Duplication and distribution of repetitive elements and non-unique regions in the human genome

Gene

Volumn 205, Issue 1-2, 1997, Pages 29-38

  Mazzarella, Richard ^a   Schlessinger, David ^a,b  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b NATIONAL INSTITUTE ON AGING   (United States)

Author keywords

Alu; Duplication; L1; Repetitive elements; X chromosome

Indexed keywords

REPETITIVE DNA;

CHROMOSOME MAP; CONFERENCE PAPER; COSMID; DNA SEQUENCE; GENE CLUSTER; GENE DUPLICATION; GENE INSERTION; GENE MAPPING; GENE SEQUENCE; GENETIC DISORDER; GENETIC RECOMBINATION; GENOME; HUMAN; HUMAN CELL; PRIORITY JOURNAL; TELOMERE; X CHROMOSOME;

GENETIC DISEASES, INBORN; GENOME, HUMAN; HUMANS; MULTIGENE FAMILY; REPETITIVE SEQUENCES, NUCLEIC ACID;

EID: 0031593215     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1119(97)00477-0     Document Type: Conference Paper

References (75)

1. Acampora, D., D'Esposito, M., Faiella, A., Pannese, M., Migliaccio, E., Morelli, F., Stornaiuolo, A., Nigro, V., Simeone, A., Boncinelli, E., 1989. The human HOX family. Nucleic Acids Res. 17, 10385-10402.
2. Antignac, C., Arduy, C.H., Beckmann, J.S., Benessy, F., Gros, F., Medhioub, M., Hildebrandt, F., Dufier, J.L., Kleinknecht, C., Broyer, M., Weissenbach, J., Habib, R., Cohen, D., 1993. A gene for familial juvenile nephronophthisis (recessive medullary cystic kidney disease) maps to chromosome 2p. Nat. Genet. 3, 342-345.
3. Arveiler, B., Porteus, D.J., 1992. Distribution of Alu and L1 in human YAC recombinants. Mammal. Gen. 3, 661-668.
4. Ballabio, A., Bardoni, B., Guioli, S., Basler, E., Camerino, G., 1990. Two families of low-copy number repeats are interspersed on Xp22.3: implications for the high frequency of deletions in this region. Genomics 8, 263-270.
5. Bernardi, G., 1995. The human genome: organization and evolutionary history. Annu. Rev. Genet. 29, 445-476.
6. Boer, P.H., Adra, C.N., Lau, Y.F., McBurney, M.W., 1987. The testisspecific phosphoglycerate kinase gene pgk-2 is a recruited retroposon. Mol. Cell Biol. 7, 3107-3112.
7. Bondeson, M.L., Dahl, N., Malmgren, H., Kleijer, W.J., Tonnesen, T., Carlberg, B.M., Pettersson, U., 1995b. Inversion of the IDS gene resulting from recombination with IDS-related sequences is a common cause of the Hunter syndrome. Hum. Mol. Genet. 4, 615-621.
8. Bondeson, M.L., Malmgren, H., Dahl, N., Carlberg, B.M., Pettersson, U., 1995a. Presence of an IDS-related locus (IDS2) in Xq28 complicates the mutational analysis of Hunter syndrome. Eur. J. Hum. Genet. 3, 219-227.
9. Bonetta, L., Juehn, S.E., Huang, A., Law, D.J., Kalikin, L.M., Koi, M., Reeve, A.E., Brownstein, B.H., Yeger, H., Williams, B.R.G., Feinberg, A.P., 1990. Wilms tumore locus on 11013 defined by multiple CpG island-associated transcripts. Science 250, 994-997.
10. Botto, M., Fong, K.Y., So, A.K., Barlow, R., Routier, R., Moreley, B.J., Walport, M.J., 1992. Homozygous hereditary C3 deficiency due to a partial gene deletion. Proc. Natl. Acad. Sci. USA 89, 4957-4961.
11. Cattanach, B.M., Beechey, C.V., 1990. Autosomal and X-chromosome imprinting. Development Suppl., 63-72.
12. Chang, P.L., Mueller, O.T., Lafrenie, R.M., Varey, P.A., Rosa, N.E., Davidson, R.G., Henry, W.M., Shows, T.B., 1990. The human arylsulfatase-C isoenzymes: two distinct genes that escape from X inactivation. Am. J. Hum. Genet. 46, 729-737.
13. Chen, E.Y., Liao, Y.-C., Smith, D.H., Barrera-Saldana, H.A., Gelinas, R.E., Seeburg, P., 1989. The human growth hormone locus: nucleotide sequence, biology, and evolution. Genomics 4, 479-497.
14. Chen, E.Y., Zollo, M., Mazzarella, R., Ciccodicola, A., Chen, C., Zuo, L., Heiner, C., Burough, F., Repetto, M., Schlessinger, D., D'Urso, M., 1996. Long range sequence analysis in Xq28: thirteen known and six candidate genes in 219.4 kb of high GC DNA between the RCP/GCP and G6PD loci. Hum. Molec. Genet. 5, 659-668.
15. Crackower, M.A., Scherer, S.W., Rommens, J.M., Hui, C.C., Poorkaj, P., Soder, S., Cobben, J.M., Hudgins, L., Evans, J.P., Tsui, L.-C., 1996. Characterization of the split hand/split foot malformation locus SHGM1 at 7q21.3-q22.1 and analysis of a candidate gene for its expression during limb development. Hum. Mol. Genet. 5, 571-579.
16. Deeb, S.S., Lindsey, D.T., Hibiya, Y., Sanocki, E., Winderickx, J., Teller, D.Y., Motulsky, A.G., 1992. Genotype-phenotype relation-ships in human red/green color-vision defects: molecular and psychophysical studies. Am. J. Hum. Genet. 51, 687-700.
17. Eichler, E.E., Lu, F., Shen, Y., Antonacci, R., Jurecic, V., Doggett, N.A., Moyzis, R.K., Baldini, A., Gibbs, R.A., Nelson, D.L., 1996. Duplication of a gene-rich cluster between 16p11.1 and Xq28: a novel pericentromeric-directed mechanism for paralogous genome evolution. Hum. Mol. Genet. 5, 899-912.
18. Eyal, N., Wilder, S., Horowitz, M., 1990. Prevalent and rare mutations among Gaucher patients. Gene 96, 277-283.
19. Filatov, L., Mamaeva, S., Tomilin, N., 1987. Non-random distribution of Alu family DNA repeats in human chromosomes. Mol. Biol. Rep. 12, 117-121.
20. Flint, J., Harding, R.M., Clegg, J.B., Boyce, A.J., 1993. Why are some genetic diseases common? Distinguishing selection from other processes by molecular analysis of globin gene variants. Hum. Genet. 91, 91-117.
21. Frippiat, J.P., Williams, S.C., Tomlinson, I.M., Cook, G.P., Cherif, D., LePaslier, D., Collins, J.E., Dunham, I., Winter, G., Lefranc, M.P., 1995. Organization of the human immunoglobulin lambda light-chain locus on chromosome 22q11.2. Hum. Molec. Genet. 4, 983-991.
22. Gardiner, K., Aissani, B., Bernardi, G., 1990. A compositional map of human chromosome 21. EMBO J. 9, 1853-1858.
23. Grimsby, J., Chen, K., Wang, L.J., Lan, N.C., Shih, J.C., 1991. Human monoamine oxidase A and B genes exhibit identical exon-intron organization. Proc. Natl. Acad. Sci. USA 88, 3637-3641.
24. Harris, P.C., Ward, C.J., Peral, B., Hughes, J., 1995. Autosomal dominant polycystic kidney disease: molecular analysis. Hum. Mol. Genet. 4, 1745-1749.
25. Henco, K., Brosius, J., Fujisawa, A., Fujisawa, J.-I., Haynes, J.R., Hochstadt, J., Kovacic, T., Pasek, M., Schambock, A., Schmid, J., Todokoro, K., Walchli, M., Nagata, S., Weissmann, C., 1985. Structural relationship of human interferon alpha genes and pseudogenes. J. Mol. Biol. 185, 227-260.
26. Hood, L., Rowen, L., Koop, B.F., 1995. Human and mouse T-cell receptor loci: genomics, evolution, diversity and serendipity. Ann. NY Acad. Sci. 758, 390-412.
27. Hori, T., Tomatsu, S., Nakashima, Y., Uchiyama, A., Fukuda, S., Sukegawa, K., Shimozawa, N., Suzuki, Y., Kondo, N., Horiuchi, T. et al., 1995. Mucopolysaccharidosis type IVA; common double deletion in the N-acetylgalactosamine-6-sulfatase gene (GALNS). Genomics 26, 535-542.
28. Huber, R., Crisponi, L., Mazzarella, R., Chen, C.-N., Su, Y., Shizua, H., Chen, E., Cao, A., Pilia, G., 1997. Analysis of exon/intron structure and 400 kb of genomic sequence surrounding the 5′-promoter and 3′-terminal ends of the human glypican 3 (GPC3) gene. Genomics, 45, in press.
29. Hunkapillar, T., Hood, L., 1989. Diversity of the immunoglobulin gene superfamily. Adv. Immunol. 44, 1-63.
30. Huxley, C., Fried, M., 1990. The mouse surfeit locus contains a cluster of six genes associated with four CpG-rich islands in 32 kilobases of genomic DNA. Mol. Cell. Biol. 10, 605-614.
31. Jurka, J., Klonowski, P., Dagman, V., Pelton, P., 1996. CENSOR -a program for identification and elimination of repetitive elements from DNA sequences. Computers and Chemistry 20 (No. 1), 119-122.
32. Kapitonov, V., Jurka, J., 1996. The age of Alu subfamilies. J. Mol. Evol. 42, 59-65.
33. Kasahara, M., Nakaya, J., Satta, Y., Takahata, N., 1997. Chromosomal duplication and the emergence of the adaptive immune system. Trends Genet. 13, 90-92.
34. Konrad, M., Saunier, S., Heidet, L., Silbermann, F., Benessy, F., Calado, J., Le Paslier, D., Broyer, M., Gubler, M.-C., Antignac, C., 1996. Large homozygous deletions of the 2q13 region are a major cause of juvenile nephronophthisis. Hum. Mol. Genet. 3, 367-371.
35. Koop, B.F., Siemieniak, D., Slightom, J.L., Goodman, M., Dunbar, J., Wright, P.C., Simons, E.L., 1989. Tarsius delta- and beta-globin genes: conversions, evolution, and systematic implications. J. Biol. Chem. 264, 68-79.
36. Korenberg, J.R., Rykowski, M.C., 1988. Human genome organization: Alu, lines, and molecular structure of metaphase chromosome bands. Cell 53, 391-400.
37. Kricker, M.C., Drake, J.W., Radman, M., 1992. Duplication-targeted DNA methylation and mutagenesis in the evolution of eukaryotic chromosomes. Proc. Natl. Acad. Sci. USA 89, 1075-1079.
38. Kvaløy, K., Galvagni, F., Brown, W.R.A., 1994. The sequence organization of the long arm pseudoautosomal region of the human sex chromosomes. Hum. Molec. Genet. 3, 771-778.
39. Lakich, D., Kazazian, H.H., Antonarakis, S.E., Gitschier, J., 1993. Inversions disrupting the factor VIII gene are a common cause of severe haemophilia A. Nat. Genet. 5, 236-241.
40. Larsen, F., Solheim, J., Kristensen, T., Kolsto, A.B., Prydz, H., 1993. A tight cluster of five unrelated human genes on chromosome 16q22.1. Hum. Mol. Genet. 2, 1589-1595.
41. Ledbetter, D.H., Engel, E., 1995. Uniparental disomy in humans: development of an imprinting map and its implications for prenatal diagnosis. Hum. Mol. Genet. 4, 1757-1764.
42. Lehrman, M.A., Russell, D.W., Goldstein, J.L., Brown, M.S., 1986. Exon-Alu recombination deletes 5 kilobases from the low density lipoprotein receptor gene, producing a null phenotype in familial hypercholesterolemia. Proc. Natl. Acad. Sci. USA 83, 3679-3683.
43. Levinson, B., Kenwrick, S., Gamel, P., Fisher, K., Gitschier, J., 1992. Evidence for a third transcript from the human factor VIII gene. Genomics 14, 585-589.
44. Levinson, B., Kenwrick, S., Lakich, D., Hammonds, G., Gitschier, J., 1990. A transcribed gene in an intron of the human factor VIII gene. Genomics 7, 1-11.
45. Li, M., Yen, P.H., Shapiro, L.J., 1992. Characterization of a low copy repetitive element S232 involved in the generation of frequent deletions of the distal short arm of the human X chromosome. Nucleic Acids Res. 20, 1117-1122.
46. Miller, A.P., Gustashaw, K., Wolff, D.J., Rider, S.H.J., Monaco, A.P., Eble, B., Schlessinger, D., Gorski, J.L., van Ommen, G.-J., Weissenbach, J., Willard, H.F., 1995. Three genes that escape X chromosome inactivation are clustered within a 6 Mb YAC contig and STS map in Xp11.21-p11.22. Hum. Mol. Genet. 4, 731-739.
47. Muscatelli, F., Walker, A.P., De Plaen, E., Stafford, A.N., Monaco, A.P., 1995. Isolation and characterization of a MAGE gene family in the Xp21.3 region. Proc. Natl. Acad. Sci. USA 92, 4987-4991.
48. Nagaraja, R., MacMillan, S., Kere, J., Jones, C., Griffin, S., Schmatz, M., Terell, J., Shomaker, M., Jermak, C., Hott, C., Masisi, M., Mumm, S., Srivastava, A., Pilia, G., Featherstone, T., Mazzarella, R., Kesterson, S., McCauley, B., Railey, B., Burough, F., Nowotny, V., D'Urso, M., States, D., Brownstein, B., Schlessinger, D., 1997. X chromosome map at 75-kb STS resolution, revealing extremes of recombination and GC content. Genome Res. 7, 210-222.
49. Nathans, J., Merbs, S.L., Sung, C.H., Weitz, C.J., Wang, Y., 1992. Molecular genetics of human visual pigments. Ann. Rev. Genet. 26, 403-424.
50. Naylor, J., Brinke, A., Hassock, S., Green, P.M., Giannelli, F., 1993. Characteristic mRNA abnormality found in half the patients with severe haemophilia A is due to large DNA inversions. Hum. Mol. Genet. 2, 1773-1778.
51. Naylor, J.A., Buck, D., Green, P., Williamson, H., Bentley, D., Giannelli, F., 1995. Investigation of the factor VIII intron 22 repeated region (int22h) and the associated inversion junctions. Hum. Mol. Genet. 4, 1217-1224.
52. Neitz, M., Neitz, J., 1995. Numbers and ratios of visual pigment genes for normal red-green color vision. Science 267, 1013-1016.
53. Nickerson, E., Greenberg, F., Keating, M.T., McCaskill, C., Shaffer, L.G., 1995. Deletions of the elastin gene at 7q11.23 occur in approximately 90% of patients with Williams syndrome. Am. J. Hum. Genet. 56, 1156-1161.
54. Ohno, S., 1970. Evolution by Gene Duplication. Springer, New York, 150 pp.
55. Ohta, K., Mizutani, A., Kawakami, A., Murakami, Y., Kasuya, Y., Takagi, S., Tanaka, H., Fujisawa, H., 1995. Plexin: a novel neuronal cell surface molecule that mediates cell adhesion via a homophilic binding mechanism in the presence of calcium ions. Neuron 14, 1189-1199.
56. Osborne, L.R., Duane Martindale, D., Scherer, S.W., Shi, X.-M., Huizenga, J., Heng, H.H.Q., Costa, T., Pober, B., Lew, L., Brinkman, J., Rommens, J.M., Koop, B., Tsui, L.-C., 1996. Identification of genes from a 500 kb region at 7q11.23 that is commonly deleted in Williams syndrome. Genomics 36, 328-336.
57. Poorkaj, P., Soder, S., Cobben, J.M., Hudgins, L., Evans, J.P., Tsui, L.-C., 1996. Characterization of the split hand/split foot malformation locus SHGM1 at 7q21.3-q22.1 and analysis of a candidate gene for its expression during limb development. Hum. Mol. Genet. 5, 571-579.
58. Porta, G., MacMillan, S., Nagaraja, R., Mumm, S., Zucchi, I., Pilia, G., Maio, S., Featherstone, T., Schlessinger, D., 1997. 4.5 Mb YAC/ STS contig at 50 kb resolution, spanning Xq25 deletions in two patients with lymphoproliferative syndrome (LYP). Genome Res. 7, 27-36.
59. Porta, G., Zucchi, I., Hillier, L., Green, P., Nowotny, V., D'Urso, M., Schlessinger, D., 1993. Alu and L1 sequence distribution in Xq24-q28, and their comparative utility in YAC contig assembly and verification. Genomics 16, 417-425.
60. Powell, C.M., Taggart, R.T., Drumheller, T.C., Wangsa, D., Qian, C., Nelson, L.M., White, B.J., 1994. Molecular and cytogenetic studies of an X'autosome translocation in a patient with premature ovarian failure and review of the literature. Am. J. Med. Genet. 52, 19-26.
61. Reiter, L.T., Murakami, T., Koeuth, T., Pentao, L., Muzny, D.M., Gibbs, R.A., Lupski, J.R., 1996. A recombination hotspot responsible for two inherited peripheral neuropathies is located near a mariner transposon-like element. Nat. Genet. 12, 288-297.
62. Robinson, W.P., Waslynka, J., Bernasconi, F., Wang, M., Clark, S., Kotzot, D., Schinzel, A., 1996. Delineation of 7q11.2 deletions associated with Williams-Beuren Syndrome and mapping of a repetitive sequence to within and to either side of the common deletion. Genomics 34, 17-23.
63. Rothenfluh, H.S., Blanden, R.V., Steele, E.J., 1995. Evolution of V genes: DNA sequence structure and functional germline genes and pseudogenes. Immunogenetics 42, 159-171.
64. Saccone, S., Caccio, S., Kusuda, J., Andreozzi, L., Bernardi, G., 1996. Identification of the gene-richest bands in human chromosomes. Gene 174, 85-94.
65. Scherer, S.W., 1996. Duplication of DNA and disease. Mol. Med. Today 2, 187
66. Simeone, A., Acampora, D., Arcioni, L., Andrews, P.W., Boncinelli, E., Mavilio, F., 1990. Sequential activation of HOX2 homeobox genes by retinoic acid in human embryonal carcinoma cells. Nature 346, 763-766.
67. Small, K., Iber, J., Warren, S.T., 1997. Emerin deletion reveals a common X-chromosome inversion mediated by inverted repeats. Nat. Genet. 16, 96-99.
68. Smit, A.F.A., 1996. The origin of interspersed repeats in the human genome. Curr. Opin. Genet. Dev. 6, 743-748.
69. Soriano, P., Meunier-Rotival, M., Bernardi, G., 1983. The distribution of interspersed repeats is nonuniform and conserved in the mouse and human genomes. Proc. Natl. Acad. Sci. USA 80, 1816-1820.
70. Taussig, M.J., 1988. Molecular genetics of immunoglobulins. Immunol. Suppl. 1, 7-15.
71. Timms, K.M., Lu, F., Shen, Y., Pierson, C.A., Muzny, D.M., Gu, Y., Nelson, D.L., Gibbs, R.A., 1995. 130 kb of DNA sequence reveals two new genes and a regional duplication distal to the human iduronate-2-sulfate sulfatase locus. Genome Res. 5, 71-78.
72. Trowsdale, J., 1993. Genome structure and function in the MHC. Trends Genet. 9, 117-122.
73. Tuddenham, E.G., Schwaab, R., Seehafer, J., Millar, D.S., Gitschier, J., Higuchi, M., Bidichandani, S., Connor, J.M., Hoyer, L.W., Yoshioka, A., Peake, I.R., Olek, K., Kazazian, H.H., Lavergne, J.-M., Gianelli, F., Antonarakis, S.E., Cooper, D.N., 1994. Haemophilia A: database of nucleotide substitutions, deletions, insertions and rearrangements of the factor VIII gene, second edition. Nucleic Acids Res. 22, 3511-3533 (corrected: NAR 22, 4851-4868).
74. Zerial, M., Salinas, J., Filipski, J., Bernardi, G., 1986. Gene distribution and nucleotide sequence organization in the human genome. Eur. J. Biochem. 160, 479-485.
75. Zollo, M., Mazzarella, R., Bione, S., Toniolo, D., Schlessinger, D., D'Urso, M., Chen, E.Y., 1995. Sequence and gene content in 52 kb including and centromeric to the G6PD gene in Xq28. DNA Seq. 6, 1-11.