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. 1988 Sep;7(9):2687–2695. doi: 10.1002/j.1460-2075.1988.tb03122.x

The genes for the alpha 1(IV) and alpha 2(IV) chains of human basement membrane collagen type IV are arranged head-to-head and separated by a bidirectional promoter of unique structure.

E Pöschl 1, R Pollner 1, K Kühn 1
PMCID: PMC457057  PMID: 2846280

Abstract

The human basement membrane specific collagen type IV is a heterotrimer composed of two alpha 1(IV) chains and one alpha 2(IV) chain. A partial genomic EcoRI library was screened with cDNA clones representing the 5' end regions of the alpha 1(IV) and the alpha 2(IV) mRNA. A 2.2-kb genomic fragment was isolated and sequenced, which contains the 5' terminal exons of both genes located in close vicinity. The two genes were found to be arranged in opposite direction, head-to-head, separated only by a short region of 127 bp, apparently representing promoters of both genes as indicated by the existence of typical sequence motifs (CAT-box, SP1 consensus sequence). These data suggest that the alpha 1(IV) and alpha 2(IV) genes use a common, bidirectional promoter. The striking symmetrical arrangement of sequence elements within the promoter may be of basic importance for the coordination of bidirectional transcription. The promoter region had no detectable transcriptional activity in transient gene expression assays after fusion to the chloramphenicol acetylase (CAT) gene in either direction, indicating the necessity of additional elements for efficient and tissue-specific expression of both genes. Constructs containing different segments of both genes failed to identify regions with enhancing activity for the homologous collagen type IV promoter. When the heterologous HSV thymidine kinase promoter was used, a negatively acting region was identified. This indicates that the alpha 1(IV) and alpha 2(IV) promoter activity is controlled by additional regulatory elements present on distant portions of both genes.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Adams S. L., Sobel M. E., Howard B. H., Olden K., Yamada K. M., de Crombrugghe B., Pastan I. Levels of translatable mRNAs for cell surface protein, collagen precursors, and two membrane proteins are altered in Rous sarcoma virus-transformed chick embryo fibroblasts. Proc Natl Acad Sci U S A. 1977 Aug;74(8):3399–3403. doi: 10.1073/pnas.74.8.3399. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Alitalo K., Vaheri A., Krieg T., Timpl R. Biosynthesis of two subunits of type IV procollagen and of other basement membrane proteins by a human tumor cell line. Eur J Biochem. 1980 Aug;109(1):247–255. doi: 10.1111/j.1432-1033.1980.tb04790.x. [DOI] [PubMed] [Google Scholar]
  3. Babel W., Glanville R. W. Structure of human-basement-membrane (type IV) collagen. Complete amino-acid sequence of a 914-residue-long pepsin fragment from the alpha 1(IV) chain. Eur J Biochem. 1984 Sep 17;143(3):545–556. doi: 10.1111/j.1432-1033.1984.tb08404.x. [DOI] [PubMed] [Google Scholar]
  4. Beier D. R., Sledziewski A., Young E. T. Deletion analysis identifies a region, upstream of the ADH2 gene of Saccharomyces cerevisiae, which is required for ADR1-mediated derepression. Mol Cell Biol. 1985 Jul;5(7):1743–1749. doi: 10.1128/mcb.5.7.1743. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Berk A. J., Sharp P. A. Sizing and mapping of early adenovirus mRNAs by gel electrophoresis of S1 endonuclease-digested hybrids. Cell. 1977 Nov;12(3):721–732. doi: 10.1016/0092-8674(77)90272-0. [DOI] [PubMed] [Google Scholar]
  6. Blin N., Stafford D. W. A general method for isolation of high molecular weight DNA from eukaryotes. Nucleic Acids Res. 1976 Sep;3(9):2303–2308. doi: 10.1093/nar/3.9.2303. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Bonner T. I., Oppermann H., Seeburg P., Kerby S. B., Gunnell M. A., Young A. C., Rapp U. R. The complete coding sequence of the human raf oncogene and the corresponding structure of the c-raf-1 gene. Nucleic Acids Res. 1986 Jan 24;14(2):1009–1015. doi: 10.1093/nar/14.2.1009. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Bonner T. I., Oppermann H., Seeburg P., Kerby S. B., Gunnell M. A., Young A. C., Rapp U. R. The complete coding sequence of the human raf oncogene and the corresponding structure of the c-raf-1 gene. Nucleic Acids Res. 1986 Jan 24;14(2):1009–1015. doi: 10.1093/nar/14.2.1009. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Bornstein P., McKay J. The first intron of the alpha 1(I) collagen gene contains several transcriptional regulatory elements. J Biol Chem. 1988 Feb 5;263(4):1603–1606. [PubMed] [Google Scholar]
  10. Bram R. J., Lue N. F., Kornberg R. D. A GAL family of upstream activating sequences in yeast: roles in both induction and repression of transcription. EMBO J. 1986 Mar;5(3):603–608. doi: 10.1002/j.1460-2075.1986.tb04253.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Brazel D., Oberbäumer I., Dieringer H., Babel W., Glanville R. W., Deutzmann R., Kühn K. Completion of the amino acid sequence of the alpha 1 chain of human basement membrane collagen (type IV) reveals 21 non-triplet interruptions located within the collagenous domain. Eur J Biochem. 1987 Nov 2;168(3):529–536. doi: 10.1111/j.1432-1033.1987.tb13450.x. [DOI] [PubMed] [Google Scholar]
  12. Brazel D., Pollner R., Oberbäumer I., Kühn K. Human basement membrane collagen (type IV). The amino acid sequence of the alpha 2(IV) chain and its comparison with the alpha 1(IV) chain reveals deletions in the alpha 1(IV) chain. Eur J Biochem. 1988 Feb 15;172(1):35–42. doi: 10.1111/j.1432-1033.1988.tb13852.x. [DOI] [PubMed] [Google Scholar]
  13. Bächinger H. P., Fessler L. I., Fessler J. H. Mouse procollagen IV. Characterization and supramolecular association. J Biol Chem. 1982 Aug 25;257(16):9796–9803. [PubMed] [Google Scholar]
  14. Chen E. Y., Seeburg P. H. Supercoil sequencing: a fast and simple method for sequencing plasmid DNA. DNA. 1985 Apr;4(2):165–170. doi: 10.1089/dna.1985.4.165. [DOI] [PubMed] [Google Scholar]
  15. Efrat S., Hanahan D. Bidirectional activity of the rat insulin II 5'-flanking region in transgenic mice. Mol Cell Biol. 1987 Jan;7(1):192–198. doi: 10.1128/mcb.7.1.192. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Feinberg A. P., Vogelstein B. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal Biochem. 1983 Jul 1;132(1):6–13. doi: 10.1016/0003-2697(83)90418-9. [DOI] [PubMed] [Google Scholar]
  17. Finer M. H., Aho S., Gerstenfeld L. C., Boedtker H., Doty P. Unusual DNA sequences located within the promoter region and the first intron of the chicken pro-alpha 1(I) collagen gene. J Biol Chem. 1987 Sep 25;262(27):13323–13332. [PubMed] [Google Scholar]
  18. Goodbourn S., Maniatis T. Overlapping positive and negative regulatory domains of the human beta-interferon gene. Proc Natl Acad Sci U S A. 1988 Mar;85(5):1447–1451. doi: 10.1073/pnas.85.5.1447. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Gorman C. M., Moffat L. F., Howard B. H. Recombinant genomes which express chloramphenicol acetyltransferase in mammalian cells. Mol Cell Biol. 1982 Sep;2(9):1044–1051. doi: 10.1128/mcb.2.9.1044. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Greenberg M. E., Siegfried Z., Ziff E. B. Mutation of the c-fos gene dyad symmetry element inhibits serum inducibility of transcription in vivo and the nuclear regulatory factor binding in vitro. Mol Cell Biol. 1987 Mar;7(3):1217–1225. doi: 10.1128/mcb.7.3.1217. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Griffin C. A., Emanuel B. S., Hansen J. R., Cavenee W. K., Myers J. C. Human collagen genes encoding basement membrane alpha 1 (IV) and alpha 2 (IV) chains map to the distal long arm of chromosome 13. Proc Natl Acad Sci U S A. 1987 Jan;84(2):512–516. doi: 10.1073/pnas.84.2.512. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Henikoff S. Unidirectional digestion with exonuclease III creates targeted breakpoints for DNA sequencing. Gene. 1984 Jun;28(3):351–359. doi: 10.1016/0378-1119(84)90153-7. [DOI] [PubMed] [Google Scholar]
  23. Hofmann H., Fietzek P. P., Kühn K. Comparative analysis of the sequences of the three collagen chains alpha 1(I), alpha 2 and alpha 1(III) Functional and genetic aspects. J Mol Biol. 1980 Aug 15;141(3):293–314. doi: 10.1016/0022-2836(80)90182-5. [DOI] [PubMed] [Google Scholar]
  24. Horton W., Miyashita T., Kohno K., Hassell J. R., Yamada Y. Identification of a phenotype-specific enhancer in the first intron of the rat collagen II gene. Proc Natl Acad Sci U S A. 1987 Dec;84(24):8864–8868. doi: 10.1073/pnas.84.24.8864. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Hostikka S. L., Tryggvason K. Extensive structural differences between genes for the alpha 1 and alpha 2 chains of type IV collagen despite conservation of coding sequences. FEBS Lett. 1987 Nov 30;224(2):297–305. doi: 10.1016/0014-5793(87)80473-8. [DOI] [PubMed] [Google Scholar]
  26. Huerre C., Junien C., Weil D., Chu M. L., Morabito M., Van Cong N., Myers J. C., Foubert C., Gross M. S., Prockop D. J. Human type I procollagen genes are located on different chromosomes. Proc Natl Acad Sci U S A. 1982 Nov;79(21):6627–6630. doi: 10.1073/pnas.79.21.6627. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Johnston M., Davis R. W. Sequences that regulate the divergent GAL1-GAL10 promoter in Saccharomyces cerevisiae. Mol Cell Biol. 1984 Aug;4(8):1440–1448. doi: 10.1128/mcb.4.8.1440. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Junien C., Weil D., Myers J. C., Van Cong N., Chu M. L., Foubert C., Gross M. S., Prockop D. J., Kaplan J. C., Ramirez F. Assignment of the human pro alpha 2(I) collagen structural gene (COLIA2) to chromosome 7 by molecular hybridization. Am J Hum Genet. 1982 May;34(3):381–387. [PMC free article] [PubMed] [Google Scholar]
  29. Khoury G., Gruss P. Enhancer elements. Cell. 1983 Jun;33(2):313–314. doi: 10.1016/0092-8674(83)90410-5. [DOI] [PubMed] [Google Scholar]
  30. Killen P. D., Francomano C. A., Yamada Y., Modi W. S., O'Brien S. J. Partial structure of the human alpha 2(IV) collagen chain and chromosomal localization of the gene (COL4A2). Hum Genet. 1987 Dec;77(4):318–324. doi: 10.1007/BF00291418. [DOI] [PubMed] [Google Scholar]
  31. Lennard A. C., Egly J. M. The bidirectional upstream element of the adenovirus-2 major late promoter binds a single monomeric molecule of the upstream factor. EMBO J. 1987 Oct;6(10):3027–3034. doi: 10.1002/j.1460-2075.1987.tb02608.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Lovell-Badge R. H., Bygrave A., Bradley A., Robertson E., Tilly R., Cheah K. S. Tissue-specific expression of the human type II collagen gene in mice. Proc Natl Acad Sci U S A. 1987 May;84(9):2803–2807. doi: 10.1073/pnas.84.9.2803. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Luckow B., Schütz G. CAT constructions with multiple unique restriction sites for the functional analysis of eukaryotic promoters and regulatory elements. Nucleic Acids Res. 1987 Jul 10;15(13):5490–5490. doi: 10.1093/nar/15.13.5490. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Mlodzik M., Gehring W. J. Expression of the caudal gene in the germ line of Drosophila: formation of an RNA and protein gradient during early embryogenesis. Cell. 1987 Feb 13;48(3):465–478. doi: 10.1016/0092-8674(87)90197-8. [DOI] [PubMed] [Google Scholar]
  35. Nader W. F., Edlind T. D., Huettermann A., Sauer H. W. Cloning of Physarum actin sequences in an exonuclease-deficient bacterial host. Proc Natl Acad Sci U S A. 1985 May;82(9):2698–2702. doi: 10.1073/pnas.82.9.2698. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Oberbäumer I. New pUC-derived expression vectors for rapid construction of cDNA libraries. Gene. 1986;49(1):81–91. doi: 10.1016/0378-1119(86)90387-2. [DOI] [PubMed] [Google Scholar]
  37. Oberbäumer I., Wiedemann H., Timpl R., Kühn K. Shape and assembly of type IV procollagen obtained from cell culture. EMBO J. 1982;1(7):805–810. doi: 10.1002/j.1460-2075.1982.tb01251.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Osley M. A., Gould J., Kim S., Kane M. Y., Hereford L. Identification of sequences in a yeast histone promoter involved in periodic transcription. Cell. 1986 May 23;45(4):537–544. doi: 10.1016/0092-8674(86)90285-0. [DOI] [PubMed] [Google Scholar]
  39. Overbeek P. A., Merlino G. T., Peters N. K., Cohn V. H., Moore G. P., Kleinsmith L. J. Characterization of five members of the actin gene family in the sea urchin. Biochim Biophys Acta. 1981 Dec 28;656(2):195–205. doi: 10.1016/0005-2787(81)90087-3. [DOI] [PubMed] [Google Scholar]
  40. Pihlajaniemi T., Tryggvason K., Myers J. C., Kurkinen M., Lebo R., Cheung M. C., Prockop D. J., Boyd C. D. cDNA clones coding for the pro-alpha1(IV) chain of human type IV procollagen reveal an unusual homology of amino acid sequences in two halves of the carboxyl-terminal domain. J Biol Chem. 1985 Jun 25;260(12):7681–7687. [PubMed] [Google Scholar]
  41. Rosenfeld P. J., Kelly T. J. Purification of nuclear factor I by DNA recognition site affinity chromatography. J Biol Chem. 1986 Jan 25;261(3):1398–1408. [PubMed] [Google Scholar]
  42. Rosenthal N. Identification of regulatory elements of cloned genes with functional assays. Methods Enzymol. 1987;152:704–720. doi: 10.1016/0076-6879(87)52075-4. [DOI] [PubMed] [Google Scholar]
  43. Rossi P., Karsenty G., Roberts A. B., Roche N. S., Sporn M. B., de Crombrugghe B. A nuclear factor 1 binding site mediates the transcriptional activation of a type I collagen promoter by transforming growth factor-beta. Cell. 1988 Feb 12;52(3):405–414. doi: 10.1016/s0092-8674(88)80033-3. [DOI] [PubMed] [Google Scholar]
  44. Rossi P., de Crombrugghe B. Identification of a cell-specific transcriptional enhancer in the first intron of the mouse alpha 2 (type I) collagen gene. Proc Natl Acad Sci U S A. 1987 Aug;84(16):5590–5594. doi: 10.1073/pnas.84.16.5590. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Rossouw C. M., Vergeer W. P., du Plooy S. J., Bernard M. P., Ramirez F., de Wet W. J. DNA sequences in the first intron of the human pro-alpha 1(I) collagen gene enhance transcription. J Biol Chem. 1987 Nov 5;262(31):15151–15157. [PubMed] [Google Scholar]
  46. Sanger F., Coulson A. R., Barrell B. G., Smith A. J., Roe B. A. Cloning in single-stranded bacteriophage as an aid to rapid DNA sequencing. J Mol Biol. 1980 Oct 25;143(2):161–178. doi: 10.1016/0022-2836(80)90196-5. [DOI] [PubMed] [Google Scholar]
  47. Schibler U., Sierra F. Alternative promoters in developmental gene expression. Annu Rev Genet. 1987;21:237–257. doi: 10.1146/annurev.ge.21.120187.001321. [DOI] [PubMed] [Google Scholar]
  48. Schwarz-Magdolen U., Oberbäumer I., Kühn K. cDNA and protein sequence of the NC1 domain of the alpha 2-chain of collagen IV and its comparison with alpha 1(IV). FEBS Lett. 1986 Nov 24;208(2):203–207. doi: 10.1016/0014-5793(86)81018-3. [DOI] [PubMed] [Google Scholar]
  49. Schwarz U., Schuppan D., Oberbäumer I., Glanville R. W., Deutzmann R., Timpl R., Kühn K. Structure of mouse type IV collagen. Amino-acid sequence of the C-terminal 511-residue-long triple-helical segment of the alpha 2(IV) chain and its comparison with the alpha 1(IV) chain. Eur J Biochem. 1986 May 15;157(1):49–56. doi: 10.1111/j.1432-1033.1986.tb09636.x. [DOI] [PubMed] [Google Scholar]
  50. Soininen R., Haka-Risku T., Prockop D. J., Tryggvason K. Complete primary structure of the alpha 1-chain of human basement membrane (type IV) collagen. FEBS Lett. 1987 Dec 10;225(1-2):188–194. doi: 10.1016/0014-5793(87)81155-9. [DOI] [PubMed] [Google Scholar]
  51. Timpl R., Wiedemann H., van Delden V., Furthmayr H., Kühn K. A network model for the organization of type IV collagen molecules in basement membranes. Eur J Biochem. 1981 Nov;120(2):203–211. doi: 10.1111/j.1432-1033.1981.tb05690.x. [DOI] [PubMed] [Google Scholar]
  52. Trüeb B., Gröbli B., Spiess M., Odermatt B. F., Winterhalter K. H. Basement membrane (type IV) collagen is a heteropolymer. J Biol Chem. 1982 May 10;257(9):5239–5245. [PubMed] [Google Scholar]
  53. Weil D., Mattei M. G., Passage E., N'Guyen V. C., Pribula-Conway D., Mann K., Deutzmann R., Timpl R., Chu M. L. Cloning and chromosomal localization of human genes encoding the three chains of type VI collagen. Am J Hum Genet. 1988 Mar;42(3):435–445. [PMC free article] [PubMed] [Google Scholar]
  54. Wood W. I., Gitschier J., Lasky L. A., Lawn R. M. Base composition-independent hybridization in tetramethylammonium chloride: a method for oligonucleotide screening of highly complex gene libraries. Proc Natl Acad Sci U S A. 1985 Mar;82(6):1585–1588. doi: 10.1073/pnas.82.6.1585. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Wyman A. R., Wertman K. F., Barker D., Helms C., Petri W. H. Factors which equalize the representation of genome segments in recombinant libraries. Gene. 1986;49(2):263–271. doi: 10.1016/0378-1119(86)90287-8. [DOI] [PubMed] [Google Scholar]
  56. Wyman A. R., Wolfe L. B., Botstein D. Propagation of some human DNA sequences in bacteriophage lambda vectors requires mutant Escherichia coli hosts. Proc Natl Acad Sci U S A. 1985 May;82(9):2880–2884. doi: 10.1073/pnas.82.9.2880. [DOI] [PMC free article] [PubMed] [Google Scholar]
  57. Yurchenco P. D., Furthmayr H. Self-assembly of basement membrane collagen. Biochemistry. 1984 Apr 10;23(8):1839–1850. doi: 10.1021/bi00303a040. [DOI] [PubMed] [Google Scholar]

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