The DNA sequence of the human X chromosome

Nature

Volumn 434, Issue 7031, 2005, Pages 325-337

  Ross, Mark T ^a   Grafham, Darren V ^a   Coffey, Alison J ^a   Scherer, Steven ^b   McLay, Kirsten ^a   Muzny, Donna ^b   Platzer, Matthias ^c   Howell, Gareth R ^a   Burrows, Christine ^a   Bird, Christine P ^a   Prankish, Adam ^a   Lovell, Frances L ^a   Howe, Kevin L ^a   Ashurst, Jennifer L ^a   Fulton, Robert S ^d   Sudbrak, Ralf ^e,f   Wen, Gaiping ^c   Jones, Matthew C ^a   Hurles, Matthew E ^a   Andrews, T Daniel ^a   Scott, Carol E ^a   Searle, Stephen ^a   Ramser, Juliane ^g   Whittaker, Adam ^a   Deadman, Rebecca ^a   Carter, Nigel P ^a   Hunt, Sarah E ^a   Chen, Rui ^b   Cree, Andrew ^b   Gunaratne, Preethi ^b   Havlak, Paul ^b   Hodgson, Anne ^b   Metzker, Michael L ^b   Richards, Stephen ^b   Scott, Graham ^b   Steffen, David ^b   Sodergren, Erica ^b   Wheeler, David A ^b   Worley, Kim C ^b   Alnscough, Rachael ^a   Ambrose, Kerrie D ^a   Ansari Lari, M Ali ^b   Aradhya, Swaroop ^b   Ashwell, Robert I S ^a   Babbage, Anne K ^a   Bagguley, Claire L ^a   Ballabio, Andrea ^b   Banerjee, Ruby ^a   Barker, Gary E ^a   Barlow, Karen F ^a   Barrett, Ian P ^a   Bates, Karen N ^a   Beare, David M ^a   Beasley, Helen ^a   Beasley, Oliver ^a   Beck, Alfred ^e   Bethel, Graeme ^a   Blechschmidt, Karin ^c   Brady, Nicola ^a   Bray Allen, Sarah ^a   Bridgeman, Anne M ^a   Brown, Andrew J ^a   Brown, Mary J ^b   Bonnin, David ^b   Bruford, Elspeth A ^h   Buhay, Christian ^b   Burch, Paula ^b   Burford, Deborah ^a   Burgess, Joanne ^a   Burrill, Wayne ^a   Burton, John ^a   Bye, Jackie M ^a   Carder, Carol ^a   Carrel, Laura ⁱ   Chako, Joseph ^b   Chapman, Joanne C ^a   Chavez, Dean ^b   Chen, Ellson ^j   Chen, Guan ^b   Chen, Yuan ^k   Chen, Zhijian ^b   Chinault, Craig ^b   Ciccodicola, Alfredo ^l   Clark, Sue Y ^a   Clarke, Graham ^a   Clee, Chris M ^a   Clegg, Sheila ^a   Clerc Blankenburg, Kerstin ^b   Clifford, Karen ^a   Cobley, Vicky ^a   Cole, Charlotte G ^a   Conquer, Jen S ^a   Corby, Nicole ^a   Connor, Richard E ^a   David, Robert ^b   Davies, Joy ^a   Davis, Clay ^b   Davis, John ^a   Delgado, Oliver ^b   DeShazo, Denise ^b   Dhami, Pawandeep ^a   Ding, Yan ^b   Dinh, Huyen ^b   Dodsworth, Steve ^a   Draper, Heather ^b   Dugan Rocha, Shannon ^b   Dunham, Andrew ^a   Dunn, Matthew ^a   Durbin, K James ^b   Dutta, Ireena ^a   Eades, Tamsin ^a   Ellwood, Matthew ^a   Emery Cohen, Alexandra ^b   Errington, Helen ^a   Evans, Kathryn L ^m   Faulkner, Louisa ^a   Francis, Fiona ⁿ   Frankland, John ^a   Fraser, Audrey E ^a   Galgoczy, Petra ^c   Gilbert, James ^a   Gill, Rachel ^b   Glöckner, Gernot ^c   Gregory, Simon G ^a   Gribble, Susan ^a   Griffiths, Coline ^a   Grocock, Russell ^a   Gu, Yanghong ^b   Gwilliam, Rhian ^a   Hamilton, Cerissa ^b   Hart, Elizabeth A ^a   Hawes, Alicia ^b   Heath, Paul D ^a   Heitmann, Katja ^e   Hennig, Steffen ^e   Hernandez, Judith ^b   Hinzmann, Bernd ^c   Ho, Sarah ^a   Hoffs, Michael ^a   Howden, Phillip J ^a   Huckle, Elizabeth J ^a   Hume, Jennifer ^b   Hunt, Paul J ^a   Hunt, Adrienne R ^a   Isherwood, Judith ^a   Jacob, Leni ^b   Johnson, David ^a   Jones, Sally ^b   De Jong, Pieter J ^o   Joseph, Shirin S ^a   Keenan, Stephen ^a   Kelly, Susan ^b   Kershaw, Joanne K ^a   Khan, Ziad ^b   Kloschis, Petra ^p   Klages, Sven ^e   Knights, Andrew J ^a   Kosiura, Anna ^e   Kovar Smith, Christie ^b   Laird, Gavin K ^a   Langford, Cordelia ^a   Lawlor, Stephanie ^a   Leversha, Margaret ^a   Lewis, Lora ^b   Liu, Wen ^b   Lloyd, Christine ^a   Lloyd, David M ^a   Loulseged, Hermela ^b   Loveland, Jane E ^a   Lovell, Jamieson D ^a   Lozado, Ryan ^b   Lu, Jing ^b   Lyne, Rachael ^a   Ma, Jie ^b   Maheshwari, Manjula ^b   Matthews, Lucy H ^a   McDowall, Jennifer ^a   McLaren, Stuart ^a   McMurray, Amanda ^a   Meidl, Patrick ^a   Meitinger, Thomas ^q   Milne, Sarah ^a   Miner, George ^b   Mistry, Shailesh L ^a   Morgan, Margaret ^b   Morris, Sidney ^b   Müller, Ines ^e,r   Mullikin, James C ^s   Nguyen, Ngoc ^b   Nordsiek, Gabriele ^c   Nyakatura, Gerald ^c   O'Dell, Christopher N ^a   Okwuonu, Geoffery ^b   Palmer, Sophie ^a   Pandian, Richard ^a   Parker, David ^b   Parrish, Julia ^b   Pasternak, Shiran ^b   Patel, Dina ^a   Pearce, Alex V ^a   Pearson, Danita M ^a   Pelan, Sarah E ^a   Perez, Lesette ^b   Porter, Keith M ^a   Ramsey, Yvonne ^a   Reichwald, Kathrin ^c   Rhodes, Susan ^a   Ridler, Kerry A ^a   Schlessinger, David ^t   Schueler, Mary G ^s   Sehra, Harminder K ^a   Shaw Smith, Charles ^a   Shen, Hua ^b   Sheridan, Elizabeth M ^a   Shownkeen, Ratna ^a   Skuce, Carl D ^a   Smith, Michelle L ^a   Sotheran, Elizabeth C ^a   Steingruber, Helen E ^a   Steward, Charles A ^a   Storey, Roy ^a   Swann, R Mark ^a   Swarbreck, David ^a   Tabor, Paul E ^b   Taudien, Stefan ^c   Taylor, Tineace ^b   Teague, Brian ^b   Thomas, Karen ^a   Thorpe, Andrea ^a   Timms, Kirsten ^b   Tracey, Alan ^a   Trevanion, Steve ^a   Tromans, Anthony C ^a   D'Urso, Michele ^l   Verduzco, Daniel ^b   Villasana, Donna ^b   Waldron, Lenee ^b   Wall, Melanie ^a   Wang, Qiaoyan ^b   Warren, James ^b   Warry, Georgina L ^a   Wei, Xuehong ^b   West, Anthony ^a   Whitehead, Siobhan L ^a   Whiteley, Mathew N ^a   Wilkinson, Jane E ^a   Willey, David L ^a   Williams, Gabrielle ^b   Williams, Leanne ^a   Williamson, Angela ^b   Williamson, Helen ^a   Wilming, Laurens ^a   Woodmansey, Rebecca L ^a   Wray, Paul W ^a   Yen, Jennifer ^b   Zhang, Jingkun ^b   Zhou, Jianling ^b   Zoghbi, Huda ^b   Zorilla, Sara ^b   Buck, David ^a   Reinhardt, Richard ^e   Poustka, Annemarie ^p   Rosenthal, André ^c   Lehrach, Hans ^e   Meindl, Alfons ^g   Minx, Patrick J ^d   Hillier, LaDeana W ^d   Willard, Huntington F ^u   Wilson, Richard K ^d   Waterston, Robert H ^d   Rice, Catherine M ^a   Vaudin, Mark ^a   Coulson, Alan ^a   Nelson, David L ^b   Weinstock, George ^b   Sulston, John E ^a   Durbin, Richard ^a   Hubbard, Tim ^a   Gibbs, Richard A ^b   Beck, Stephan ^a   Rogers, Jane ^a   Bentley, David R ^a   more..

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b BAYLOR COLLEGE OF MEDICINE   (United States)

^c FRITZ LIPMANN INSTITUTE   (Germany)

^d WASHINGTON UNIVERSITY   (United States)

^e MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^f UNIVERSITY OF KIEL   (Germany)

^g UNIVERSITY OF MUNICH   (Germany)

^h UNIVERSITY COLLEGE LONDON   (United Kingdom)

ⁱ PENN STATE COLLEGE OF MEDICINE   (United States)

^j APPLIED BIOSYSTEMS   (United States)

^k EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^l INSTITUTE OF GENETICS AND BIOPHYSICS ADRIANO BUZZATI TRAVERSO   (Italy)

^m UNIVERSITY OF EDINBURGH   (United Kingdom)

ⁿ INSTITUT COCHIN   (France)

^o CHILDREN S HOSPITAL OAKLAND RESEARCH INSTITUTE   (United States)

^p GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^q INSTITUTE OF EPIDEMIOLOGY   (Germany)

^r German Genome Resource Center RZPD   (Germany)

^s NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^t NATIONAL INSTITUTE ON AGING   (United States)

^u DUKE UNIVERSITY   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

CHARACTERIZATION; CHROMOSOMES; DEGRADATION; DISEASE CONTROL; MUTAGENESIS; PROTEINS;

MUTATIONS; PROTEIN ENCODING; SEX CHROMOSOMES; X CHROMOSOMES;

DNA SEQUENCES;

GENETICS;

ARTICLE; AUTOSOMAL INHERITANCE; CELL TYPE; DEGRADATION; DNA SEQUENCE; FEMALE; GENDER; GENE MUTATION; HUMAN; MALE; MOLECULAR EVOLUTION; PRIORITY JOURNAL; PROTEIN EXPRESSION; SEX CHROMOSOME; TESTIS; X CHROMOSOME; X CHROMOSOME INACTIVATION; X CHROMOSOME LINKED DISORDER; Y CHROMOSOME; ANIMAL; CENTROMERE; CONTIG MAPPING; CROSSING OVER; GENE EXPRESSION REGULATION; GENETIC LINKAGE; GENETICS; GENOMICS; MEDICAL GENETICS; METABOLISM; NUCLEOTIDE REPEAT; SEQUENCE HOMOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM;

MAMMALIA;

RNA; TUMOR ANTIGEN;

ANIMALS; ANTIGENS, NEOPLASM; CENTROMERE; CHROMOSOMES, HUMAN, X; CHROMOSOMES, HUMAN, Y; CONTIG MAPPING; CROSSING OVER, GENETIC; DOSAGE COMPENSATION, GENETIC; EVOLUTION, MOLECULAR; FEMALE; GENETICS, MEDICAL; GENOMICS; HUMANS; LINKAGE (GENETICS); MALE; POLYMORPHISM, SINGLE NUCLEOTIDE; REPETITIVE SEQUENCES, NUCLEIC ACID; RNA; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; TESTIS;

EID: 15244363491     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/nature03440     Document Type: Article

References (68)

1. Ohno, S. Sex Chromosomes and Sex-linked Genes (Springer, Berlin, 1967).
2. McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University and National Center for Biotechnology Information, National Library of Medicine. OMIM: Online Mendelian Inheritance in Man. (http://www.ncbi.nlm.nih. gov/omim/) (2000).
3. Royer-Pokora, B. et al. Cloning the gene for an inherited human disorder-chronic granulomatous disease - on the basis of its chromosomal location. Nature 322, 32-38 (1986).
4. Monaco, A. P. et al. Isolation of candidate cDNAs for portions of the Duchenne muscular dystrophy gene. Nature 323, 646-650 (1986).
5. Bentley, D. R. et al. The physical maps for sequencing human chromosomes 1, 6, 9, 10, 13, 20 and X. Nature 409, 942-943 (2001).
6. Humphray, S. J. et al. DNA sequence and analysis of human chromosome 9. Nature 429, 369-374 (2004).
7. International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001).
8. Schmutz, J. et al. Quality assessment of the human genome sequence. Nature 429, 365-368 (2004).
9. Mahtani, M. M. & Willard, H. F. Physical and genetic mapping of the human X chromosome centromere: repression of recombination. Genome Res. 8, 100-110 (1998).
10. Kong, A. et al. A high-resolution recombination map of the human genome. Nature Genet. 31, 241-247 (2002).
11. Pruitt, K. D., Katz, K. S., Sicotte, H. & Maglott, D. R. Introducing RefSeq and LocusLink: curated human genome resources at the NCBI. Trends Genet. 16, 44-47 (2000).
12. Mungall, A. J. et al. The DNA sequence and analysis of human chromosome 6. Nature 425, 805-811 (2003).
13. Deloukas, P. et al. The DNA sequence and comparative analysis of human chromosome 10. Nature 429, 375-381 (2004).
14. Dunham, A. et al. The DNA sequence and analysis of human chromosome 13. Nature 428, 522-528 (2004).
15. Griffiths-Jones, S., Bateman, A., Marshall, M., Khanna, A. & Eddy, S. R. Rfam: an RNA family database. Nucleic Acids Res. 31, 439-441 (2003).
16. Lowe, T. M. & Eddy, S. R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955-964 (1997).
17. Griffiths-Jones, S. The microRNA Registry. Nucleic Acids Res. 32 (Database issue), D109-111 (2004).
18. Brown, C. J. et al. A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome. Nature 349, 38-44 (1991).
19. Brown, C. J. et al. The human XIST gene: analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus. Cell 71, 527-542 (1992).
20. Lee, J. T., Davidow, L. S. & Warshawsky, D. Tsix, a gene antisense to Xist at the X-inactivation centre. Nature Genet. 21, 400-404 (1999).
21. Migeon, B. R., Chowdhury, A. K., Dunston, J. A. & McIntosh, I. Identification of TSIX, encoding an RNA antisense to human XIST, reveals differences from its murine counterpart: implications for X inactivation. Am. J. Hum. Genet. 69, 951-960 (2001).
22. Chow, J. C., Hall, L. L., Clemson, C. M., Lawrence, J. B. & Brown, C. J. Characterization of expression at the human XIST locus in somatic, embryonal carcinoma, and transgenic cell lines. Genomics 82, 309-322 (2003).
23. Chureau, C. et al. Comparative sequence analysis of the X-inactivation center region in mouse, human, and bovine. Genome Res. 12, 894-908 (2002).
24. Bateman, A. et al. The Pfam protein families database. Nucleic Acids Res. 32 (Database issue), D138-141 (2004).
25. Scanlan, M. J., Simpson, A. J. & Old, L. J. The cancer/testis genes: review, standardization, and commentary. Cancer Immun. [online] 4, 1 (2004).
26. Hurst, L. D. Evolutionary genomics: Sex and the X. Nature 411, 149-150(2001).
27. Chomez, P. et al. An overview of the MAGE gene family with the identification of all human members of the family. Cancer Res. 61, 5544-5551 (2001).
28. Cheung, J. et al. Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence. Genome Biol. 4, R25 (2003).
29. Stankiewicz, P. & Lupski, J. R. Genome architecture, rearrangements and genomic disorders. Trends Genet. 18, 74-82 (2002).
30. Pegoraro, E. et al. Familial skewed X inactivation: a molecular trait associated with high spontaneous-abortion rate maps to Xq28. Am. J. Hum. Genet. 61, 160-170 (1997).
31. Schueler, M. G., Higgins, A. W., Rudd, M. K., Gustashaw, K. & Willard, H. F. Genomic and genetic definition of a functional human centromere. Science 294, 109-115 (2001).
32. Spence, J. M. et al. Co-localization of centromere activity, proteins and topoisomerase II within a subdomain of the major human X alpha-satellite array. EMBO J. 21, 5269-5280 (2002).
33. Rudd, M. K. & Willard, H. F. Analysis of the centromeric regions of the human genome assembly. Trends Genet. 20, 529-533 (2004).
34. She, X. et al. The structure and evolution of centromeric transition regions within the human genome. Nature 430, 857-864 (2004).
35. The International SNP Map Working Group. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409, 928-933 (2001).
36. Schmid, M. et al. First report on chicken genes and chromosomes 2000. Cytogenet. Cell Genet. 90, 169-218 (2000).
37. Kohn, M., Kehrer-Sawatzki, H., Vogel, W., Graves, J. A. & Hameister, H. Wide genome comparisons reveal the origins of the human X chromosome. Trends Genet. 20, 598-603 (2004).
38. Graves, J. A. The origin and function of the mammalian Y chromosome and Y-borne genes - an evolving understanding. Bioessays 17, 311-320 (1995).
39. Hillier, L. W. et al. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432, 695-716 (2004).
40. Freije, D., Helms, C., Watson, M. S. & Donis-Keller, H. Identification of a second pseudoautosomal region near the Xq and Yq telomeres. Science 258, 1784-1787 (1992).
41. Skaletsky, H. et al. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 423, 825-837 (2003).
42. Page, D. C., Harper, M. E., Love, J. & Botstein, D. Occurrence of a transposition from the X-chromosome long arm to the Y-chromosome short arm during human evolution. Nature 311, 119-123 (1984).
43. Sargent, C. A. et al. The sequence organization of Yp/proximal Xq homologous regions of the human sex chromosomes is highly conserved. Genomics 32, 200-209 (1996).
44. Toder, R., Wakefield, M. J. & Graves, J. A. The minimal mammalian Y chromosome - the marsupial Y as a model system. Cytogenet. Cell Genet. 91, 285-292 (2000).
45. Delbridge, M. L. et al. TSPY, the candidate gonadoblastoma gene on the human Y chromosome, has a widely expressed homologue on the X - implications for Y chromosome evolution. Chromosome Res. 12, 345-356 (2004).
46. Lahn, B. T. & Page, D. C. Four evolutionary strata on the human X chromosome. Science 286, 964-967 (1999).
47. Lyon, M. F. Gene action in the X-chromosome of the mouse (Mus musculus L.). Nature 190, 372-373 (1961).
48. Carrel, L. & Willard, H. F. X-inactivation profile reveals extensive variability in X-linked gene expression in females. Nature doi:10.1038/ nature03479 (this issue).
49. Jegalian, K. & Page, D. C. A proposed path by which genes common to mammalian X and Y chromosomes evolve to become X inactivated. Nature 394, 776-780 (1998).
50. Gartler, S. M. & Riggs, A. D. Mammalian X-chromosome inactivation. Annu. Rev. Genet. 17, 155-190 (1983).
51. Lyon, M. F. X-chromosome inactivation: a repeat hypothesis. Cytogenet. Cell Genet. 80, 133-137 (1998).
52. Bailey, I. A., Carrel, L., Chakravarti, A. & Eichler, E. E. Molecular evidence for a relationship between LINE-1 elements and X chromosome inactivation: the Lyon repeat hypothesis. Proc. Natl Acad. Sci. USA 97, 6634-6639 (2000).
53. Smit, A. F., Toth, G., Riggs, A. D. & Jurka, J. Ancestral, mammalian-wide subfamilies of LINE-1 repetitive sequences. J. Mol. Biol. 246, 401-417 (1995).
54. Ke, X. & Collins, A. CpG islands in human X-inactivation. Ann. Hum. Genet. 67, 242-249 (2003).
55. Coffey, A. J. et al. Host response to EBV infection in X-linked lymphoproliferative disease results from mutations in an SH2-domain encoding gene. Nature Genet. 20, 129-135 (1998).
56. Stromme, P. et al. Mutations in the human ortholog of Aristaless cause X-linked mental retardation and epilepsy. Nature Genet. 30, 441-445 (2002).
57. Amir, R. E. et al. Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2. Nature Genet. 23, 185-188 (1999).
58. Orrico, A. et al. MECP2 mutation in male patients with non-specific X-linked mental retardation. FEBS Lett. 481, 285-288 (2000).
59. Ropers, H. H. et al. Nonsyndromic X-linked mental retardation: where are the missing mutations? Trends Genet. 19, 316-320 (2003).
60. The International Human Genome Mapping Consortium. A physical map of the human genome. Nature 409, 934-941 (2001).
61. Ning, Z., Cox, A. J. & Mullikin, J. C. SSAHA: a fast search method for large DNA databases. Genome Res. 11, 1725-1729 (2001).
62. Brudno, M. et al. LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 13, 721-731 (2003).
63. Frazer, K. A., Pachter, L., Poliakov, A., Rubin, E. M. & Dubchak, I. VISTA: computational tools for comparative genomics. Nucleic Acids Res. 32, W273-W279 (2004).
64. Bourque, G. & Pevzner, P. A. Genome-scale evolution: reconstructing gene orders in the ancestral species. Genome Res. 12, 26-36 (2002).
65. Francke, U. Digitized and differentially shaded human chromosome ideograms for genomic applications. Cytogenet. Cell Genet. 65, 206-218 (1994).
66. Gibbs, R. A. et al. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428, 493-521 (2004).
67. Iwase, M. et al. The amelogenin loci span an ancient pseudoautosomal boundary in diverse mammalian species. Proc. Natl Acad. Sci. USA 100, 5258-5263 (2003).
68. Lahn, B. T. & Page, D. C. A human sex-chromosomal gene family expressed in male germ cells and encoding variably charged proteins. Hum. Mol. Genet. 9, 311-319 (2000).