Article

Nature 434, 325-337 (17 March 2005) | doi:10.1038/nature03440; Received 1 February 2005; Accepted 7 February 2005

The DNA sequence of the human X chromosome

Mark T. Ross1, Darren V. Grafham1, Alison J. Coffey1, Steven Scherer2, Kirsten McLay1, Donna Muzny2, Matthias Platzer3, Gareth R. Howell1, Christine Burrows1, Christine P. Bird1, Adam Frankish1, Frances L. Lovell1, Kevin L. Howe1, Jennifer L. Ashurst1, Robert S. Fulton4, Ralf Sudbrak5,6, Gaiping Wen3, Matthew C. Jones1, Matthew E. Hurles1, T. Daniel Andrews1, Carol E. Scott1, Stephen Searle1, Juliane Ramser7, Adam Whittaker1, Rebecca Deadman1, Nigel P. Carter1, Sarah E. Hunt1, Rui Chen2, Andrew Cree2, Preethi Gunaratne2, Paul Havlak2, Anne Hodgson2, Michael L. Metzker2, Stephen Richards2, Graham Scott2, David Steffen2, Erica Sodergren2, David A. Wheeler2, Kim C. Worley2, Rachael Ainscough1, Kerrie D. Ambrose1, M. Ali Ansari-Lari2, Swaroop Aradhya2, Robert I. S. Ashwell1, Anne K. Babbage1, Claire L. Bagguley1, Andrea Ballabio2, Ruby Banerjee1, Gary E. Barker1, Karen F. Barlow1, Ian P. Barrett1, Karen N. Bates1, David M. Beare1, Helen Beasley1, Oliver Beasley1, Alfred Beck5, Graeme Bethel1, Karin Blechschmidt3, Nicola Brady1, Sarah Bray-Allen1, Anne M. Bridgeman1, Andrew J. Brown1, Mary J. Brown2, David Bonnin2, Elspeth A. Bruford8, Christian Buhay2, Paula Burch2, Deborah Burford1, Joanne Burgess1, Wayne Burrill1, John Burton1, Jackie M. Bye1, Carol Carder1, Laura Carrel9, Joseph Chako2, Joanne C. Chapman1, Dean Chavez2, Ellson Chen10, Guan Chen2, Yuan Chen11, Zhijian Chen2, Craig Chinault2, Alfredo Ciccodicola12, Sue Y. Clark1, Graham Clarke1, Chris M. Clee1, Sheila Clegg1, Kerstin Clerc-Blankenburg2, Karen Clifford1, Vicky Cobley1, Charlotte G. Cole1, Jen S. Conquer1, Nicole Corby1, Richard E. Connor1, Robert David2, Joy Davies1, Clay Davis2, John Davis1, Oliver Delgado2, Denise DeShazo2, Pawandeep Dhami1, Yan Ding2, Huyen Dinh2, Steve Dodsworth1, Heather Draper2, Shannon Dugan-Rocha2, Andrew Dunham1, Matthew Dunn1, K. James Durbin2, Ireena Dutta1, Tamsin Eades1, Matthew Ellwood1, Alexandra Emery-Cohen2, Helen Errington1, Kathryn L. Evans13, Louisa Faulkner1, Fiona Francis14, John Frankland1, Audrey E. Fraser1, Petra Galgoczy3, James Gilbert1, Rachel Gill2, Gernot Glöckner3, Simon G. Gregory1, Susan Gribble1, Coline Griffiths1, Russell Grocock1, Yanghong Gu2, Rhian Gwilliam1, Cerissa Hamilton2, Elizabeth A. Hart1, Alicia Hawes2, Paul D. Heath1, Katja Heitmann5, Steffen Hennig5, Judith Hernandez2, Bernd Hinzmann3, Sarah Ho1, Michael Hoffs1, Phillip J. Howden1, Elizabeth J. Huckle1, Jennifer Hume2, Paul J. Hunt1, Adrienne R. Hunt1, Judith Isherwood1, Leni Jacob2, David Johnson1, Sally Jones2, Pieter J. de Jong15, Shirin S. Joseph1, Stephen Keenan1, Susan Kelly2, Joanne K. Kershaw1, Ziad Khan2, Petra Kioschis16, Sven Klages5, Andrew J. Knights1, Anna Kosiura5, Christie Kovar-Smith2, Gavin K. Laird1, Cordelia Langford1, Stephanie Lawlor1, Margaret Leversha1, Lora Lewis2, Wen Liu2, Christine Lloyd1, David M. Lloyd1, Hermela Loulseged2, Jane E. Loveland1, Jamieson D. Lovell1, Ryan Lozado2, Jing Lu2, Rachael Lyne1, Jie Ma2, Manjula Maheshwari2, Lucy H. Matthews1, Jennifer McDowall1, Stuart McLaren1, Amanda McMurray1, Patrick Meidl1, Thomas Meitinger17, Sarah Milne1, George Miner2, Shailesh L. Mistry1, Margaret Morgan2, Sidney Morris2, Ines Müller5,18, James C. Mullikin19, Ngoc Nguyen2, Gabriele Nordsiek3, Gerald Nyakatura3, Christopher N. O'Dell1, Geoffery Okwuonu2, Sophie Palmer1, Richard Pandian1, David Parker2, Julia Parrish2, Shiran Pasternak2, Dina Patel1, Alex V. Pearce1, Danita M. Pearson1, Sarah E. Pelan1, Lesette Perez2, Keith M. Porter1, Yvonne Ramsey1, Kathrin Reichwald3, Susan Rhodes1, Kerry A. Ridler1, David Schlessinger20, Mary G. Schueler19, Harminder K. Sehra1, Charles Shaw-Smith1, Hua Shen2, Elizabeth M. Sheridan1, Ratna Shownkeen1, Carl D. Skuce1, Michelle L. Smith1, Elizabeth C. Sotheran1, Helen E. Steingruber1, Charles A. Steward1, Roy Storey1, R. Mark Swann1, David Swarbreck1, Paul E. Tabor2, Stefan Taudien3, Tineace Taylor2, Brian Teague2, Karen Thomas1, Andrea Thorpe1, Kirsten Timms2, Alan Tracey1, Steve Trevanion1, Anthony C. Tromans1, Michele d'Urso12, Daniel Verduzco2, Donna Villasana2, Lenee Waldron2, Melanie Wall1, Qiaoyan Wang2, James Warren2, Georgina L. Warry1, Xuehong Wei2, Anthony West1, Siobhan L. Whitehead1, Mathew N. Whiteley1, Jane E. Wilkinson1, David L. Willey1, Gabrielle Williams2, Leanne Williams1, Angela Williamson2, Helen Williamson1, Laurens Wilming1, Rebecca L. Woodmansey1, Paul W. Wray1, Jennifer Yen2, Jingkun Zhang2, Jianling Zhou2, Huda Zoghbi2, Sara Zorilla2, David Buck1, Richard Reinhardt5, Annemarie Poustka16, André Rosenthal3, Hans Lehrach5, Alfons Meindl7, Patrick J. Minx4, LaDeana W. Hillier4, Huntington F. Willard21, Richard K. Wilson4, Robert H. Waterston4, Catherine M. Rice1, Mark Vaudin1, Alan Coulson1, David L. Nelson2, George Weinstock2, John E. Sulston1, Richard Durbin1, Tim Hubbard1, Richard A. Gibbs2, Stephan Beck1, Jane Rogers1 & David R. Bentley1

  1. The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK;
  2. Baylor College of Medicine Human Genome Sequencing Center, Department of Molecular and Human Genetics, One Baylor Plaza, Houston, Texas 77030, USA;
  3. Genomanalyse, Institut für Molekulare Biotechnologie, Beutenbergstr. 11, 07745 Jena, Germany;
  4. Washington University Genome Sequencing Center, Box 8501, 4444 Forest Park Avenue, St. Louis, Missouri 63108, USA;
  5. Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany;
  6. Institute for Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany;
  7. Medizinische Genetik, Ludwig-Maximilian-Universität, Goethestr. 29, 80336 München, Germany;
  8. HUGO Gene Nomenclature Committee, The Galton Laboratory, Department of Biology, University College London, Wolfson House, 4 Stephenson Way, London NW1 2HE, UK;
  9. Department of Biochemistry and Molecular Biology, Pennsylvania State College of Medicine, Hershey, Pennsylvania 17033, USA;
  10. Advanced Center for Genetic Technology, PE-Applied Biosystems, Foster City, California 94404, USA;
  11. European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK;
  12. Institute of Genetics and Biophysics, Adriano Buzzati-Traverso, Via Marconi 12, 80100 Naples, Italy;
  13. Medical Genetics Section, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK;
  14. Laboratoire de Génétique et de Physiopathologie des Retards Mentaux, Institut Cochin. Inserm U567, Université Paris V., 24 rue du Faubourg Saint Jacques, 75014 Paris, France;
  15. BACPAC Resources, Children's Hospital Oakland Research Institute, 747 52nd Street, Oakland, California 94609, USA;
  16. Molekulare Genomanalyse, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany;
  17. Institute of Human Genetics, GSF National Research Center for Environment and Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany;
  18. RZPD Resource Center for Genome Research, 14059 Berlin, Germany;
  19. National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
  20. Laboratory of Genetics, National Institute on Aging, 333 Cassell Drive, Baltimore, Maryland 21224, USA;
  21. Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina 27708, USA

Correspondence to: Mark T. Ross1 Correspondence and requests for materials should be addressed to M.T.R. (Email: mtr@sanger.ac.uk).
All DNA sequences reported in this study have been deposited in the EMBL or GenBank databases, and accession numbers are given in Supplementary Fig. 1.

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The human X chromosome has a unique biology that was shaped by its evolution as the sex chromosome shared by males and females. We have determined 99.3% of the euchromatic sequence of the X chromosome. Our analysis illustrates the autosomal origin of the mammalian sex chromosomes, the stepwise process that led to the progressive loss of recombination between X and Y, and the extent of subsequent degradation of the Y chromosome. LINE1 repeat elements cover one-third of the X chromosome, with a distribution that is consistent with their proposed role as way stations in the process of X-chromosome inactivation. We found 1,098 genes in the sequence, of which 99 encode proteins expressed in testis and in various tumour types. A disproportionately high number of mendelian diseases are documented for the X chromosome. Of this number, 168 have been explained by mutations in 113 X-linked genes, which in many cases were characterized with the aid of the DNA sequence.

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