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

Nature. 2003 Jun 19;423(6942):825-37. doi: 10.1038/nature01722.


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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Chromosomes, Human, X / genetics
  • Chromosomes, Human, Y / genetics*
  • Crossing Over, Genetic / genetics
  • DNA Transposable Elements / genetics
  • Euchromatin / genetics
  • Evolution, Molecular*
  • Female
  • Gene Amplification / genetics
  • Gene Conversion / genetics
  • Genes / genetics
  • Heterochromatin / genetics
  • Humans
  • In Situ Hybridization, Fluorescence
  • Male
  • Models, Genetic
  • Multigene Family / genetics
  • Organ Specificity
  • Pseudogenes / genetics
  • Sequence Homology, Nucleic Acid
  • Sex Characteristics
  • Sex Determination Processes*
  • Species Specificity
  • Testis / metabolism
  • Transcription, Genetic / genetics
  • Transducin*


  • DNA Transposable Elements
  • Euchromatin
  • Heterochromatin
  • TBL1Y protein, human
  • Transducin