WO1992012163A1 - A method for determining the nucleotide sequence of the gene for the alpha5(iv) chain of human type iv collagen - Google Patents

A method for determining the nucleotide sequence of the gene for the alpha5(iv) chain of human type iv collagen Download PDF

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WO1992012163A1
WO1992012163A1 PCT/FI1991/000410 FI9100410W WO9212163A1 WO 1992012163 A1 WO1992012163 A1 WO 1992012163A1 FI 9100410 W FI9100410 W FI 9100410W WO 9212163 A1 WO9212163 A1 WO 9212163A1
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collagen
gene
human
chain
genomic
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PCT/FI1991/000410
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French (fr)
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Karl Tryggvason
Sirkka Liisa Hostikka
Jing Zhou
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Karl Tryggvason
Sirkka Liisa Hostikka
Jing Zhou
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/78—Connective tissue peptides, e.g. collagen, elastin, laminin, fibronectin, vitronectin or cold insoluble globulin [CIG]
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6881—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers

Definitions

  • the present invention relates to a method for isolating and identifying the nucleotide sequence of the human gene for the type IV collagen o5(IV) chain.
  • the present invention is directed to the determination of the nucleotide sequence of the gene for the ⁇ 5(TV) collagen chain in individuals by any method known to the art e.g. cloning from genomic DNA libraries or amplifying gene regions with the polymerase chain reaction (PCR) and studying their physical properties or nucleotide sequences.
  • the invention is directed to the use of the nucleotide sequences of the ⁇ 5(IV) gene to amplify or identify the nucleotide sequences of the ⁇ 5(IV) gene.
  • BM Basement membranes
  • the BM protein components can have different subunits and molecular compositions that possess the necessary functional elements for the tissues concerned. This has become more apparent as new chains with restricted tissue distributions have been found e.g. for type IV collagen and iaminin.
  • the basement membranes have also an important role in the correct regeneration of tissues following injuries such as during post-wound reformation of skin and nerves.
  • Basement membranes also function as macromoiecular filters e.g. in kidneys where the glo erular basement membrane is the sole filtration barrier between the capillary lumen and the urinary space, hindering the macromolecules and blood cells to leak from blood to urine.
  • Basement membranes are composed of several specific components that include type IV collagen, Iaminin, entactin (nidogen) and proteogiycans.
  • Type IV collagen is the major structural component of basement membranes and it forms the framework of these extracellular structures.
  • basement membranes contain SPARK (BM-40), fibronectin and type VII collagen that are also present in other extracellular structures.
  • SPARK BM-40
  • fibronectin fibronectin
  • type VII collagen type VII collagen that are also present in other extracellular structures.
  • the exact molecular compositions of basement membranes in different tissues is not well known but there is growing evidence that even the ubiquitous basement membrane components as type IV collagen and Iaminin have different chain compositions in different tissues. Additionally, there are some proteins such as pemphigoid antigen that is present only in the basement membranes of skin.
  • Type IV collagen is the major structural component of basement membranes and it can provide up to 60 % of the structure.
  • the type IV collagen molecule is formed by three a chains coiled around each other to form the collagen triple helix with the repeated Gly-X-Y-triplet amino acid sequence containing regions.
  • the molecule has a triple-helical 400 nm-long collagenous part and a C-terminal globule with a diameter of about 15 nm.
  • the collagenous domain sequence has several interruptions in the otherwise continuous collagenous Gly-X-Y repeat sequence that give flexibility to the type IV collagen molecules as opposed to the rigid rod-like molecules of fibrillar collagens with uninterrupted helices.
  • the triple-helical type IV collagen molecules can form dimers by the attachment of two NC domains and tetramers by the 30 nm overlapping cross-linking of four molecules of their amino terminal ends (Timpl, Eur. J. Biochem., 180: 487-502, 1989).
  • the major form of the molecules consists of two ⁇ l(IV) and one ⁇ 2(IV) chain.
  • the applicants have determined the entire amino acid sequence of these two chains from man by cloning and sequencing cDNA clones covering the coding region (Soininen et al, FEBS Lett, 225: 188-194, 1987; Hostikka and Tryggvason, J. Biol. Chem., 263: 19488-19493, 1988).
  • the results showed that the ⁇ l(IV) chain in synthesized as a 1969 amino acid residue polypeptide as compared to 1712 residues in the ⁇ 2(IV) chain.
  • the carboxyl terminal NC domains of the two chains are very similar with 63 % identical amino acid residues.
  • ⁇ l(IV) and ⁇ 2(IV) chains are transcribed by different DNA strands from a common bidirectional promoter in opposite directions, so that the transcription initiation sites are separated by only 42-127 bp (P ⁇ schl et al., EMBO J., 7: 2687-2695, 1988; Soininen et al., J. Biol. Chem.,
  • the applicants have determined the complete structure of the human ⁇ l(IV) gene (Soininen et al., J. Biol. Chem., 264: 23565-13571, 1989) and the partial structure for the human ⁇ 2(IV) gene (Hostikka and Tryggvason, FEBS Lett, 224: 297-305.
  • the ol(IV) gene contains 52 exons spread over at least 100 kb of genomic DNA The sizes of translated exons vary from 27 to 213 bp.
  • the collagenous domain is encoded by 47 exons with sizes varying between 27 and 192 bp.
  • the exon size pattern of this gene is very different from the highly conserved structure of the genes for the fibrillar collagens.
  • the largest exon coding for a translated sequence is the junction econ coding for the carboxyl-terminal part of the collagenous domain and the a ⁇ uno-te ⁇ ninal part of the NC domain.
  • Four more exons code for the NC domain, the last of them containing the 3' untranslated region (Soininen et al., J. Biol. Chem., 264: 13565-13571, 1989).
  • the region characterized from the human ⁇ 2(IV) gene shows a different pattern.
  • the NC domain is encoded by three exons as comapred to five in the ⁇ l(IV) gene.
  • the similarity of the two genes is demonstrated by the fact that although the exon sizes differ, the locations of the introns are exactly the same when comparing to the aligned amino acid sequences of the chains.
  • the exons in the collagenous domain coding region of the ⁇ 2(IV) gene are different so that only one intron location seems to coincide, whereas all the exon sizes differ nor do they obey the fibrillar 54 bp pattern.
  • the exons in the collagenous region coding part begin with split glycine codons (Hostikka and Tryggvason, FEBS Lett, 224: 297-305).
  • basement membranes Due to the wide distribution of basement membranes in the body, they are frequently affected in local and systemic diseases, and in many instances the consequent pathological changes lead to severe clinical complications. These diseases may be acquired i.e. complications of a disease that do not primarily involve basement membrane, or they can be genetically determined inherited diseases that are due to gene mutations leading to abnormal structure and function of the basement membrane.
  • the best known example of an acquired disease is diabetes mellitus where the basement membrane structure is affected in almost all tissues in the body, resulting in dysfunction of small blood vessels (microangiopathy), kidneys (nephropathy), and nerves (neuropathy). The biochemical alterations leading to these malfunctions are still poorly understood.
  • autoimmune diseases such as Goodpasture syndrome, affected the basement membranes. The antibody binds to the glomerular basement membrane and triggers its destruction by complement binding and phagocytosis.
  • Examples of inherited diseases are: (1) the congenital nephrotic syndrome that is characterized by extensive leakage of blood proteins through the renal glomerular basement membrane into the urine (proteinuria); and (2) the Alport syndrome where malfunction of the glomerular basement membrane leads to the passage of blood cells into urine (hematuria), eye lesions and hearing loss.
  • the actual gene defect leading to the congenital nephrotic syndrome is yet completely unknown.
  • the Alport syndrome is primarily an X-linked inherited kidney disease that has been linked by chromosomal markers to chromosome X region q22-26 (Atkin et al., Am. J. Hum. Genet, 42: 249-255, 1988; Flinter et al., Genomics 4: 335-338).
  • the present invention provides for a method for isolation and partially characterizing the nucleotide sequencing of the gene coding for the human type IV collagen ⁇ 5(IV) chain.
  • the invention provides for the use of the identified nucleotide sequence (or DNA fragment thereof) to detect mutation(s) in individual genes specific for the ⁇ 5(IV) chain which can, directly or indirectly, produce human diseases.
  • the invention relates to the use of noncoding intervening sequences (introns) between and flanking the ⁇ 5(IV) polypeptide chain coding regions (exons) of the ⁇ 5(IV) gene to amplify and determine the physical properties and nucleotide sequence of the said gene for both protein coding regions and noncoding regions.
  • the invention relates to the use of gene fragments generated through amplification from human genomic or cloned DNA for the detection and analysis of the gene, such as in detection of mutations. Additionally, the invention provides for the use of the identified recombinant DNA cloning vectors and transformed hosts which contain a vector which has a fragment of the c_5(IV) gene inserted into.
  • the invention related to the detection of variation of an individual's COL4A5 gene in comparison with the known normal COL4A5 gene. In one embodyment this is done by RFLP analysis, wherein and individual's genomic DNA is cut by restriction enzyme, size-fractionated and tested for the sizes of DNA fragments of the ⁇ 5(IV) gene.
  • the invention relates to nucleotide sequences flanking the polypeptide chain coding region (intron requences) that can be used to amplify coding regions (exons) with the flanking consensus sequences needed for the proper splicing of the pre-mRNA to mRNA by cloning or the method polymerase chain reaction (PCR) or any other method known to the art; and to determining the differences of those sequences with the normal COL4A5 gene by various techniques, such as single-strand conformation polymorphism analysis, denaturing gradient gel electrophoresis, SI nuclease mapping nucleotide sequencing or any other method known to the art.
  • the invention related to the fragments of the normal human ⁇ 5(IV) gene that may by used to correct a defective gene by gene therapy.
  • FIGURE 1 is a restriction map of eight cloned fragments of the ⁇ 5(IV) gene.
  • a scale demonstrating the size differences in kilo base pairs is shown below the cloned gene fragments (in the middle).
  • the EcoRI restriction sites (E) and the aligned positions of the eight 1 clones are shown.
  • On top is a diagram of the gene with ⁇ 5(IV) polypeptide chain coding regions (exons) indicated by shadowed boxes and noncoding regions (introns and the 3' flanking region) indicated by a solid line. The exons are numbered from the 3' end of the gene.
  • FIGURE 2 shows the nucleotide sequence of the 19 most 3' exons of the ⁇ 5(IV) gene and flanking regions. Exon sequences are shown in capital letters and intron sequences in lowe case letters. The exons are numbered from the 3' end.
  • FIGURE 3 is a table. where the sizes of the exons and introns of the ⁇ 5(IV) gene is compared with those of the ⁇ l(IV) gene. The exon sizes differ only once, in exon 19 where one amino acid residue is missing from the ⁇ 5(IV) chain when comparing the aligned amino acid sequences with those of the ⁇ l(IV) chain. On the other hand, the introns show no similarity in their size pattern.
  • FIGURE 4 shows partial sequence of a PCR-amplification segment of the ⁇ 5(IV) gene from normal individuals and individuals carrying a mutated gene.
  • the amplified fragments were cloned into an M13 vector and sequenced with the dideoxynucleotide chain termination method.
  • the sequencing reaction samples were electrophoresed on a polyacrylamide gel followed by autoradiography. The results show sequence differences between normal and mutated DNA
  • the coding nucleotide sequence of the cDNAs was used to make oligonucleotide primers for sequencing the exons and their flanking regions from the genomic clones.
  • ML-5, MG-2, EB-4, FM-13, F-2 and F-7 cover about 9.5 kb of the 3' flanking region and about 36 kb of the gene, including 14 most 3' exons.
  • Exon 15 was shown to be one exon and sequenced by amplifying the coding region with PCR reaction, using cDNA derived primers.
  • the exons 1-5 code for the NC domain.
  • Exon 5 is a junction exon that contains 142 bp coding for the NC domain and 71 bp coding for the collagenous region.
  • Exons 6-19 code for collagenous Gly-X-Y-repeat sequence and have sizes differing between 51 and 186 bp. The exons and their flanking intron sequences are shown in the figure 2. The intron sizes analyzed very between 133 and 7000 bp and show no correlation with the sizes of the corresponding introns in the ⁇ l(IV) gene.
  • Example 1 Isolation and characterization of the gene clones for the human g5(IV) gene.
  • coli LE 392 planting bacteria (in 20 mM MgS0 4 ) at 37° C for 20 minutes and planted in 7 ml top-agar (1 % tryptone, 0.8% NaCl, 1.4 % LMP-agar) on agar plates containing 1 % tryptone, 0.5 % NaCl and 100 txg ml ampicillin. The ⁇ phage were grown at 37° C overnight.
  • Duplicate nitrocelluloce filters were made by allowing them to stand on the plate for 1 and 2 minutes following 5 minutes denaturation in 0.5 M NaOH, 1.5 M NaCl; neutralizing in 1 M Tris (Tris[hydroxymethyl]- aminomethane), pH 8.0, 1.5 M NaCl for 5 minutes and balancing to 2 x SSC (1 x SSC is 0.15 M NaCl, 0.015 M sodium citrate, pH 7.0) before air drying and backing at 80° C for 2 h.
  • the nitrocellulose filters were balanced in 5 x SSC.
  • Nick translation labeling of the cDNA inserts with deoxycytidine S'-J ⁇ Jtriphosphate was carried out with a Promega kit according to the manufacturer's instructions.
  • the filters were prehybridized for 2 h and hybridized with the labeled cDNA probes overnight at 65° C in 5 x SSC, 5 x Denhardt's solution, 0.1 % SDS, 50 ⁇ g/ml denatured salmon sperm DNA (50 x Denhardt's solution is 1 % Ficoll, 1 % polyvinylpyrrolidone, 1 % BSA).
  • nitrocellulose filters were washed first in 2 x SSC, 0.1 % SDS at RT and then at 65 °C with several changes and washing solution up to 0.2 x SSC, 0.1 % SDS. Autoradiography was done at -70° C overnight
  • RNAse A treatment of the lyzed growing medium PEG precipitation, proteinase K treatment, phenol and chloroform extractions and ethanol precipitations.
  • ⁇ -DNA of the clones was digested with different restriction endonucleases and eletrophoresed in 1 % agarose gel containing ethidium bromide to separate the genomic inserts from the ⁇ -vector and to determine the sizes of gene fragments in order to make a restriction map of the gene.
  • DNA was transferred from the gel to a nitrocellulose filter by Southern blotting and hybridized with the cDNA mixture.
  • the genomic fragments that hybridized with the cDNA clones were isolated and subcloned into M13 or pUC vectors for sequencing and further restriction mapping. The clones and a partial restriction map is shown in Figure 1.
  • the Southern filter could be hybridized with an oligonucleotide probe. Knowing the exon present in a fragment, the exon could be sequenced using the same oligonucleotide as a primer for sequencing.
  • oligonucleotide hybridization 5 the nitrocellulose filter was prewashed in 3 x SSC, 0.1 % SDS at 65° C overnight, prehybridized in 6 x SSC, 5 x Denhardt's, 0.5 % SDS, 100 ⁇ g/ml denatured salmon sperm DNA, 0.05 % Na-pyrophosphate for 2 h at 37° C and hybridized with labeled oligonucleotide mixture in 6 x SSC, 5 x Denhardt's solution, 250 ⁇ g/ml denatured salmon sperm DN 0.05 % Na-pyrphosphate overnight at
  • oligonucleotide probe 500 ng of the oligonucleotide was labeled with 100 ⁇ Ci adenosine (in 10 ⁇ l; Amersham, PB 10168) in 20 mM MgCl* 200 mM Tris, pH 7.6, 40 mM b-mercaptoethanol with 1 U T4-polynucleotide kinase in 40 ⁇ l reaction mixture at 37° C for 1 hour. After the hybridization, the nitrocellulose filter was washed with 6 x SSC, 0.05
  • the genomic fragments containing coding regions of the ⁇ 5(IV) gene were subcloned into M13 opr pUC vectors for sequencing.
  • Nucleotide sequencing 5 was sone with the Sanger dideoxy nucleotide sequencing method using Sequenase (United States Biochemical Corporation) and deoxyadenosine 5'-( ⁇ [ 35 S]thio)triphosphate (Amersham, SJ1304) according to manufacturer's instructions. Both "universal primer” and sequence specific oligonucleotides were used as primers. The sequences were determined from both strands, 0 yielding the entire sequence of each exon together with sequences of the adjacent intervening regions (introns).
  • exons 1-14 and 16-19 together with varying length of intron sequences are shown in Figure 2.
  • the sequence of exon 15 was determined after amplification from genomic DNA by PCR reaction (see example 3.) using cDNA derived primers with flanking 5 restriction sites. The PCR product was purified, linker sequences were digested to produce cohesice cloning sites and the fragment was subcloned into M13-vectors for sequencing.
  • Example 3 Polvmerase chain reaction amplification of fragments of the c.5(IV) gene.
  • oligonucleotide primers PI 5 '-CTAGAATTCGGTGAGCCTTGGTCTGCCT-3 '
  • P2 5'-CCGAAGCTTCTGGGAATCCAGGAAGGC-3'
  • the reaction was performed with a Perking-Elmer/Cetus PCR kit using 1 ⁇ g of human lymphocyte DNA as template and 25 pmol of primers according to manufacturer's recommendations.
  • the DNA was denatured at 94° C for 10 minutes and cooling on ice for 3 minutes.
  • a 1038 bp fragment containing the exons 2 and 3 was amplified.
  • Oligonucleotide primers P3 (5'-GACTCTAGAAAGGCC ATTGCACTGGTT-3') upstream (to the 5') from exon 3 and P4 (5'-AGCGAATTCCTGACCTGAGTCATGTAT-3') to the downstream (3') from exon 2, with Xbal and EcoRI restriction sites, respectively.
  • the PCR reaction of 35 cycles denaturing at 94° C for 1.5 minutes, annealing at 65 °C for 2 minutes, and extension at 72° C for 2 minutes), subcloning and sequencing were carried out as above.
  • the sequence of the exon 3 showed a difference in a DNA sample from an Alport patient compared to normal individual's gene and an isolated genomic clone.
  • the amplified gene, fragments can be separated according to their physical properties showing base differences between samples.
  • the amplified fragments of different individuals were separated according to melting temperatures in denaturing gradient gel electrophoresis (DGGE).
  • DGGE denaturing gradient gel electrophoresis
  • the denaturing gradient gel electrophoresis was performed in 10 % polyacrylamide gels with a linerar gradient from 40 % denaturant to 75 % denaturant (100 % is 7 M urea, 40 %

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Abstract

The present invention relates to a method for isolating and identifying the nucleotide sequence of the human gene for the type IV collagen α5(IV) chain. The present invention is directed to the determination of the nucleotide sequence of the gene for the α5(IV) collagen chain in individuals by any method known in the art, e.g. cloning from genomic DNA libraries or amplifying gene regions with the polymerase chain reaction (PCR) and studying their physical properties or nucleotide sequences. In addition, the invention is directed to the use of the nucleotide sequences of the α5(IV) gene to amplify or identify the nucleotide sequences of the α5(IV) gene.

Description

A METHOD FOR DETERMINING THE NUCLEOTIDE SEQUENCE OF THE GENE FOR THE α5(TV) CHAIN OF HUMAN TYPE IV COLLAGEN
pfcjd of the Invention
The present invention relates to a method for isolating and identifying the nucleotide sequence of the human gene for the type IV collagen o5(IV) chain. The present invention is directed to the determination of the nucleotide sequence of the gene for the α5(TV) collagen chain in individuals by any method known to the art e.g. cloning from genomic DNA libraries or amplifying gene regions with the polymerase chain reaction (PCR) and studying their physical properties or nucleotide sequences. In addition, the invention is directed to the use of the nucleotide sequences of the α5(IV) gene to amplify or identify the nucleotide sequences of the α5(IV) gene.
Backround of the Invention Basement membranes (BM) are special extracellular, sheet-like structures that separate the cells of organs from the underlying connective tissues. They form flexible boundaries that provide physical support and biological signals required for maintainance of morphology and orderly development of distinct tissue patterns. The BM protein components can have different subunits and molecular compositions that possess the necessary functional elements for the tissues concerned. This has become more apparent as new chains with restricted tissue distributions have been found e.g. for type IV collagen and iaminin. The basement membranes have also an important role in the correct regeneration of tissues following injuries such as during post-wound reformation of skin and nerves. Basement membranes also function as macromoiecular filters e.g. in kidneys where the glo erular basement membrane is the sole filtration barrier between the capillary lumen and the urinary space, hindering the macromolecules and blood cells to leak from blood to urine.
Basement membranes are composed of several specific components that include type IV collagen, Iaminin, entactin (nidogen) and proteogiycans. Type IV collagen is the major structural component of basement membranes and it forms the framework of these extracellular structures. In addition, basement membranes contain SPARK (BM-40), fibronectin and type VII collagen that are also present in other extracellular structures. The exact molecular compositions of basement membranes in different tissues is not well known but there is growing evidence that even the ubiquitous basement membrane components as type IV collagen and Iaminin have different chain compositions in different tissues. Additionally, there are some proteins such as pemphigoid antigen that is present only in the basement membranes of skin.
Type IV collagen is the major structural component of basement membranes and it can provide up to 60 % of the structure. As all collageπs, the type IV collagen molecule is formed by three a chains coiled around each other to form the collagen triple helix with the repeated Gly-X-Y-triplet amino acid sequence containing regions. The molecule has a triple-helical 400 nm-long collagenous part and a C-terminal globule with a diameter of about 15 nm. The collagenous domain sequence has several interruptions in the otherwise continuous collagenous Gly-X-Y repeat sequence that give flexibility to the type IV collagen molecules as opposed to the rigid rod-like molecules of fibrillar collagens with uninterrupted helices. The triple-helical type IV collagen molecules can form dimers by the attachment of two NC domains and tetramers by the 30 nm overlapping cross-linking of four molecules of their amino terminal ends (Timpl, Eur. J. Biochem., 180: 487-502, 1989).
The major form of the molecules consists of two αl(IV) and one α2(IV) chain. The applicants have determined the entire amino acid sequence of these two chains from man by cloning and sequencing cDNA clones covering the coding region (Soininen et al, FEBS Lett, 225: 188-194, 1987; Hostikka and Tryggvason, J. Biol. Chem., 263: 19488-19493, 1988). The results showed that the αl(IV) chain in synthesized as a 1969 amino acid residue polypeptide as compared to 1712 residues in the α2(IV) chain. The carboxyl terminal NC domains of the two chains are very similar with 63 % identical amino acid residues. The sequence identity of the two chains is much less conserved in the triple-helical region with only 49 % identity; where only 22 % of the X and Y residues in the collagenous Gly-X-Y-repeat sequence are conserved.. Two other distinct type IV collagen a chains, referred α3(IV) and α4(IV), have been described (Butkowski et al., J. Biol. Chem. 262: 7874-7877, 1987; Saus et al., J. Biol. Chem. 263: 13374-13380, 1988; Gunwar et al., J. Biol. Chem. 265: 5466-5469, 1990).
Of importance with respect to the present invention is our recent discovery of yet another novel human type IV collagen α5(IV) chain by cDNA cloning (Hostikka et al., Proc. Natl. Acad. Sci. USA, 87: 1606-1610, 1990 and the parent U.S. patent application "A Method for determining the nucleotide sequence of a novel α5(IV) chain of human type IV collagen" serial number 377,238, filed on July 6, 1989). Amino acid sequence comparison with the αl(IV) and α2(IV) chains and the data available of the α3(IV) and α4(IV) chains demonstrated that the α5(IV) chain is a distinct gene product which is closely related to the αl(IV) chain. In the NC domain the identity between the deduced amino acid sequences is 83 % with the αl(IV) chain and with α2(IV) chain 63 %; whereas in the collagenous domain the identities are 58 % and 46 %, respectively. Furthermore, all the interruptions in the collagenous Gly-X-Y-repeat sequence of the α5(IV) chain coincide with those in the αl(IV) chain but only partially with those in the α2(IV) chain (Hostikka et al., Proc. Natl. Acad. Sci. USA, 87: 1606-1610, 1990 and the parent U.S. patent application "A Method for determining the nucleotide sequence of a novel α5(IV) chain of human type IV collagen" serial number 377,238, filed on July 6, 1989).
With α5(IV)-specific peptide-antibodies, the chain was shown to be almost exclucively present in the GBM in the kidney (Hostikka et al., Proc. Natl. Acad. Sci. USA, 87: 1606-1610, 1990 and the parent U.S. patent application "A Method for determining the nucleotide sequence of a novel α5(IV) chain of human type IV collagen" serial number 377,238, filed on July 6, 1989 and the continuation- in-part application "Immunological methods for the detection of the human type IV collagen α5(IV) chain", filed...); whereas the well characterized αl(IV) and α2(IV) chain are believed to be ubiquitous basement membrane (BM) components present in all BMs.
Using cDNA probes and both somatic cell-hybrids and in situ hybridization, the gene for the human type IV collagen α5 chain COL4A5 was localized to the q22 region on the long arm of chromosome X (Hostikka et al., Proc. Natl. Acad. Sci. USA, 87: 1606-1610, 1990 and the parent U.S. patent application "A Method for determining the nucleotide sequence of a novel α5(IV) chain of human type IV collagen" serial number 377,238, filed on July 6, 1989). This is different from the human genes COL4A1 and COL4A2 coding for the αl(IV) and α2(IV) chains that both are located on the terminal end of the long arm of the chromosome 13 (Boyd et al., Hum. Genet, 74: 121-125, 1986; Griffin et al., Proc. Natl. Acad. Sci. USA 87: 512-516, 1987). The αl(IV) and α2(IV) chains are transcribed by different DNA strands from a common bidirectional promoter in opposite directions, so that the transcription initiation sites are separated by only 42-127 bp (Pδschl et al., EMBO J., 7: 2687-2695, 1988; Soininen et al., J. Biol. Chem.,
UTE SHEET 263: 17217-17220, 1988).
The applicants have determined the complete structure of the human αl(IV) gene (Soininen et al., J. Biol. Chem., 264: 23565-13571, 1989) and the partial structure for the human α2(IV) gene (Hostikka and Tryggvason, FEBS Lett, 224: 297-305. The ol(IV) gene contains 52 exons spread over at least 100 kb of genomic DNA The sizes of translated exons vary from 27 to 213 bp. The collagenous domain is encoded by 47 exons with sizes varying between 27 and 192 bp. About half of them begin with complete codons whereas the other half of the gene has mainly split codons, usually beginning with the second base for glycine, but also two exons begin with the third base of a codon. Thus, the exon size pattern of this gene is very different from the highly conserved structure of the genes for the fibrillar collagens. The largest exon coding for a translated sequence is the junction econ coding for the carboxyl-terminal part of the collagenous domain and the aπuno-teπninal part of the NC domain. Four more exons code for the NC domain, the last of them containing the 3' untranslated region (Soininen et al., J. Biol. Chem., 264: 13565-13571, 1989).
The region characterized from the human α2(IV) gene shows a different pattern. The NC domain is encoded by three exons as comapred to five in the αl(IV) gene. The similarity of the two genes is demonstrated by the fact that although the exon sizes differ, the locations of the introns are exactly the same when comparing to the aligned amino acid sequences of the chains. On the other hand, the exons in the collagenous domain coding region of the α2(IV) gene are different so that only one intron location seems to coincide, whereas all the exon sizes differ nor do they obey the fibrillar 54 bp pattern. The exons in the collagenous region coding part begin with split glycine codons (Hostikka and Tryggvason, FEBS Lett, 224: 297-305).
Due to the wide distribution of basement membranes in the body, they are frequently affected in local and systemic diseases, and in many instances the consequent pathological changes lead to severe clinical complications. These diseases may be acquired i.e. complications of a disease that do not primarily involve basement membrane, or they can be genetically determined inherited diseases that are due to gene mutations leading to abnormal structure and function of the basement membrane. The best known example of an acquired disease is diabetes mellitus where the basement membrane structure is affected in almost all tissues in the body, resulting in dysfunction of small blood vessels (microangiopathy), kidneys (nephropathy), and nerves (neuropathy). The biochemical alterations leading to these malfunctions are still poorly understood. Also, autoimmune diseases, such as Goodpasture syndrome, affected the basement membranes. The antibody binds to the glomerular basement membrane and triggers its destruction by complement binding and phagocytosis.
Examples of inherited diseases are: (1) the congenital nephrotic syndrome that is characterized by extensive leakage of blood proteins through the renal glomerular basement membrane into the urine (proteinuria); and (2) the Alport syndrome where malfunction of the glomerular basement membrane leads to the passage of blood cells into urine (hematuria), eye lesions and hearing loss. The actual gene defect leading to the congenital nephrotic syndrome is yet completely unknown. The Alport syndrome is primarily an X-linked inherited kidney disease that has been linked by chromosomal markers to chromosome X region q22-26 (Atkin et al., Am. J. Hum. Genet, 42: 249-255, 1988; Flinter et al., Genomics 4: 335-338). It leads to malfunction of kidneys and it can be treated only by dialysis or renal transplantation. The disease has been shown to be associated with progressive ultrastructural abnormalities, such as patchy thickening and thinning of the glomerular basement membrane and splitting of the lamina densa. These results and the more recent immunological studies have suggested that the cause of the Alport syndrome would be an abnormal or absent type IV collagen a chain (Spear, Clin.Nephrol. 1: 336-337, 1973; Kashtan et al., J. Clin. Invest, 78: 1035-1044, 1986).
Of importance with respect to the present invention is our recent discovery that a mutation in the type IV collagen α5(IV) gene, that changes the structure of the produced polypeptide chain, causes Alport syndrome. Eighteen Alport kindreds were studied and in three of them an abnormal fragment pattern was shown with restriction fragment length polymorphism (RFLP) analysis for the α5(IV) gene (Barker et al., Science 248: 1224-1227, 1990; and the U.S. patent application "Method for detection of Alport syndrome", serial No. 07/534,786, filed June 7, 1990 and the parent U.S. patent application "A Method for determining the nucleotide sequence of a novel α5(IV) chain of human type IV collagen" serial number 377,238, filed on July 6, 1989). In kindred EP, there was a deletion of about 15 kb of the gene, containing exons 5 through 10 as counted from the 3' end. In kindred P, there was a point mutation that changed a codon for a conserved cysteine residue to a codon for serine and created restriction sites for PstI and Bglll restriction endonucleases (Barker et al., Science 248:
BSTITUTE SHEET 1224-1227, 1990; and the U.S. patent application "Method for detection of Alport syndrome", serial No. 07/534,786, filed June 7, 1990 and the parent U.S. patent application "A Method for determining the nucleotide sequence of a novel α5(IV) chain of human type IV collagen" serial number 377,238, filed on July 6, 1989; and Zhou et al., 1991a, Genomics, in press). Later studies have shown that in about 10 % of the Alport patients, a gene rearrangement can be observed with the α5(IV) cDNA clones in RFLP analysis.
Summary of the Invention The present invention provides for a method for isolation and partially characterizing the nucleotide sequencing of the gene coding for the human type IV collagen α5(IV) chain. The invention provides for the use of the identified nucleotide sequence (or DNA fragment thereof) to detect mutation(s) in individual genes specific for the α5(IV) chain which can, directly or indirectly, produce human diseases. The invention relates to the use of noncoding intervening sequences (introns) between and flanking the α5(IV) polypeptide chain coding regions (exons) of the α5(IV) gene to amplify and determine the physical properties and nucleotide sequence of the said gene for both protein coding regions and noncoding regions. Also, the invention relates to the use of gene fragments generated through amplification from human genomic or cloned DNA for the detection and analysis of the gene, such as in detection of mutations. Additionally, the invention provides for the use of the identified recombinant DNA cloning vectors and transformed hosts which contain a vector which has a fragment of the c_5(IV) gene inserted into.
The invention related to the detection of variation of an individual's COL4A5 gene in comparison with the known normal COL4A5 gene. In one embodyment this is done by RFLP analysis, wherein and individual's genomic DNA is cut by restriction enzyme, size-fractionated and tested for the sizes of DNA fragments of the α5(IV) gene. The invention relates to nucleotide sequences flanking the polypeptide chain coding region (intron requences) that can be used to amplify coding regions (exons) with the flanking consensus sequences needed for the proper splicing of the pre-mRNA to mRNA by cloning or the method polymerase chain reaction (PCR) or any other method known to the art; and to determining the differences of those sequences with the normal COL4A5 gene by various techniques, such as single-strand conformation polymorphism analysis, denaturing gradient gel electrophoresis, SI nuclease mapping nucleotide sequencing or any other method known to the art. Finally, the invention related to the fragments of the normal human α5(IV) gene that may by used to correct a defective gene by gene therapy.
Description of the Drawings The following is a description of the drawings which are presented for the purpose of illustrating the invention and not for the purpose of limiting same.
FIGURE 1 is a restriction map of eight cloned fragments of the α5(IV) gene. A scale demonstrating the size differences in kilo base pairs is shown below the cloned gene fragments (in the middle). The EcoRI restriction sites (E) and the aligned positions of the eight 1 clones are shown. On top is a diagram of the gene with α5(IV) polypeptide chain coding regions (exons) indicated by shadowed boxes and noncoding regions (introns and the 3' flanking region) indicated by a solid line. The exons are numbered from the 3' end of the gene.
FIGURE 2 shows the nucleotide sequence of the 19 most 3' exons of the α5(IV) gene and flanking regions. Exon sequences are shown in capital letters and intron sequences in lowe case letters. The exons are numbered from the 3' end.
FIGURE 3 is a table. where the sizes of the exons and introns of the α5(IV) gene is compared with those of the αl(IV) gene. The exon sizes differ only once, in exon 19 where one amino acid residue is missing from the α5(IV) chain when comparing the aligned amino acid sequences with those of the αl(IV) chain. On the other hand, the introns show no similarity in their size pattern.
FIGURE 4 shows partial sequence of a PCR-amplification segment of the α5(IV) gene from normal individuals and individuals carrying a mutated gene. The amplified fragments were cloned into an M13 vector and sequenced with the dideoxynucleotide chain termination method. The sequencing reaction samples were electrophoresed on a polyacrylamide gel followed by autoradiography. The results show sequence differences between normal and mutated DNA
Detailed Description of the Invention The applicants have isolated and characterized fragments of the gene for the human type IV collagen α5(IV) chain and determined the structure and partial sequence for the gene. The gene clones in 1 phage were screened with the cDNA clones coding for the human α5(IV) chain (Hostikka et al., Proc. Natl.
BSTITUTE SHEET Acad. Sci. US 87: 1606-1610, 1990 and the parent U.S. patent application "A Method for determining the nucleotide sequence of a novel α5(IV) chain of human type IV collagen" serial number 377,238, filed on July 6, 1989). The genomic clones obtained, cover approximately 50 kb or about half of the COΪ_4A5 gene in eight overlapping clones (Zhou et al., Genomics, 9: 10-18, 1991). Map of the clones with respect to each other and the encoded exons with the restriction sites for EcoRI are shown in Figure 1.
Fragments of the genomic clones for the COL4A5 gene that hybridized with the cDNA clones and therefore contained coding regions, were subcloned into M13 and/or pUC-vectors for sequencing and further restriction mapping. The coding nucleotide sequence of the cDNAs was used to make oligonucleotide primers for sequencing the exons and their flanking regions from the genomic clones. By the sequence identity of the α5(IV) chain with the αl(IV) chain, it was anticipated that the exon-intron boundaries would concide, as compared to the aligned amino acid sequences. This was shown to be the case, as shown in Figure 3. Six overlapping genomic clones (ML-5, MG-2, EB-4, FM-13, F-2 and F-7) cover about 9.5 kb of the 3' flanking region and about 36 kb of the gene, including 14 most 3' exons. Two additional clones (F-8 and ML-2) that do not overlap the previous clones, contain exons 16 through 19. Exon 15 was shown to be one exon and sequenced by amplifying the coding region with PCR reaction, using cDNA derived primers. The exons 1-5 code for the NC domain. Exon 5 is a junction exon that contains 142 bp coding for the NC domain and 71 bp coding for the collagenous region. Exons 6-19 code for collagenous Gly-X-Y-repeat sequence and have sizes differing between 51 and 186 bp. The exons and their flanking intron sequences are shown in the figure 2. The intron sizes analyzed very between 133 and 7000 bp and show no correlation with the sizes of the corresponding introns in the αl(IV) gene.
Examples
Example 1. Isolation and characterization of the gene clones for the human g5(IV) gene.
Human genomic libraries in λ Charons 4A, in λ EMBL-3 or λ Fix, made from genomic DNA isolated from human lymphocytes, were screened with the cDNA clones coding for the human α5(IV) chain (Hostikka et al., Proc. Natl. Acad. Sci. USA 87: 1606-1610, 1990 and the parent U.S. patent application "A Method for determining the nucleotide sequence of a novel α5(IV) chain of human type IV collagen" serial number 377,238, filed on July 6, 1989). For each plate, a sample of 30,000 plaque forming units of a library was infected to 300 μl E. coli LE 392 planting bacteria (in 20 mM MgS04) at 37° C for 20 minutes and planted in 7 ml top-agar (1 % tryptone, 0.8% NaCl, 1.4 % LMP-agar) on agar plates containing 1 % tryptone, 0.5 % NaCl and 100 txg ml ampicillin. The λ phage were grown at 37° C overnight. Duplicate nitrocelluloce filters were made by allowing them to stand on the plate for 1 and 2 minutes following 5 minutes denaturation in 0.5 M NaOH, 1.5 M NaCl; neutralizing in 1 M Tris (Tris[hydroxymethyl]- aminomethane), pH 8.0, 1.5 M NaCl for 5 minutes and balancing to 2 x SSC (1 x SSC is 0.15 M NaCl, 0.015 M sodium citrate, pH 7.0) before air drying and backing at 80° C for 2 h.
For hybridization, the nitrocellulose filters were balanced in 5 x SSC. Nick translation labeling of the cDNA inserts with deoxycytidine S'-Jα^Jtriphosphate (Amersham, PB 10205) was carried out with a Promega kit according to the manufacturer's instructions. The filters were prehybridized for 2 h and hybridized with the labeled cDNA probes overnight at 65° C in 5 x SSC, 5 x Denhardt's solution, 0.1 % SDS, 50 μg/ml denatured salmon sperm DNA (50 x Denhardt's solution is 1 % Ficoll, 1 % polyvinylpyrrolidone, 1 % BSA). The nitrocellulose filters were washed first in 2 x SSC, 0.1 % SDS at RT and then at 65 °C with several changes and washing solution up to 0.2 x SSC, 0.1 % SDS. Autoradiography was done at -70° C overnight
Clones showing duplicate positive signals for the cDNA clones were picked and rescreened until pure plaques were isolated. Phage were grown in larger amounts and isolated as pure λ-DNA with a rapid method containing DNAse
I and RNAse A treatment of the lyzed growing medium, PEG precipitation, proteinase K treatment, phenol and chloroform extractions and ethanol precipitations. λ-DNA of the clones was digested with different restriction endonucleases and eletrophoresed in 1 % agarose gel containing ethidium bromide to separate the genomic inserts from the λ-vector and to determine the sizes of gene fragments in order to make a restriction map of the gene. DNA was transferred from the gel to a nitrocellulose filter by Southern blotting and hybridized with the cDNA mixture. The genomic fragments that hybridized with the cDNA clones were isolated and subcloned into M13 or pUC vectors for sequencing and further restriction mapping. The clones and a partial restriction map is shown in Figure 1.
STITUTE SHEET For the detection of a gene fragment containing a certain exon, the Southern filter could be hybridized with an oligonucleotide probe. Knowing the exon present in a fragment, the exon could be sequenced using the same oligonucleotide as a primer for sequencing. For oligonucleotide hybridization, 5 the nitrocellulose filter was prewashed in 3 x SSC, 0.1 % SDS at 65° C overnight, prehybridized in 6 x SSC, 5 x Denhardt's, 0.5 % SDS, 100 μg/ml denatured salmon sperm DNA, 0.05 % Na-pyrophosphate for 2 h at 37° C and hybridized with labeled oligonucleotide mixture in 6 x SSC, 5 x Denhardt's solution, 250 μg/ml denatured salmon sperm DN 0.05 % Na-pyrphosphate overnight at
10 37° C. For making the oligonucleotide probe, 500 ng of the oligonucleotide was labeled with 100 μCi adenosine
Figure imgf000012_0001
(in 10 μl; Amersham, PB 10168) in 20 mM MgCl* 200 mM Tris, pH 7.6, 40 mM b-mercaptoethanol with 1 U T4-polynucleotide kinase in 40 μl reaction mixture at 37° C for 1 hour. After the hybridization, the nitrocellulose filter was washed with 6 x SSC, 0.05
15 % Na-pyrophosphate once at room temperature, twice 10 minutes at 37° C and at least twice 10 minutes at 42° C. Autoradiography was performed at -70° C for two days (DuPont Cronex).
Example 2. 0 Determining the nucleotide sequencing of the exons and flanking intron sequences
The genomic fragments containing coding regions of the α5(IV) gene were subcloned into M13 opr pUC vectors for sequencing. Nucleotide sequencing 5 was sone with the Sanger dideoxy nucleotide sequencing method using Sequenase (United States Biochemical Corporation) and deoxyadenosine 5'-(α [35S]thio)triphosphate (Amersham, SJ1304) according to manufacturer's instructions. Both "universal primer" and sequence specific oligonucleotides were used as primers. The sequences were determined from both strands, 0 yielding the entire sequence of each exon together with sequences of the adjacent intervening regions (introns). The sequences of exons 1-14 and 16-19 together with varying length of intron sequences are shown in Figure 2. The sequence of exon 15 was determined after amplification from genomic DNA by PCR reaction (see example 3.) using cDNA derived primers with flanking 5 restriction sites. The PCR product was purified, linker sequences were digested to produce cohesice cloning sites and the fragment was subcloned into M13-vectors for sequencing. Example 3. Polvmerase chain reaction amplification of fragments of the c.5(IV) gene.
For the amplification of exon 15, oligonucleotide primers PI (5 '-CTAGAATTCGGTGAGCCTTGGTCTGCCT-3 ') and P2 (5'-CCGAAGCTTCTGGGAATCCAGGAAGGC-3') were designed to contain EcoRI and Hindlll restriction sites, respectively. The reaction was performed with a Perking-Elmer/Cetus PCR kit using 1 μg of human lymphocyte DNA as template and 25 pmol of primers according to manufacturer's recommendations. The DNA was denatured at 94° C for 10 minutes and cooling on ice for 3 minutes. After the addition of Taq polymerase, 25 cycles (denaturing at 94° C for 1.5 minutes, annealing at 55° C for 2 minutes, and extension at 72° for 2 minutes) were carried out. The amplified product was extracted with phenol/chlorophorm, digested with EcoRI and Hindlll endonucleases, and electrophoresed in NuSieve GTG low-melting-point agarose (FMC BioProducts) gel. A DNA fragment of about expected size (145 bp) was excised from the gel and subcloned into M13 vectors for sequencing.
For the comparison of normal and altered gene sequences, a 1038 bp fragment containing the exons 2 and 3 was amplified. Oligonucleotide primers P3 (5'-GACTCTAGAAAGGCC ATTGCACTGGTT-3') upstream (to the 5') from exon 3 and P4 (5'-AGCGAATTCCTGACCTGAGTCATGTAT-3') to the downstream (3') from exon 2, with Xbal and EcoRI restriction sites, respectively. The PCR reaction of 35 cycles (denaturing at 94° C for 1.5 minutes, annealing at 65 °C for 2 minutes, and extension at 72° C for 2 minutes), subcloning and sequencing were carried out as above. The sequence of the exon 3 showed a difference in a DNA sample from an Alport patient compared to normal individual's gene and an isolated genomic clone.
Example 4.
Denaturing gradient gel electrophoresis of PCR-amplified a5(YV) gene regions.
The amplified gene, fragments can be separated according to their physical properties showing base differences between samples. The amplified fragments of different individuals were separated according to melting temperatures in denaturing gradient gel electrophoresis (DGGE). The denaturing gradient gel electrophoresis was performed in 10 % polyacrylamide gels with a linerar gradient from 40 % denaturant to 75 % denaturant (100 % is 7 M urea, 40 %
v TITUTE SHEET (vol vol) formamide) at 150 V for 5 hours or 80 V overnight The gel was stained with ethidium bromide solution destained with water and photographed.

Claims

CLAIMS:
1. A process for isolating genomic DNA clones which code for the α5(IV) gene of the human type IV collagen comprising the steps of: a) labeling cDNA clone or oligonucleotide containing sequences that are derived from the cDNA coding for the human type IV collagen α5(IV) chain with radioactive or other detecteble label; b) screening a genomic library with the said DNAs or fragments thereof in order to isolate those genomic clones containing coding regions of the human type IV collagen α5(IV) chain; c) isolating the genomic clones that contain coding regions of the gene for the human type IV collagen α5(IV) chain; d) cloning the said isolated genomic clones or fragments thereof into a vector and inserting the vector into a bacterial or other host; e) sequencing said genomic clones or fragments thereof thereby identifying the isolated gene fragments which encode for the α5(IV) polypeptide chain of human type IV collagen.
2. The process of claim 1, wherein the genomic library containing clones coding for human type IV collagen α5(IV) chain comprises a human lymphocyte genomic library or any other genomic library.
3. The process of claim 1, wherein said vector cloned with the isolated gene fragments containing sequences coding for the α5(IV) chain of human type IV collagen comprises a λCharon 4A, λEMBL-3, λFix phage or any other appropriate vectors.
4. The genomic clones or gene fragments which encode for part of the α5(IV) polypeptide chain of human type IV collagen isolated by the prosess of claim 1.
5. The gene fragments which encode for part of the α5(IV) polypeptide chain of human type IV collagen identified in Figures 1 and 2.
6. A genomic clone which codes for part of the α5(IV) polypeptide chain of human type IV collagen comprising the genomic clone identified as ML-5.
7. A genomic clone which codes for part of the α5(IV) polypeptide chain of human type IV collagen comprising the genomic clone identified as MG-2.
STITUTE SHEET
8. A genomic clone which codes for part of the α5(IV) polypeptide chain of human type IV collagen comprising the genomic clone identified as EB-4.
9. A genomic clone which codes for part of the α5(IV) polypeptide chain of 5 human type IV collagen comprising the genomic clone identified as FM-13.
10. A genomic clone which codes for part of the α5(IV) polypeptide chain of human type IV collagen comprising the genomic clone identified as F-2.
10 11. A genomic clone which codes for part of the α5(IV) polypeptide chain of human type IV collagen comprising the genomic clone identified as F-7.
12. A genomic clone which codes for part of the α5(IV) polypeptide chain of human type IV collagen comprising the genomic clone identified as F-8.
15
13. A genomic clone which codes for part of the α5(IV) polypeptide chain of human type IV collagen comprising the genomic clone identified as MI_--2.
14. A process for identifying the nucleotide sequence for part of the gene coding 0 for the α5(IV) polypeptide chain of human type IV collagen comprising the steps of: a) labeling cDNA clone or oligonucleotide containing sequences that are derived from the cDNA coding for the human type IV collagen α5(IV) chain with radioactive or other detectable label; 5 b) screening a genomic library with the said DNAs or fragments thereof in order to isolate those genomic clones containing coding regions of the human type IV collagen α5(IV) chain; c) isolating the genomic clones that contain coding regions of the gene for the human type IV collagen α5(IV) chain; 0 d) cloning the said isolated genomic clones or fragments thereof into a vector for sequencing; e) sequencing the said genomic clones or fragments thereof thereby identifying the nucleotide sequence including both coding (exon) and intervening sequences (introns) of the gene for the human α5(IV) type IV collagen chain; 5 f) identifying coding (exon), intenrening (intron) and flanking sequences of the gene for the human α5(IV) type IV collagen chain by comparing the sequence with that of the cDNA; g) identifying differences between individuals' genes for the human α5(IV) type IV collagen chain by comparing said sequences.
15. The nucleotide sequence for part of the human α5(IV) type IV collagen gene identified by the process of claim 14.
16. Human DNA sequences which contain or flank the coding sequences (exons) for the human α5(IV) type IV collagen chain as shown in Figure 2.
17. Human DNA sequences which contain or flank the coding sequences (exons) for the human α5(IV) type IV collagen chain comprising a DNA sequence which have the restriction endonuclease map of the eight genomic clones as shown in Figure 1.
18. The human DNA sequence of clain 17, wherein the eight genomic clones are ML-5, MG-2, EB-4, FM-13, F-2, F-7, F-8 and ML-2.
19. A cloning vector comprising the DNA sequence of claim 15.
20. A cloning vector comprising the DNA sequence of claim 16.
21. A cloning vector comprising the DNA sequence of claim 17.
22. A method for amplifying a nucleotide sequence specific for the human gene for the α5(IV) chain of type IV collagen from biological samples containing human genomic DNA using synthetic oligonucleotide primers containing a nucleotide sequence from said gene including sequences intervening the coding regions (introns), the coding regions (exons) and flanking regions of the gene, said method comprising the following steps: a) synthesis of oligonucleotide containing nucleotide sequences wherein said oligonucleotides are specific for the gene for the α5(IV) chain of human type IV collagen and are from each or either strand of said gene; b) allowing the oligonucleotide to anneal to the specific sequences in the sample containing human genomic DNA; c) synthesizing a copy of each or either strand of the DNA by polymerase chain reaction; and d) denaturing the sample to separate DNA strands from each other.
23. A method of identifying nucleotide sequence polymerizing in the human gene
TE SHEET coding for the α5(IV) polypeptide chain of human type IV collagen, said method comprising of: a) sequencing the product of claim 22 b) separating the amplified products of claim 22 according to physical properties.
24. A method of separating amplified fragments of the human gene coding for the α5(IV) polypeptide chain of human type IV collagen according to their physical properties, said method comprising of running amplified fragements in denaturing gradient gel in order to find differences between samples from different individuals' according to melting temperatures. A method of separating amplified fragments according to their physical properties also include single strand conformation polymorphism analysis, SI nuclease mapping nucleotide sequencing or any other method known to the art
25. A method for identifying the size or the presence or absence of fragment(s) of the COL4A5 gene which comprises: a) contacting separated restriction fragments obtained from a restriction enzyme digest of DNA of an individual with one or more detectable probes comprising a portion of the squence of the COL4A5 gene; b) comparing the restriction fragment pattern so produced with a restriction fragment pattern obtained from an identical restriction enzyme digest of DNA from another individual; c) identifying the presence or variation in fragment sizes between individuals.
PCT/FI1991/000410 1990-12-28 1991-12-27 A method for determining the nucleotide sequence of the gene for the alpha5(iv) chain of human type iv collagen WO1992012163A1 (en)

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Title
DIALOG INFORMATION SERVICES, File 154, Medline 83-92, Dialog accession no. 07430990, Medline accession no. 90337990, PIHLAJANIEMI T et al.: "Complete primary structure of the triple-helical region and the carboxyl-terminal domain of a new type IV collagen chain, alpha 5(IV)"; & J BIOL CHEM, 15 Aug 1990, 265 (23), p 13758-66. *
DIALOG INFORMATION SERVICES, File 154, Medline 85-92, Dialog accession no. 07345791, Medline accession no. 90252791, MYERS J C et al.: "Molecular cloning of alpha 5(IV) collagen and assignment of the gene to the region of the X chromosome containing the Alport syndrome locus"; & AM J HUM GENET, June 1990, 46 (6), p 1024-33. *
PROC. NATL. ACAD. SCI., Vol. 87, 1990, SIRKKA LIISA HOSTIKKA et al.: "Identification of a distinct type IV collagen x chain with restricted kidney distribution and assignment of its gene to the locus of X chromosome-linked Alport syndrome", see page 1606 - page 1610. *

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