Nature 423, 825-837 (19 June 2003) | doi:10.1038/nature01722; Received 7 March 2003; Accepted 8 April 2003

The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes

Helen Skaletsky1, Tomoko Kuroda-Kawaguchi1, Patrick J. Minx2, Holland S. Cordum2, LaDeana Hillier2, Laura G. Brown1, Sjoerd Repping3, Tatyana Pyntikova1, Johar Ali2, Tamberlyn Bieri2, Asif Chinwalla2, Andrew Delehaunty2, Kim Delehaunty2, Hui Du2, Ginger Fewell2, Lucinda Fulton2, Robert Fulton2, Tina Graves2, Shun-Fang Hou2, Philip Latrielle2, Shawn Leonard2, Elaine Mardis2, Rachel Maupin2, John McPherson2, Tracie Miner2, William Nash2, Christine Nguyen2, Philip Ozersky2, Kymberlie Pepin2, Susan Rock2, Tracy Rohlfing2, Kelsi Scott2, Brian Schultz2, Cindy Strong2, Aye Tin-Wollam2, Shiaw-Pyng Yang2, Robert H. Waterston2, Richard K. Wilson2, Steve Rozen1 & David C. Page1

  1. Howard Hughes Medical Institute, Whitehead Institute, and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
  2. Genome Sequencing Center, Washington University School of Medicine, 4444 Forest Park Boulevard, St Louis, Missouri 63108, USA
  3. Center for Reproductive Medicine, Department of Gynaecology and Obstetrics, Academic Medical Centre, Amsterdam 1105 AZ, the Netherlands

Correspondence to: David C. Page1 Correspondence and requests for materials should be addressed to D.C.P. (Email: GenBank accession numbers are listed in Fig. 2l and the Supplementary Information.


The male-specific region of the Y chromosome, the MSY, differentiates the sexes and comprises 95% of the chromosome's length. Here, we report that the MSY is a mosaic of heterochromatic sequences and three classes of euchromatic sequences: X-transposed, X-degenerate and ampliconic. These classes contain all 156 known transcription units, which include 78 protein-coding genes that collectively encode 27 distinct proteins. The X-transposed sequences exhibit 99% identity to the X chromosome. The X-degenerate sequences are remnants of ancient autosomes from which the modern X and Y chromosomes evolved. The ampliconic class includes large regions (about 30% of the MSY euchromatin) where sequence pairs show greater than 99.9% identity, which is maintained by frequent gene conversion (non-reciprocal transfer). The most prominent features here are eight massive palindromes, at least six of which contain testis genes.