification by carrying out an identical experiment excluding the reverse transcriptase. In all cases, no amplification was obtained (data not shown).
FIG. 5(A) (SEQ ID NOS:7-8) depicts an alignment of the predicted amino acid sequence of the RoRet gene to the 52 kD Ro/SSA auto-antigen protein. The asterisks under the alignment represent conserved amino acids; the "dots" represent conserved amino acids substitutions. The putative DNA binding cysteine-rich domain and the B30-2 exon domain are boxed. FIG. 5(B) (SEQ ID NOS:9-10) depicts an alignment of the predicted amino acid sequence of the two novel putative sodium phosphate transport proteins to that of the NPT1.
FIG. 6, panel (A) depicts a Northern blot analysis of the RoRet gene. The RoRet cDNA hybridized to 4 different transcripts, ranging from 7.1 kb to 2.2 kb. Autoradiography was performed for 4 days. The re-hybridization of the blot with a b-actin probe showed the variation in poly (A)+ RNA between the lanes. Autoradiography was for 1 hour. Panel (B) depicts RT-PCR analysis of the RoRet gene. Included in the (+) lane was a cDNA 27 positive control. Weak amplification of the correct size was observed in the small intestine, kidney and liver. The other tissues were negative as was the no DNA control lane (-). The RFP primers demonstrated the integrity of the cDNA. Panel (C) depicts Northern blot analysis of NPT3 and NPT4. NPT3 was expressed at high abundance in the heart and muscle as a single 7.2 kb transcript. Lesser amounts were found in the other tissues. The expression pattern of NPT4 was more restricted, being found only in the liver and kidney as a smear of transcripts ranging from 2.6 to 1.7 kb. Panel (D) depicts RT-PCR analysis of the NPT3 and NPT4 genes. Included in the (+) lane were the respective cDNA22E and 22B positive controls. The NPT3 gene was expressed as the proper size PCR fragment in kidney, liver, spleen and testis. A smaller fragment was detected in all tissues with the exception of the liver. The no DNA control lane (-) was negative. NPT4 was expressed as the proper size fragment in the small intestine, kidney, liver and testis. Larger and smaller size fragments were found in all other tissues with the exception of the brain. For both genes these different size fragments may indicate alternative splice events. The no DNA control lane (-) was negative. The RFP primers demonstrated the integrity of the cDNA.
FIG. 7 depicts the sequences of cDNA 21 (BTF1) (SEQ ID NO:12), cDNA 29 (BTF3) (SEQ ID NO:13), cDNA 23 (BTF4) (SEQ ID NO:14), cDNA 44 (BTF5) (SEQ ID NO:15), cDNA 32 (BTF2) (SEQ ID NO:16), cDNA 27 (RoRet) (SEQ ID NO:17), cDNA 22B (NPT3) (SEQ ID NO:18), cDNA22E (NPT4) (SEQ ID NO:19).
FIG. 8 (SEQ ID NOS:20-22) depicts the nucleotide sequence of approximately 250 KB in the HH subregion.
DETAILED DESCRIPTION OF THE SPECIFIC EMBODIMENT
A. Definitions
Abbreviations for the twenty naturally occurring amino acids follow conventional usage. In the polypeptide notation used herein, the left-hand direction is the amino terminal direction and the right-hand direction is the carboxyl-terminal direction, in accordance with standard usage and convention. Similarly, unless specified otherwise, the left hand end of single-stranded polynucleotide sequences is the 5' end; the left hand direction of double-stranded polynucleotide sequences is referred to as the 5' direction. The direction of 5' to 3' addition of nascent RNA transcripts is referred to as the transcription direction; sequence regions on the DNA strand having the same sequence as the RNA and which are 5' to the 5' end of the RNA transcript are referred to as "upstream sequences"; sequence regions on the DNA strand having the same sequence as the RNA and which are 3' to the 3' end of the RNA transcript are referred to as "downstream sequences".
The term "nucleic acids", as used herein, refers to either DNA or RNA. "Nucleic acid sequence" or "polynucleotide sequence" refers to a single- or double-stranded polymer of deoxyribonucleotide or ribonucleotide bases read from the 5' to the 3' end. It includes both self-replicating plasmids, infectious polymers of DNA or RNA and nonfunctional DNA or RNA.
"Nucleic acid probes" may be DNA or RNA fragments. DNA fragments can be prepared, for example, by digesting plasmid DNA, or by use of PCR, or synthesized by either the phosphoramidite method described by Beaucage and Carruthers, Tetrahedron Lett. 22:1859-1862 (1981), or by the triester method according to Matteucci, et al., J. Am. Chem. Soc. 103:3185 (1981), both incorporated herein by reference. A double stranded fragment may then be obtained, if desired, by annealing the chemically synthesized single strands together under appropriate conditions or by synthesizing the complementary strand using DNA polymerase with an appropriate primer sequence. Where a specific sequence for a nucleic acid probe is given, it is understood that the complementary strand is also identified and included. The complementary strand will work equally well in situations where the target is a double-stranded nucleic acid.
The phrase "selectively hybridizing to" refers to a nucleic acid probe that hybridizes, duplexes or binds only to a particular target DNA or RNA sequence when the target sequences are present in a preparation of total cellular DNA or RNA. "Complementary" or "target" nucleic acid sequences refer to those nucleic acid sequences which selectively hybridize to a nucleic acid probe. Proper annealing conditions depend, for example, upon a probe's length, base composition, and the number of mismatches and their position on the probe, and must often be determined empirically. For discussions of nucleic acid probe design and annealing conditions, see, for example, Sambrook et al., Molecular Cloning: A Laboratory Manual (2nd ed.), Vols. 1-3, Cold Spring Harbor Laboratory, (1989) or Current Protocols in Molecular Biology, F. Ausubel et al., ed. Greene Publishing and Wiley-Interscience, New York (1987).
The phrase "nucleic acid sequence encoding" refers to a nucleic acid which directs the expression of a specific protein or peptide. The nucleic acid sequences include both the DNA strand sequence that is transcribed into RNA and the RNA sequence that is translated into protein. The nucleic acid sequences include both the full length nucleic acid sequences as well as non-full length sequences derived from the full length protein. It being further understood that the sequence includes the degenerate codons of the native sequence or sequences which may be introduced to provide codon preference in a specific host cell.
The phrase "isolated" or "substantially pure" refers to nucleic acid preparations that lack at least one protein or nucleic acid normally associated with the nucleic acid in a host cell.
The phrase "expression cassette", refers to nucleotide sequences which are capable of affecting expression of a structural gene in hosts compatible with such sequences. Such cassettes include at least promoters and optionally, transcription termination signals. Additional factors necessary or helpful in effecting expression may also be used as described herein.
The term "operably linked" as used herein refers to linkage of a promoter upstream from a DNA sequence such that the promoter mediates transcription of the DNA sequence.
The term "vector", refers to viral expression systems, autonomous self-replicating circular DNA (plasmids), and includes both expression and nonexpression plasmids. Where a recombinant microorganism or cell culture is described as hosting an "expression vector," this includes both extrachromosomal circular DNA and DNA that has been incorporated into the host chromosome(s). Where a vector is being maintained by a host cell, the vector may either be stably replicated by the cells during mitosis as an autonomous structure, or is incorporated within the host's genome.
The term "gene" as used herein is intended to refer to a nucleic acid sequence which encodes a polypeptide. This definition includes various sequence polymorphisms, mutations, and/or sequence variants wherein such alterations do not affect the function of the gene product. The term "gene" is intended to include not only coding sequences but also regulatory regions such as promoters, enhancers, and termination regions. The term further includes all introns and other DNA sequences spliced from the mRNA transcript, along with variants resulting from alternative splice sites.
The term "plasmid" refers to an autonomous circular DNA molecule capable of replication in a cell, and includes both the expression and nonexpression types. Where a recombinant microorganism or cell culture is described as hosting an "expression plasmid", this includes both extrachromosomal circular DNA molecules and DNA that has been incorporated into the host chromosome(s). Where a plasmid is being maintained by a host cell, the plasmid is either being stably replicated by the cells during mitosis as an autonomous structure or is incorporated within the host's genome.
The phrase "recombinant protein" or "recombinantly produced protein" refers to a peptide or protein produced using non-native cells that do not have an endogenous copy of DNA able to express the protein. The cells produce the protein because they have been genetically altered by the introduction of the appropriate nucleic acid sequence. The recombinant protein will not be found in association with proteins and other subcellular components normally associated with the cells producing the protein. The terms "protein" and "polypeptide" are used interchangeably herein.
The following terms are used to describe the sequence relationships between two or more nucleic acids or polynucleotides: "reference sequence", "comparison window", "sequence identity", "percentage of sequence identity", and "substantial identity". A "reference sequence" is a defined sequence used as a basis for a sequence comparison; a reference sequence may be a subset of a larger sequence, for example, as a segment of a full-length cDNA or gene sequence given in a sequence listing, or may comprise a complete cDNA or gene sequence.
Optimal alignment of sequences for aligning a comparison window may, for example, be conducted by the local homology algorithm of Smith and Waterman Adv. Appl. Math. 2:482 (1981), by the homology alignment algorithm of Needleman and Wunsch J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson and Lipman Proc. Natl. Acad. Sci. U.S.A. 85:2444 (1988), or by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package Release 7.0, Genetics Computer Group, 575 Science Dr., Madison, Wis.).
The terms "substantial identity" or "substantial sequence identity" as applied to nucleic acid sequences and as used herein and denote a characteristic of a polynucleotide sequence, wherein the polynucleotide comprises a sequence that has at least 85 percent sequence identity, preferably at least 90 to 95 percent sequence identity, and more preferably at least 99 percent sequence identity as compared to a reference sequence over a comparison window of at least 20 nucleotide positions, frequently over a window of at least 25-50 nucleotides, wherein the percentage of sequence identity is calculated by comparing the reference sequence to the polynucleotide sequence which may include deletions or additions which total 20 percent or less of the reference sequence over the window of comparison. The reference sequence may be a subset of a larger sequence.
As applied to polypeptides, the terms "substantial identity" or "substantial sequence identity" mean that two peptide sequences, when optimally aligned, such as by the programs GAP or BESTFIT using default gap weights, share at least 80 percent sequence identity, preferably at least 90 percent sequence identity, more preferably at least 95 percent sequence identity or more. "Percentage amino acid identity" or "percentage amino acid sequence identity" refers to a comparison of the amino acids of two polypeptides which, when optimally aligned, have approximately the designated percentage of the same amino acids. For example, "95% amino acid identity" refers to a comparison of the amino acids of two polypeptides which when optimally aligned have 95% amino acid identity. Preferably, residue positions which are not identical differ by conservative amino acid substitutions. For example, the substitution of amino acids having similar chemical properties such as charge or polarity are not likely to effect the properties of a protein. Examples include glutamine for asparagine or glutamic acid for aspartic acid.
The phrase "substantially purified" or "isolated" when referring to a peptide or protein, means a chemical composition which is essentially free of other cellular components. It is preferably in a homogeneous state although it can be in either a dry or aqueous solution. Purity and homogeneity are typically determined using analytical chemistry techniques such as polyacrylamide gel electrophoresis or high performance liquid chromatography. A protein which is the predominant species present in a preparation is substantially purified. Generally, a substantially purified or isolated protein will comprise more than 80% of all macromolecular species present in the preparation. Preferably, the protein is purified to represent greater than 90% of all macromolecular species present. More preferably the protein is purified to greater than 95%, and most preferably the protein is purified to essential homogeneity, wherein other macromolecular species are not detected by conventional techniques.
The phrase "specifically binds to an antibody" or "specifically immunoreactive with", when referring to a protein or peptide, refers to a binding reaction which is determinative of the presence of the protein in the presence of a heterogeneous population of proteins and other biologies. Thus, under designated immunoassay conditions, the specified antibodies bind to a particular protein and do not bind in a significant amount to other proteins present in the sample. Specific binding to an antibody under such conditions may require an antibody that is selected for its specificity for a particular protein. A variety of immunoassay formats may be used to select antibodies specifically immunoreactive with a particular protein. For example, solid-phase ELISA immunoassays are routinely used to select monoclonal antibodies specifically immunoreactive with a protein. See Harlow and Lane (1988) Antibodies, A Laboratory Manual, Cold Spring Harbor Publications, New York, for a description of immunoassay formats and conditions that can be used to determine specific immunoreactivity.
As used herein, "EST" or "Expressed Sequence Tag" is meant a partial DNA or cDNA sequence of about 150 to 500, more preferably about 300, sequential nucleotides of a longer sequence obtained from a genomic or cDNA library prepared from a selected cell, cell type, tissue or tissue type, or organisms which longer sequence corresponds to an mRNA or a gene found in that library. An EST is generally DNA. One or more libraries made from a single tissue type typically provide at least 3000 different (i.e. unique) EST's and potentially the full complement of all possible EST's representing all possible cDNAs, e.g., 50,000-100,000 in an animal such as a human. (See, for example, Adams et al. Science 252:1651-1656 (1991)).
B. Nucleic Acid Markers and the Proteins Encoded Thereby
The instant invention provides a fine structure map of the 1 megabase region surrounding the candidate HH gene. As part of that map the instant invention provides 250 KB of DNA sequence (FIG. 8) and eight loci of particular interest corresponding to candidate genes within the 1 megabase region. These loci are useful as genetic and physical markers for further mapping studies. Additionally, the eight cDNA sequences corresponding to those loci are useful, for example, for the isolation of other genes in putative gene families, the identification of homologs from other species, and as probes for diagnostic assays. In particular, isolated nucleic acid sequences of at least 18 nucleotides substantially identical to contiguous nucleotides of a cDNA of the invention are useful as PCR primers. Typically, the PCR primer will be used as part of a pair of primers in a PCR reaction. Isolated nucleic acid sequences preferably comprising about 18-100 nucleotides, more preferably at least 18 nucleotides, substantially identical to contiguous nucleotides in a cDNA of the invention are useful in the design of PCR primers and probes for hybridization assays. Additionally, the proteins encoded by those cDNAs are useful in the generation of antibodies for analysis of gene expression and in diagnostic assays, and in the purification of related proteins.
Thus, in one embodiment of the invention, a 250 KB sequence is provided for the HH subregion within the 1 megabase region mapped. This sequence can serve as a reference in genetic or physical analysis of deletions, substitutions, and insertions in that region. Additionally, the sequence information provides a resource for the further identification of new genes in that region. Thus, nucleic acid sequences substantially identically to the 250 KB sequence are also included in the scope of this invention.
In a further embodiment of the invention, a family of five genes, BTF1-5, is provided which are related by sequence homology to the milk protein butyrophilin (BT) (FIGS. 1, 3, and 7). The predicted amino acid sequences of the proteins encoded by these genes are provided in FIG. 3. These cDNAs are useful for the identification of further members of the BT family and to study regulation of expression of this family of genes. The proteins encoded by these cDNAs can be useful in the identification and isolation of ligands for the BT protein, and in the generation of agonists or antagonists of BT function. Nucleic acid sequences substantially identically to BTF1-5 and the proteins encoded by them are also included in the scope of this invention, including allelic forms.
In a further embodiment of the invention, a novel gene RoRet is provide, which is related by sequence homology to the 52 KD Ro/SSA Lupus and Sjogren's syndrome autoantigen. This sequence is especially useful in the identification of other genes that may be involved in Lupus or Sjorgen's syndrome. The protein encoded by this cDNA can be useful in the identification and isolation of ligands for the autoantigen, and in the generation of agonists or antagonists of the antigen. Nucleic acid sequences substantially identically to RoRet and the proteins encoded by them are also included in the scope of this invention.
In a further embodiment of the invention, two genes, NPT3 and NPT4, with structural homology to a type 1 sodium transport gene are provided. These cDNAs and the proteins expressed by them are useful in determining the etiology of hypophosphatemia, along with being useful as probes in the identification and isolation of further members of the gene family. Nucleic acid sequences substantially identically to the NPT1-like sequences and the proteins encoded by them are also included in the scope of this invention.
C. General Methods
The nucleic acid compositions of this invention, whether RNA, cDNA, genomic DNA, or a hybrid of the various combinations, may be isolated from natural sources, including cloned DNA, or may be synthesized in vitro. The nucleic acids claimed may be present in transformed or transfected whole cells, in a transformed or transfected cell lysate, or in a partially purified or substantially pure form.
The nucleic acid sequences of the invention are typically identical to or show substantial sequence identity (determined as described above) to the nucleic acid sequences of FIGS. 7 and 8. Included in this definition are nucleic acids which hybridize to the nucleic acid sequences of FIGS. 7 and 8 under stringent conditions. "Stringent" as used herein refers to hybridization and wash conditions of 50% formamide at 42.degree. C. Other stringent hybridization conditions may also be selected. Generally, stringent conditions are selected to be about 5.degree. C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. The Tm is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. Typically, stringent conditions will be those in which the salt concentration is at least about 0.02 molar at pH 7 and the temperature is at least about 60.degree. C. As other factors may significantly affect the stringency of hybridization, including, among others, base composition and size of the complementary strands, the presence of organic solvents and the extent of base mismatching, the combination of parameters is more important than the absolute measure of any one.
Techniques for nucleic acid manipulation of the nucleic acid sequences of the invention such as subcloning nucleic acid sequences encoding polypeptides into expression vectors, labelling probes, DNA hybridization, and the like are described generally in Sambrook et al., Molecular Cloning--A Laboratory Manual (2nd Ed.), Vol. 1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., (1989), which is incorporated herein by reference. This manual is hereinafter referred to as "Sambrook et al."
There are various methods of isolating the nucleic acid sequences of the invention. For example, DNA is isolated from a genomic or cDNA library using labelled oligonucleotide probes having sequences complementary to the sequences disclosed herein. Such probes can be used directly in hybridization assays. Alternatively probes can be designed for use in amplification techniques such as PCR.
To prepare a cDNA library, mRNA is isolated from tissue such as heart or pancreas, preferably a tissue wherein expression of the gene or gene family is likely to occur. cDNA is prepared from the mRNA and ligated into a recombinant vector. The vector is transfected into a recombinant host for propagation, screening and cloning. Methods for making and screening cDNA libraries are well known. See Gubler, U. and Hoffman, B. J. Gene 25:263-269 (1983) and Sambrook et al.
For a genomic library, the DNA is extracted from tissue and either mechanically sheared or enzymatically digested to yield fragments of about 12-20 kb. The fragments are then separated by gradient centrifugation from undesired sizes and are constructed in bacteriophage lambda vectors. These vectors and phage are packaged in vitro, as described in Sambrook, et al. Recombinant phage are analyzed by plaque hybridization as described in Benton and Davis, Science 196:180-182 (1977). Colony hybridization is carried out as generally described in M. Grunstein et al. Proc. Natl. Acad. Sci. USA. 72:3961-3965 (1975).
DNA of interest is identified in either cDNA or genomic libraries by its ability to hybridize with nucleic acid probes, for example on Southern blots, and these DNA regions are isolated by standard methods familiar to those of skill in the art. See Sambrook, et al.
Various methods of amplifying target sequences, such as the polymerase chain reaction, can also be used to prepare DNA encoding ATP-sensitive potassium channel protein. Polymerase chain reaction (PCR) technology is used to amplify such nucleic acid sequences directly from mRNA, from cDNA, and from genomic libraries or cDNA libraries. The isolated sequences encoding ATP-sensitive potassium channel protein may also be used as templates for PCR amplification.
In PCR techniques, oligonucleotide primers complementary to the two 3' borders of the DNA region to be amplified are synthesized. The polymerase chain reaction is then carried out using the two primers. See PCR Protocols: A Guide to Methods and Applications (Innis, M, Gelfand, D., Sninsky, J. and White, T., eds.), Academic Press, San Diego (1990). Primers can be selected to amplify the entire regions encoding a full-length sequence of interest or to amplify smaller DNA segments as desired.
PCR can be used in a variety of protocols to isolate cDNA's encoding a sequence of interest. In these protocols, appropriate primers and probes for amplifying DNA encoding a sequence of interest are generated from analysis of the DNA sequences listed herein. Once such regions are PCR-amplified, they can be sequenced and oligonucleotide probes can be prepared from sequence obtained.
Oligonucleotides for use as probes are chemically synthesized according to the solid phase phosphoramidite triester method first described by Beaucage, S. L. and Carruthers, M. H., Tetrahedron Lett., 22(20):1859-1862 (1981) using an automated synthesizer, as described in Needham-VanDevanter, D. R., et al., Nucleic Acids Res. 12:6159-6168 (1984). Purification of oligonucleotides is by either native acrylamide gel electrophoresis or by anion-exchange HPLC as described in Pearson, J. D. and Regnier, F. E., J. Chrom., 255:137-149 (1983). The sequence of the synthetic oligonucleotide can be verified using the chemical degradation method of Maxam, A. M. and Gilbert, W., in Grossman, L. and Moldave, D., eds. Academic Press, New York, Methods in Enzymology 65:499-560 (1980).
C. Expression
Once DNA encoding a sequence of interest is isolated and cloned, one can express the encoded proteins in a variety of recombinantly engineered cells. It is expected that those of skill in the art are knowledgeable in the numerous expression systems available for expression of DNA encoding A. No attempt to describe in detail the various methods known for the expression of proteins in prokaryotes or eukaryotes is made here.
In brief summary, the expression of natural or synthetic nucleic acids encoding a sequence of interest will typically be achieved by operably linking the DNA or cDNA to a promoter (which is either constitutive or inducible), followed by incorporation into an expression vector. The vectors can be suitable for replication and integration in either prokaryotes or eukaryotes. Typical expression vectors contain transcription and translation terminators, initiation sequences, and promoters useful for regulation of the expression of polynucleotide sequence of interest. To obtain high level expression of a cloned gene, it is desirable to construct expression plasmids which contain, at the minimum, a strong promoter to direct transcription, a ribosome binding site for translational initiation, and a transcription/translation terminator. The expression vectors may also comprise generic expression cassettes containing at least one independent terminator sequence, sequences permitting replication of the plasmid in both eukaryotes and prokaryotes, i.e., shuttle vectors, and selection markers for both prokaryotic and eukaryotic systems. See Sambrook et al. Examples of expression of ATP-sensitive potassium channel proteins in both prokaryotic and eukaryotic systems are described below.
1. Expression in Prokaryotes
A variety of procaryotic expression systems may be used to express the proteins of the invention. Examples include E. coli, Bacillus, Streptomyces, and the like.
It is preferred to construct expression plasmids which contain, at the minimum, a strong promoter to direct transcription, a ribosome binding site for translational initiation, and a transcription/translation terminator. Examples of regulatory regions suitable for this purpose in E. coli are the promoter and operator region of the E. coli tryptophan biosynthetic pathway as described by Yanofsky, C., J. Bacteriol. 158:1018-1024 (1984) and the leftward promoter of phage lambda (P.lambda.) as described by Herskowitz, I. and Hagen, D., Ann. Rev. Genet. 14:399-445 (1980). The inclusion of selection markers in DNA vectors transformed in E. coli is also useful. Examples of such markers include genes specifying resistance to ampicillin, tetracycline, or chloramphenicol. See Sambrook et al. for details concerning selection markers for use in E. coli.
To enhance proper folding of the expressed recombinant protein, during purification from E. coli, the expressed protein may first be denatured and then renatured. This can be accomplished by solubilizing the bacterially produced proteins in a chaotropic agent such as guanidine HCl and reducing all the cysteine residues with a reducing agent such as beta-mercaptoethanol. The protein is then renatured, either by slow dialysis or by gel filtration. See U.S. Pat. No. 4,511,503.
Detection of the expressed antigen is achieved by methods known in the art as radioimmunoassay, or Western blotting techniques or immunoprecipitation. Purification from E. coli can be achieved following procedures such as those described in U.S. Pat. No. 4,511,503.
2. Expression in Eukaryotes
A variety of eukaryotic expression systems such as yeast, insect cell lines, bird, fish, and mammalian cells, are known to those of skill in the art. As explained briefly below, a sequence of interest may be expressed in these eukaryotic systems.
Synthesis of heterologous proteins in yeast is well known. Methods in Yeast Genetics, Sherman, F., et al., Cold Spring Harbor Laboratory, (1982) is a well recognized work describing the various methods available to produce the protein in yeast.
Suitable vectors usually have expression control sequences, such as promoters, including 3-phosphoglycerate kinase or other glycolytic enzymes, and an origin of replication, termination sequences and the like as desired. For instance, suitable vectors are described in the literature (Botstein, et al., Gene 8:17-24 (1979); Broach, et al., Gene 8:121-133 (1979)).
Two procedures are used in transforming yeast cells. In one case, yeast cells are first converted into protoplasts using zymolyase, lyticase or glusulase, followed by addition of DNA and polyethylene glycol (PEG). The PEG-treated protoplasts are then regenerated in a 3% agar medium under selective conditions. Details of this procedure are given in the papers by J. D. Beggs, Nature (London) 275:104-109 (1978); and Hinnen, A., et al., Proc. Natl. Acad. Sci. U.S.A. 75:1929-1933 (1978). The second procedure does not involve removal of the cell wall. Instead the cells are treated with lithium chloride or acetate and PEG and put on selective plates (Ito, H., et al., J. Bact. 153:163-168 (1983)).
The proteins of the invention, once expressed, can be isolated from yeast by lysing the cells and applying standard protein isolation techniques to the lysates. The monitoring of the purification process can be accomplished by using Western blot techniques or radioimmunoassay of other standard immunoassay techniques.
The sequences encoding the proteins of the invention can also be ligated to various expression vectors for use in transforming cell cultures of, for instance, mammalian, insect, bird or fish origin. Illustrative of cell cultures useful for the production of the polypeptides are mammalian cells. Mammalian cell systems often will be in the form of monolayers of cells although mammalian cell suspensions may also be used. A number of suitable host cell lines capable of expressing intact proteins have been developed in the art, and include the HEK293, BHK21, and CHO cell lines, and various human cells such as COS cell lines, HeLa cells, myeloma cell lines, Jurkat cells, etc. Expression vectors for these cells can include expression control sequences, such as an origin of replication, a promoter (e.g., the CMV promoter, a HSV tk promoter or pgk (phosphoglycerate kinase) promoter), an enhancer (Queen et al. Immunol. Rev. 89:49 (1986)), and necessary processing information sites, such as ribosome binding sites, RNA splice sites, polyadenylation sites (e.g., an SV40 large T Ag poly A addition site), and transcriptional terminator sequences. Other animal cells useful for production of ATP-sensitive potassium channel proteins are available, for instance, from the American Type Culture Collection Catalogue of Cell Lines and Hybridomas (7th edition, (1992)).
Appropriate vectors for expressing the proteins of the invention in insect cells are usually derived from the SF9 baculovirus. Suitable insect cell lines include mosquito larvae, silkworm, armyworm, moth and Drosophila cell lines such as a Schneider cell line (See Schneider J. Embryol. Exp. Morphol. 27:353-365 (1987).
As indicated above, the vector, e.g., a plasmid, which is used to transform the host cell, preferably contains DNA sequences to initiate transcription and sequences to control the translation of the protein. These sequences are referred to as expression control sequences.
As with yeast, when higher animal host cells are employed, polyadenlyation or transcription terminator sequences from known mammalian genes need to be incorporated into the vector. An example of a terminator sequence is the polyadenlyation sequence from the bovine growth hormone gene. Sequences for accurate splicing of the transcript may also be included. An example of a splicing sequence is the VP1 intron from SV40 (Sprague, J. et al., J. Virol. 45: 773-781 (1983)).
Additionally, gene sequences to control replication in the host cell may be incorporated into the vector such as those found in bovine papilloma virus type-vectors. Saveria-Campo, M., 1985, "Bovine Papilloma virus DNA a Eukaryotic Cloning Vector" in DNA Cloning Vol. II a Practical Approach Ed. D. M. Glover, IRL Press, Arlington, Va. pp. 213-238.
The host cells are competent or rendered competent for transformation by various means. There are several well-known methods of introducing DNA into animal cells. These include: calcium phosphate precipitation, fusion of the recipient cells with bacterial protoplasts containing the DNA, treatment of the recipient cells with liposomes containing the DNA, DEAE dextran, electroporation and micro-injection of the DNA directly into the cells.
The transformed cells are cultured by means well known in the art. Biochemical Methods in Cell Culture and Virology, Kuchler, R. J., Dowden, Hutchinson and Ross, Inc., (1977). The expressed polypeptides are isolated from cells grown as suspensions or as monolayers. The latter are recovered by well known mechanical, chemical or enzymatic means.
D. Purification
The proteins produced by recombinant DNA technology may be purified by standard techniques well known to those of skill in the art. Recombinantly produced proteins can be directly expressed or expressed as a fusion protein. The protein is then purified by a combination of cell lysis (e.g., sonication) and affinity chromatography. For fusion products, subsequent digestion of the fusion protein with an appropriate proteolytic enzyme releases the desired polypeptide.
The polypeptides of this invention may be purified to substantial purity by standard techniques well known in the art, including selective precipitation with such substances as ammonium sulfate, column chromatography, immunopurification methods, and others. See, for instance, R. Scopes, Protein Purification: Principles and Practice, Springer-Verlag: New York (1982), incorporated herein by reference. For example, antibodies may be raised to the proteins of the invention as described herein. Cell membranes are isolated from a cell line expressing the recombinant protein, the protein is extracted from the membranes and immunoprecipitated. The proteins may then be further purified by standard protein chemistry techniques as described above.
E. In Vitro Diagnostic Methods
The present invention provides methods for detecting DNA or RNA encoding the proteins of the invention and for measuring the proteins by immunoassay techniques. These methods are useful for two general purposes. First, assays for detection of nucleic acids encoding the proteins of the invention are useful for the isolation of these nucleic acids from a variety of vertebrate species according to the methods described in section (B) above and by use of the nucleic acid hybridization assays described below.
The nucleic acid hybridization assays and the immunoassays described below are also useful as in vitro diagnostic assays for disorders in which alterations in the proteins of the invention or related proteins play a role.
1. Nucleic Acid Hybridization Assays
A variety of methods for specific DNA and RNA measurement using nucleic acid hybridization techniques are known to those of skill in the art. See Sambrook, et al. For example, one method for evaluating the presence or absence of the nucleic acids of the invention in a sample involves a Southern transfer. Briefly, the digested genomic DNA is run on agarose slab gels in buffer and transferred to membranes. Hybridization is carried out using the nucleic acid probes discussed above. As described above, nucleic acid probes are designed based on the nucleic acid sequences of the invention. The probes can be full length or less than the full length of the nucleic acid sequence encoding the potassium channel protein. Shorter probes are empirically tested for specificity. Preferably nucleic acid probes are 20 bases or longer in length. (See Sambrook, et al. for methods of selecting nucleic acid probe sequences for use in nucleic acid hybridization.) Visualization of the hybridized portions allows the qualitative determination of the presence or absence of DNA encoding ATP-sensitive potassium channel proteins.
Similarly, a Northern transfer may be used for the detection of mRNA encoding the proteins of the invention. In brief, the mRNA is isolated from a given cell sample using an acid guanidinium-phenol-chloroform extraction method. The mRNA is then electrophoresed to separate the mRNA species and the mRNA is transferred from the gel to a nitrocellulose membrane. As with the Southern blots, labeled probes are used to identify the presence or absence of the proteins of the invention
A variety of nucleic acid hybridization formats are known to those skilled in the art. For example, common formats include sandwich assays and competition or displacement assays. Hybridization techniques are generally described in Nucleic Acid Hybridization, A Practical Approach Ed. Hames, B. D. and Higgins, S. J., IRL Press (1985); Gall and Pardue Proc. Natl. Acad. Sci. U.S.A. 63:378-383 (1969); and John, Burnsteil and Jones Nature 223:582-587 (1969).
For example, sandwich assays are commercially useful hybridization assays for detecting or isolating nucleic acid sequences. Such assays utilize a "capture" nucleic acid covalently immobilized to a solid support and a labelled "signal" nucleic acid in solution. The clinical sample will provide the target nucleic acid. The "capture" nucleic acid and "signal" nucleic acid probe hybridize with the target nucleic acid to form a "sandwich" hybridization complex. To be effective, the signal nucleic acid cannot hybridize with the capture nucleic acid.
Typically, labelled signal nucleic acids are used to detect hybridization. Complementary nucleic acids or signal nucleic acids may be labelled by any one of several methods typically used to detect the presence of hybridized polynucleotides. The most common method of detection is the use of autoradiography with .sup.3 H, .sup.125 I, .sup.35 S, .sup.14 C, or .sup.32 p-labelled probes or the like. Other labels include ligands which bind to labelled antibodies, fluorophores, chemiluminescent agents, enzymes, and antibodies which can serve as specific binding pair members for a labelled ligand.
Detection of a hybridization complex may require the binding of a signal generating complex to a duplex of target and probe polynucleotides or nucleic acids. Typically, such binding occurs through ligand and anti-ligand interactions as between a ligand-conjugated probe and an anti-ligand conjugated with a signal.
The label may also allow indirect detection of the hybridization complex. For example, where the label is a hapten or antigen, the sample can be detected by using antibodies. In these systems, a signal is generated by attaching fluorescent or enzyme molecules to the antibodies or, in some cases, by attachment to a radioactive label. (Tijssen, P., "Practice and Theory of Enzyme Immunoassays," Laboratory Techniques in Biochemistry and Molecular Biology Burdon, R. H., van Knippenberg, P. H., Eds., Elsevier (1985), pp. 9-20.)
The sensitivity of the hybridization assays may be enhanced through use of a nucleic acid amplification system which multiplies the target nucleic acid being detected. Examples of such systems include the polymerase chain reaction (PCR) system and the ligase chain reaction (LCR) system. Other methods recently described in the art are the nucleic acid sequence based amplification (NASBA.TM., Cangene, Mississauga, Ontario) and Q Beta Replicase systems.
An alternative means for determining the level of expression of a gene encoding the proteins of the invention is in situ hybridization. In situ hybridization assays are well known and are generally described in Angerer et al. Methods Enzymol. 152:649-660 (1987). In an in situ hybridization assay, cells are fixed to a solid support, typically a glass slide. If DNA is to be probed, the cells are denatured with heat or alkali. The cells are then contacted with a hybridization solution at a moderate temperature to permit annealing of labeled probes specific to the proteins of the invention. The probes are preferably labelled with radioisotopes or fluorescent reporters.
2. Production of Antibodies and Development of Immunoassays
Immunoassays can be used to qualitatively or quantitatively analyze for the proteins of the invention. A general overview of the applicable technology can be found in Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Pubs., N.Y. (1988), incorporated herein by reference.
a. Antibody Production
A number of immunogens may be used to produce antibodies specifically reactive with the proteins of the invention. Recombinant protein is the preferred immunogen for the production of monoclonal or polyclonal antibodies. Naturally occurring protein may also be used either in pure or impure form. Synthetic peptides made using the protein sequences described herein may also used as an immunogen for the production of antibodies to the protein. Recombinant protein can be expressed in eukaryotic or prokaryotic cells as described above, and purified as generally described above. The product is then injected into an animal capable of producing antibodies. Either monoclonal or polyclonal antibodies may be generated, for subsequent use in immunoassays to measure the protein.
Methods of production of polyclonal antibodies are known to those of skill in the art. In brief, an immunogen, preferably a purified protein, is mixed with an adjuvant and animals are immunized. The animal's immune response to the immunogen preparation is monitored by taking test bleeds and determining the titer of reactivity to the ATP-sensitive potassium channel protein. When appropriately high titers of antibody to the immunogen are obtained, blood is collected from the animal and antisera are prepared. Further fractionation of the antisera to enrich for antibodies reactive to the protein can be done if desired. (See Harlow and Lane, supra).
Monoclonal antibodies may be obtained by various techniques familiar to those skilled in the art. Briefly, spleen cells from an animal immunized with a desired antigen are immortalized, commonly by fusion with a myeloma cell (See, Kohler and Milstein, Eur. J. Immunol. 6:511-519 (1976), incorporated herein by reference). Alternative methods of immortalization include transformation with Epstein Barr Virus, oncogenes, or retroviruses, or other methods well known in the art. Colonies arising from single immortalized cells are screened for production of antibodies of the desired specificity and affinity for the antigen, and yield of the monoclonal antibodies produced by such cells may be enhanced by various techniques, including injection into the peritoneal cavity of a vertebrate host. Alternatively, one may isolate DNA sequences which encode a monoclonal antibody or a binding fragment thereof by screening a DNA library from human B cells according to the general protocol outlined by Huse, et al. Science 246:1275-1281 (1989).
Methods of production of synthetic peptides are known to those of skill in the art. Peptides preferably at least 10 amino acids in length are synthesized corresponding to these regions and the peptides are conjugated to larger protein molecules for subsequent immunization. Preferably, peptide sequences corresponding to regions of interest of a recombinant protein of the invention is used to generate antibodies specifically immunoreactive with the protein. Production of monoclonal or polyclonal antibodies is then carried out as described above.
b. Immunoassays
A particular protein can be measured by a variety of immunoassay methods. For a review of immunological and immunoassay procedures in general, see Basic and Clinical Immunology 7th Edition (D. Stites and A. Terr ed.) (1991). Moreover, immunoassays can be performed in any of several configurations, which are reviewed extensively in Enzyme Immunoassay, E. T. Maggio, ed., CRC Press, Boca Raton, Fla. (1980); "Practice and Theory of Enzyme Immunoassays," P. Tijssen, Laboratory Techniques in Biochemistry and Molecular Biology, Elsevier Science Publishers B. V. Amsterdam (1985); and, Harlow and Lane, Antibodies, A Laboratory Manual, supra, each of which is incorporated herein by reference.
Immunoassays for measurement of the proteins of the invention can be performed by a variety of methods known to those skilled in the art. In brief, immunoassays to measure the protein can be either competitive or noncompetitive binding assays. In competitive binding assays, the sample analyte competes with a labeled analyte for specific binding sites on a capture agent bound to a solid surface. Preferably the capture agent is an antibody specifically reactive with a recombinant protein of the invention produced as described above. The concentration of labeled analyte bound to the capture agent is inversely proportional to the amount of free analyte present in the sample.
Western blot analysis can also be done to determine the presence of a protein of the invention in a sample. Electrophoresis is carried out, for example, on a tissue sample suspected of containing the protein. Following electrophoresis to separate the proteins, and transfer of the proteins to a suitable solid support such as a nitrocellulose filter, the solid support is then incubated with an antibody reactive with the protein. This antibody may be labelled, or alternatively may be it may be detected by subsequent incubation with a second labelled antibody that binds the primary antibody.
The immunoassay formats described above employ labelled assay components. The label can be in a variety of forms. The label may be coupled directly or indirectly to the desired component of the assay according to methods well known in the art. A wide variety of labels may be used. The component may be labelled by any one of several methods. Traditionally a radioactive label incorporating .sup.3 H, .sup.125 I, .sup.35 S, .sup.14 C, or .sup.32 P was used. Non-radioactive labels include ligands which bind to labelled antibodies, fluorophores, chemiluminescent agents, enzymes, and antibodies which can serve as specific binding pair members for a labelled ligand. The choice of label depends on sensitivity required, ease of conjugation with the compound, stability requirements, and available instrumentation. For a review of various labelling or signal producing systems which may be used, see U.S. Pat. No. 4,391,904, which is incorporated herein by reference.
Antibodies reactive with a particular protein can also be measured by a variety of immunoassay methods. For a review of immunological and immunoassay procedures applicable to the measurement of antibodies by immunoassay techniques, see Basic and Clinical Immunology 7th Edition (D. Stites and A. Terr ed.) supra, Enzyme Immunoassay, E. T. Maggio, ed., supra, and Harlow and Lane, Antibodies, A Laboratory Manual, supra.
This invention also embraces kits for detecting the presence of a protein of the invention in tissue or blood samples which comprise a container containing antibodies selectively immunoreactive to the protein and instructional material for performing the test. The kit may also contain other components such as a protein of the invention, controls, buffer solutions, and secondary antibodies. Kits for detecting antibodies to a protein of the invention comprise a container containing an a protein of the invention, instructional material and may comprise other materials such as secondary antibodies and labels as described herein.
This invention further embraces diagnostic kits for detecting DNA or RNA encoding proteins of interest in tissue or blood samples which comprise nucleic probes as described herein and instructional material. The kit may also contain additional components such as labeled compounds, as described herein, for identification of duplexed nucleic acids.
The following examples are provided to illustrate the invention but not to limit its scope. Other variants of the invention will be readily apparent to one of ordinary skill in the art and are encompassed by the appended claims.

EXAMPLE
In these studies direct selection, exon-trapping, and genomic sample sequencing were used to generate a transcript map of a 1 megabase region approximately 8.5 megabases telomeric to HLA-A in the vicinity of HH, the candidate hematochromatosis gene. This region 6p21.3 was flanked by the genetic markers D6S2242 and D6S2241. The starting material for these experiments was a 1 megabase YAC labeled y899g1 and a bacterial clone contig of this region (Feder et al. Nature Genetics 13:399-408 (1996)). These techniques and other methods used in the study are outlined below.
Direct Selection (DS)
Poly A.sup.+ RNA from human fetal brain, liver and small intestine (Clontech, Palo Alto, Calif.) were converted into cDNA using random primers and a Superscript cDNA synthesis kit (Life Technologies, Gaithersburg, Md.). The cDNA was digested with Mbo I and ligated to cDNA Mbo I linker-adaptors. Unligated linker-adaptor were removed by passage through cDNA spun columns (Pharmacia, Piscataway, N.J.). The 5 ng of each of the ligated cDNAs were amplified using the cDNA Mbo I-S primer (SEQ ID NO:23) (5'-CCTGATGCTCGAGTGAATTC-3'). The amplified products were purified on S-400 spin columns (Pharmacia, Piscataway, N.J.), ethanol precipitated and resuspended at 1 mg/ml in TE. Gel-purified yac899g1 (Centre d'Etude du Polymorphisme Humain) was processed as described by Morgan et al. (Nucl. Acids Res. 20:5173-5179 (1992)). The cDNAs were mixed in equal molar amounts for a total of 3 mg, and blocked with a mixture of 4 mg Cot-1 DNA (Life Technologies, Gaithersburg, Md.), and a cocktail of Sau 3A-digested ribosomal and five different histone DNAs. The blocked cDNAs were hybridized to biotinylated yac899g1 DNA and streptavidin capture was carried out as described by Morgan et al. (ibid). After the second round of selection, the eluted cDNAs were amplified using the cDNA Mbo I-S primer which included a (CUA)4 repeat at the 5' end to facilitate cloning into a version of pSP72 (Promega, Madison, Wis.) constructed for use with uracil-DNA glycolyase cloning (UDG, Life Technologies, Gaithersburg, Md.). Recombinants were transformed in DH5a, 1000 clones picked into a 96 well format, and clones prepped for DNA sequencing using AGTC boiling 96-well mini-prep system (Advance Genetic Technologies, Gaitherburg, Md.).
Four hundred and sixty five clones were sequenced and the resulting data searched by BLAST (Altschul et al. J. Mol. Biol. 215:403-410 (1990)). Those clones representing repetitive, bacterial, yeast, mitochondrial and histone sequences were eliminated from future considerations. The remaining sequences were then searched for overlaps and assembled into 108 unique DS contigs. The number of clones per DS contig varied between 1 to 22 with the length of each contig ranging from 250bp to 850 bp. Small sequence-tag-sites PCR assays were developed for each DS contig and two experiments were carried out concomitantly; mapping each DS contig back to the bacterial clone contig of the region and testing for the presence of each DS contig in cDNA libraries. Overall, 86 or 80% of the DS contigs mapped back to the region and were found to be in cDNA libraries. The number of 80% mapping to the region was probably an underestimate of the fidelity of the direct-selection since PCR assays which cross exon-intron boundaries would be expected to fail or give larger size products, thereby being scored negative.
Exon-Trapping
CsCl-purified genomic P1 (Genome Systems), BAC (Research Genetics) and PAC (Genome Systems) DNAs were digested with BamHI, Bgl II, Pst I Sac 1 and Xho I and 125 ng of each digest ligated into 500 ng pSPL3 (Church et al. Nature Genetics 6:98-105 (1994)) (Life Technologies, Gaithersburg, Md.) digested with the appropriate restriction enzyme and phosphatased with calf intestinal alkaline phosphatase (USB, Cleveland, Ohio). One tenth of the ligation was used to transform XL1-Blue MRF' cells (Stratagene, La Jolla, Calif.) by electroporation. Nine tenths of the electroporation was used to inoculate 10 ml of LB+100 mg/ml of carbenicillen and after overnight growth, DNA was prepared using Qiagen Q-20 tips (Qiagen GmbH, Hilden Germany). The remaining one tenth was plated on LB+100 mg/ml carbenicillen plates to evaluated the efficiency on cloning and to test individual clones for the present of single inserts. COS-7 cells were seed overnight at a density of 1.4.times.10.sup.5 /well in 6 well dishes. One mg of DNA was transfected using 6 ml of Lipofect-Ace. Cytoplasmic RNA was isolated 48 hr post-transfection. RT-PCR was carried out as described by Church et al. (ibid) using commercially available reagents Life Technologies, Gaithersburg, Md.). The resulting CUA-tailed PCR fragments for each restriction digested bacterial clone were pooled and UDG cloned into pSP72-U (a derivative of pSP72). The DNA was transformed in DH5a and the cells plated onto nylon membranes. After overnight growth, duplicates were made and the DNA hybridized to .sup.32 p end-labeled oligos designed to detect various background products associated with the pSPL3 vector. One set of filters was hybridized with the following gel-purified oligos in 6.times.SSC aqueous hybridization solution at 42.degree. C.:
______________________________________vector-vector 5'-CGACCCAGCAACCTGGAGAT-3' (SEQ ID NO:24)splicingcryptic 5'-AGCTCGAGCGGCCGCTGCAG-3' (SEQ ID NO:25)donor-1021cryptic 5'-AGACCCCAACCCACAAGAAG-3' (SEQ ID NO:26)donor-1134______________________________________
The filters were washed twice in 6.times.SSC, 10 mM sodium pyrophosphate (NaPPi) at 60.degree. C., 30 mins.
After overnight autoradiography, non-hybridizing clones were picked and grown in 250 ml of LB+100 mg/ml of carbenicillin in 96 well mini-rack tubes. The samples were analyzed by PCR using the secondary PCR primers supplied in the kit (Life Technologies, Gaithersburg, Md.) and those clones with inserts greater than 200 bp were selected for sequencing.
Ninety-six exon traps per bacterial clone were sequenced for a total of 768 reactions and the resulting data analyzed by BLAST. In addition, each potential exon was searched against a database of the 86 DS contigs to eliminate redundant sequences. PCR assays were developed for each of the potential exons and they were tested for their presence in cDNA libraries. A total of 48 potential exons remained after these screening steps.
Sample Sequencing
A minimal set of bacterial clones chosen to cover y899g1 were prepped with the Qiagen Maxi-Prep system and purified on CsCl. Ten micrograms of DNA from each bacterial clone was sonicated in a Heat Systems Sonicator XL and end-repaired with Klenow (USB) and T4 polymerase (USB). The sheared fragments were size selected between three to four kilobases on a 0.7% agarose gel and then ligated to BstXI linkers (Invitrogen). The ligations were gel purified on a 0.7% agarose gel and cloned into a pSP72 derivative plasmid vector. The resulting plasmids were transformed into electrocompetent DH5a cells and plated on LB-carbenicillin plates. A sufficient number of colonies was picked to achieve 15-fold clone coverage. The appropriate number of colonies was calculated by the following equation to generate a single-fold sequence coverage: Number of colonies=size of bacterial clone (in kb)/average sequence read length (0.4 kb). These colonies were prepped in the 96-well AGCT system and end-sequenced with oligo MAP1 using standard ABI Dye Terminator protocols. MAP1 was CGTTAGAACGCGGCTACAAT (SEQ ID NO:27). The MAP1 sequences were screened locally with the BLAST algorithm against all available public databases. All sequence identities were catalogued and cross referenced to the DS and exon-trapped databases.
A total of 3794 end sequence reactions were run to achieve the theoretical 1.times. coverage. Eighty-five percent of these sequences contained non-bacterial non-vector inserts. An additional 1060 end sequence reactions were run from the opposite end of the cloning vector to augment the sequence coverage and to prepare for contigging across selected regions. BLAST searches to all publicly available databases identified 12 histone genes and 74 unique expressed sequence fragments (ESF). The ESF represent a collection of ESTs and other expressed sequence fragments that were selected due to their sequence identity over a significant portion of genomic DNA. The ESF were cross referenced against the DS and exon-trapped databases to eliminate redundancies. 58 unique ESF remained, representing 39 distinct clones (Table 1).
TABLE 1__________________________________________________________________________EST's found by Sample Sequencing large bacterial clones.Clone Bacterial Homology Homology Poly A+ Genomic cDNAname clone 5' blastx 3' blastx signal.sup.1 poly (A).sub..quadrature.8 Homology__________________________________________________________________________EST03556 pc157c3 na.sup.2 none.sup.3 + - cDNA 28ym33fl1 pc157c3 ZNF na na naEST04698 pc157c3 na NSH.sup.4 + -EST04812 pc157c3 na NSH - -yb89b08 pc157c3 NSH na na nayd88g11 pc157c3 na NSH + -yj49b01 pc157c3 NSH na na nayv81d05 pc157c3 HGI7 Human NSH + - cDNA 30Yg57h09 p196e20 BUTYBOVIN NSH + - cDNA 21yq23d08 p196e20 BUTYBOVIN NSH + - cDNA 21yo65f06 p196e20 NSH na na na cDNA 29yv88c09 p196e20 BUTYBOVIN na na na cDNA 29yd17d06 p196e20 NSH na na na cDNA 23ye25g03 p196e20 BUTYBOVIN NSH na na cDNA 44ys04h08 pc45p21 NSH NSH + - cDNA 44yn01c05 p196e20 BUTYBOVIN na na na cDNA 32yg78f10 pc45p21 NSH NSH na nayh54f11 p196e20 none NSH - -ys05b08 pc157c3 NSH Alu - +yb12h11 b132a12 NSH Histone H3.1 - -HSC2EE082 b132a12 na NSH + -HUM160H11B b132a12 none na na nayg04f09 b132a12 Line element Alu - + ##STR1##ym29g03 b132a12 Histone H2A NSH + - cDNA 37yi77b02 b132a12 NSH NSH - - cDNA 37yh76b05 b132a12 NSH Alu - -yu98e02 b132a12 NSH Alu - +yd72h12 b132a12 Alu NSH + +yf19d03 pc222k22 Histone H2B.1 NSH + -ye98g01 b132a12 NSH NSH + - cDNA 24yi61f07 b132a12 NSH NSH - +EST05340 b3e17 na Alu - +yd35d05 pc222k22 NSH NSH - +yc52a05 pc75L14 NSH na na nayd84a05 pc75L14 none none - ?.sup.5 ##STR2##yd83h08 b20h20 NSH none - +ye38c09 b20h20 NSH Alu - +yp74c05 b20h20 NaPi transport Alu ?.sup.6 na__________________________________________________________________________ racketed area is the critical region .sup.1 Signal of ATAAA or ATTAA .sup.2 not available .sup.3 "NONE" reported by blast .sup.4 No Sigificant Homologies .sup.5 3' splice that is not on contig .sup.6 Poor EST sequence
Included in these ESF are 5 sequences homologous to histone genes.
cDNA library screening
Superscript plasmid cDNA libraries, brain, liver and testis, were purchased by Life Technologies, Gaithersburg, Md. Colonies were plated on Hybond N filters (Amersham) using standard techniques. Insert probes from DS, exons and EST (I.M.A.G.E. clones; Genome Systems) were all isolated by PCR followed by purification in low-melting point agarose gels (Seakmen). The DNAs were labeled in gel using the Prime-it II kit (Stratagene, La Jolla, Calif.). Small exon probes were labeled using their respective STS PCR primers instead of random primers. Up to 5 different probes were pooled in a hybridization. Filters were hybridized in duplicate using standard techniques. Putative positives were screened by PCR using the probe's STSs to identify clones. Inserts from positive clones were subcloned in pSP72 and sequenced.
Northern blots and RT-PCR analysis
Multiple tissue northern blots were purchased from Clontech and hybridized according the manufacturer's instructions. RT-PCR was carried out on random primed first strand cDNA made from poly A+ RNA (Clontech) using AmpliTaq Gold (Perkin-Elmer). Control reactions were performed on RNA samples processed in the absence of reverse transcriptase to control for genomic DNA contamination.
Genomic Sequencing
The MAP1 sequences from the bacterial clones b132a2, 222K22, and 75L14 were assembled into contigs with the Staden package (available from Roger Staden, MRC). A minimal set of 3 kb clones was selected for sequencing with oligo labeled MAP2 that sits on the opposite end of the plasmid vector. The sequence of MAP2 was GCCGATTCATTAATGCAGGT (SEQ ID NO:28). The MAP2 sequences were entered into the Staden database in conjunction with the MAP1 sequences to generate a tiling path of 3 kb clones across the region. These sequences were also screened with the BLAST algorithm and all novel sequence identities were noted. The plasmid 3 kb libraries were concurrently transformed in 96 well format into pox38UR (available from C. Martin, Lawrence Berkeley Laboratories). The transformants were subsequently mated with JGM (Strathman et al. P.N.A.S. 88:1247-1250 (1991) in 96 well format. All matings of the 3 kb clones within the tiling path were streaked on LB-carbenicillin-kanamycin plates and a random selection of 12 colonies per 3 kb clone was prepped in the AGCT system. The oligos -21: CTGTAAAACGACGGCCAGTC (SEQ ID NO:29), and REV: GCAGGAAACAGCTATGACC (SEQ ID NO:30) were used to sequence off both ends of the transposon. Each 3 kb clone was assembled in conjunction with the end sequence information from all bacterial clones to generate complete sequence across the region. The genomic sequence was analyzed with the BLAST nucleotide and protein homology algorithms and the GRAIL 1.2 software to identify novel open reading frames (ORF) for gene finding.
Discussion
A compilation of 174 ESF led to the construction of an expressed sequence map of the region that served as the framework for the isolation of full-length cDNAs (FIG. 1). (The map shows the subset of ESF that were actually mapped). Probes were developed for 82 best ESFs which appeared to be derived from the coding portions of cDNAs and the appropriate cDNA libraries were screened. This led to the isolation of 19 cDNAs, 17 of which represented novel sequences. 70 of the 174 ESF were included in the cDNAs isolated (40%). 36 probes failed to produce any clones even after repeated screening of several libraries. 51 ESF which were not accounted for in the cDNAs cloned were not used in any screen. Therefore, it is possible that some additional genes within this 1 megabase region may have escaped detection.
A list of these cDNAs cloned and a comparison of the methods used to find them is presented in Table 2. Direct selection found 14 out of the 18 cDNAs contained within the boundaries of the YAC used in the experiment. Exon trapping found 15 out of the 19 cDNAs contained within the boundaries of the large insert bacterial clone contig. Sample sequencing identified 11 genes that had corresponding ESTs in the public database.
TABLE 2______________________________________Comparison of gene finding methodsBacterial clone CDNA# homology EST DS Exon trap______________________________________157c3 28 zinc finger EST03556 2 1157c3 30 nonhistone yv81d05 1 none yvh07a10157c3 46 ORF yd88g11 1157c3 20 BT none none 3P18696 21 BTF1 yn01g05 4 5 yg23d08 yg57h09 yu15h0345p21 32 BTF2 yg78f10 7 3 yn01c0545p21 29 BTF3 ye25g03 2 9 yo65f0645p21 23 BTF4 yd17d06 4 645p21 44 BTF5 ys04h08 2 43e17 41 genomic? none none 1132a2 43 genomic? none none 3132a2 36 genomic? none 1 none132a2 37 histone 2A ym29g03 3 none yh87a0375114 24 MHC class 1 ye98g01 1 2132a2 39 genomic? none none 4132a2 27 Ro/SSA none 3 4132a2 22B NPT1-like yr42a05 1 7 yf09g0620h20 22E NPT1-like none 2 520h20 NPT1 NPT1 yp74c05 N/A 3______________________________________
As a final approach, a tiling path with overlapping end sequences from the sample sequence database was generated. Each 3 kb clone within the path was shotgunned-sequenced using transposable elements as platforms for dual end sequencing. These individual clones were assembled in conjunction with the end sequences from all bacterial clones in the region. The resulting sequence (FIG. 2) was analyzed systematically with BLAST homology searches and the Grail 1.2 program to identify novel open reading frames (ORF) and other gene-like structures. The BLAST homology searches did not produce any probes that had not already been identified by sample sequencing. Grail predicted exons for all the genes in the region, but was only able assemble the histones into any representative form. A detailed analysis of BLAST homology searches to protein databases identified an enticing homology to a zinc alpha 2 glycoprotein approximately 25 kb upstream of HLA-H, but the lack of a substantial ORF and the presence of a stop codon suggested that it was a pseudogene. FIG. 2 shows the positions, the exon and intron structures, and the relative orientation of transcription of novel genes within this region. Also shown are the positions and transcriptional orientations of the histone genes. A total of 12 histone genes were identified in this study.
In an effort to account for the ESTs that did not associate with the characterized genes in the 250 kb region, the genomic sequence around the putative 3' ends were examined for polyadenylation signals to determine whether certain EST sequences may have originated from genomic DNA contamination in the normalized cDNA libraries used in EST generation. The positions of the 14 ESTs found in this region are indicated in FIG. 2 to show those associated with the cDNAs cloned and those which did not associate with genomic DNA of obvious coding potential. Four ESTs corresponded to 3 of the 4 cDNAs cloned from the region (Table 1). One EST encoded a histone H2B.1 gene and another was a repetitive element. Of the remaining 8, 6 EST clones were used as probes of cDNA libraries with negative results. Those sequences representing putative 3' ends of cDNA were searched for the presence of poly (A)+ addition signals. Five of the 13 ESTs which had 3' end sequence, had the sequence ATAAA or ATTAA. Five of the remaining 8 ESTs that did not have a poly (A)+ addition signal had genomic encoded stretches of poly (A) near the end of EST sequence and, therefore, may have been created by oligo d(T) priming of contaminating genomic DNA. This analysis was expanded to include all ESTs in the large-insert bacterial contigs with definitive 3' ends. Of the remaining 26, 15 had 3' end sequence and of these 8 had poly (A)+ addition signals. Five of these 8 ESTs were associated with the cloned cDNAs. Of the remaining 7 which did not have poly (A)+ addition signals, 4 had genomic encoded stretches of poly (A).
Butyrophilin gene family
The human homolog of the bovine butyrophilin gene (BT) was cloned and mapped to approximately 480 kb centromeric to HLA-H (FIG. 1). ET is a transmembrane protein of unknown function which constitutes 40% of the total protein associated with the fat globule of bovine milk (Jack et al. J. Biol. Chem. 265:14481-14486 (1990)). A human homolog of BT has recently been cloned by Tayloer et al. (Biocem Biophys Acta 1306:1-4 (1996)). The results in this study indicated that BT is a member of a gene family with at least five other members of the family residing in this region (FIG. 1). A comparison of these proteins is shown in FIG. 3. The proteins were aligned based on their descending order of relatedness and to minimized gaps in the sequence. Each of the five proteins display varying degrees of homology to ET. BTF1 (cDNA 21), BTF2 (cDNA 32), BTF5 (cDNA 44), and BTF3 (cDNA 29) are 45%, 48%, 46%, and 49%, identical to BT, whereas BTF4 (cDNA 32), which is more similar to BTF3 (cDNA 29), is only 26% identical. This low degree of identity to BT is largely due to a truncation at the carboxyl terminus of the protein. The BTF family falls into two groups: BTF1 and 2 which are more related to each other than to BT or the other BTF members, and BTF5, 3 and 4, which appear to have a common evolutionary origin. The order of these genes on the chromosome suggests that the BT gene has duplicated two times, giving rise to BTF1 and BTF5. Subsequently, it appears likely these two genes experienced further duplication events to give rise to the other members in their groups.
The three major components of BT, the B-G immunoglobulin superfamily domain (containing the V consensus sequence) (Miller et al. Proc. Natl. Acad. Sci. U.S.A. 88:4377-4381 (1991)), the transmembrane region, and the B30-2 exon are found in all of these proteins (with the exception of BTF4 (cDNA 29) which lacks the B30-2 exon by virtue of the carboxyl terminal truncation). The exon B30-2 is a previously noted feature of the MHC class 1 region found approximately 200 kb centromeric to the HLA-A gene (Vernet et al., (1993)). In addition this exon is found in several genes of diverse function telomeric to HLA-A namely MOG (approximately 200 kb) and RFP (approximately 1 megabase) (Amadou et al. Genomics 26:9-20 (1995)).
The levels of the BTF mRNA were analyzed by northern blot analysis (FIG. 4A). The expression of the BTF genes fell into two patterns. BTF1 and BTF2 were expressed as a single major transcript of 2.9 kb and one minor transcript of 5.0 kb. These genes were expressed at high levels in all the tissues tested with the exception of the kidney where the expression level was less. The two genes are 900 identical at the DNA sequence level, therefore, it is possible that the signal observed on the northerns was the result of cross-hybridization and only one of the two genes was actually expressed. To address this possibility RT-PCR experiments were carried out on a panel of different tissues in order to detect possible tissue dependent expression that would suggest that both genes are expressed. Identical, and thus equivocal, results were obtained with both BTF1 and BTF2 amplification (FIG. 4B).
The second group of genes, BTF3-5, are expressed as three (BTF5) (FIG. 4A) and two (BTF3 and 4) transcripts ranging from 4.0 to 3.3 kb (data not shown). BTF5 is expressed at moderate levels in all tissues tested with the exception of the kidney where the expression level is less. RT-PCR experiments showed that mRNA from the BTF5 gene can be found in all tissues tested, including the kidney (FIG. 4B). Identical results were obtained with primers from the other genes of this group (data not shown). These genes are also 90% identical to each other at the DNA sequence level (but only 58% identical to BTF1 and 2), hence like BTF1 and BTF2, cross-hybridization could account for the similarity in size and patterns on the northern blots and RT-PCR. This might be particularly true for BTF4 which lacks the B30-2 exon but still hybridizes to larger size transcripts like BTF5 and BTF3 (data not shown).
A gene with similarity to 52 kD Ro/SSA auto-antigen
Located approximately 120 kb telomeric to the HLA-H gene is a gene, RoRet, that has 58% amino acid similarity to the 52 kD Ro/SSA protein, an auto-antigen of unknown function that is frequently recognized by antibodies in patients with systemic lupus and Sjogren's syndrome (Anderson et al. Lancet 2:456-560 (1961); Clark et al. J. Immunol. 102:117-122 (1969)) (FIGS. 1 and 2). Alignment of the predicted amino acid sequence of this cDNA with that of 52 kD Ro/SSA indicated two features associated with the 52 kD Ro/SSA protein: a putative DNA binding cysteine rich motif (C-X-(I,V)-C-X(11-30)-C-X-H-X-(F,I,L)-C-X(2)-C-(I,L,M)-X(10-18)-C-P-X-C) (SEQ ID NO:31) found at the N terminus (Freemont et al. Cell 64: 483-484 (1991)) and the B30-2 exon found near the carboxyl terminus, are both conserved in RoRet (FIG. 5). Northern blot analysis indicated the RoRet gene was expressed as two major transcripts of 2.8 and 2.2 kb and two minor transcripts of 7.1 and 4.4 kb in all of the tissues on the blot at levels reflective of the RNA amounts as determined by b-actin probing (FIG. 6A). Using RT-PCR, expression can also be detected in small intestine, kidney liver, and spleen (FIG. 6B).
Two genes with homology to a sodium phosphate transporter
A cDNA for a sodium phosphate transport protein (NPT1) was previously cloned and mapped to 6p21.3 using a somatic cell hybrid panel (Chong et al. Genomics 18:355-359 (1993)). NPT1 maps 320 kb telomeric to the HLA-H gene (FIGS. 1 and 2). Two additional cDNAs were cloned which show appreciable homology to NPT1 (FIG. 5). These genes, NPT3 and NPT4, mapped 1.5 megabases and 1.3 megabases centromeric to the NPT1 gene (FIG. 1). Like NPT1, the gene products of NPT3 and NPT4 were extremely hydrophobic, which may reflect a membrane location. Both proteins gave hydrophilicity profiles which were indistinguishable from NPT1 in this study (data not shown). Northern blot analysis indicated that the two genes have different patterns of expression (FIG. 6C). NPT3 was expressed at high levels as a 7.2 kb transcript predominately in muscle and heart. Lesser amount of the mRNA were also found in brain, placenta, lung, liver and pancreas. RT-PCR analysis indicated that expression of the proper size PCR fragment for NPT3 was clearly absent in fetal brain, bone marrow and small intestine (FIG. 6D). A smaller size fragment was detectable in all tissues with the exception of the liver, which may represent evidence for alternative splicing. Although expression was apparently absent from the kidney by northern blot analysis, it was detectable by RT-PCR. Expression was also noted in the mammary gland, spleen and testis. NPT4, on the other hand, was expressed only in the liver and the kidney as a smear of transcripts approximately 2.6-1.7 kb (FIG. 6C). RT-PCR confirmed these results, although a small amount of the proper size PCR fragment was also found in the small intestine and testis (FIG. 6D). Other tissues showed amplification, but the fragments were of larger and smaller size than that produced by the cDNA 22E positive control. Hence, these two genes which apparently have the structural characteristics of a sodium phosphate transporter, appeared to be under the control of different regulatory mechanism that lead to differential patterns of expression.
All publications, patents, and patent applications cited herein are hereby incorporated by reference in their entirety.
______________________________________vector-vector 5'-CGACCCAGCAACCTGGAGAT-3' (SEQ ID NO:24)splicingcryptic 5'-AGCTCGAGCGGCCGCTGCAG-3' (SEQ ID NO:25)donor-1021cryptic 5'-AGACCCCAACCCACAAGAAG-3' (SEQ ID NO:26)donor-1134______________________________________

Megabase transcript map: novel sequences and antibodies thereto

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