The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes.
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.
Skaletsky
Helen
H
Howard Hughes Medical Institute, Whitehead Institute, and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA.
Kuroda-Kawaguchi
Tomoko
T
Minx
Patrick J
PJ
Cordum
Holland S
HS
Hillier
LaDeana
L
Brown
Laura G
LG
Repping
Sjoerd
S
Pyntikova
Tatyana
T
Ali
Johar
J
Bieri
Tamberlyn
T
Chinwalla
Asif
A
Delehaunty
Andrew
A
Delehaunty
Kim
K
Du
Hui
H
Fewell
Ginger
G
Fulton
Lucinda
L
Fulton
Robert
R
Graves
Tina
T
Hou
Shun-Fang
SF
Latrielle
Philip
P
Leonard
Shawn
S
Mardis
Elaine
E
Maupin
Rachel
R
McPherson
John
J
Miner
Tracie
T
Nash
William
W
Nguyen
Christine
C
Ozersky
Philip
P
Pepin
Kymberlie
K
Rock
Susan
S
Rohlfing
Tracy
T
Scott
Kelsi
K
Schultz
Brian
B
Strong
Cindy
C
Tin-Wollam
Aye
A
Yang
Shiaw-Pyng
SP
Waterston
Robert H
RH
Wilson
Richard K
RK
Rozen
Steve
S
Page
David C
DC
D041321:Chromosomes, Human, X / Q000235:genetics; D041322:Chromosomes, Human, Y / Q000235:genetics*; D003434:Crossing Over, Genetic / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics; D022041:Euchromatin / Q000235:genetics; D019143:Evolution, Molecular; D005260:Female; D005784:Gene Amplification / Q000235:genetics; D005785:Gene Conversion / Q000235:genetics; D005796:Genes / Q000235:genetics; D006570:Heterochromatin / Q000235:genetics; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D008297:Male; D008957:Models, Genetic; D005810:Multigene Family / Q000235:genetics; D009928:Organ Specificity; D011544:Pseudogenes / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid; D012727:Sex Characteristics; D019849:Sex Determination Processes; D013045:Species Specificity; D013737:Testis / Q000378:metabolism; D014158:Transcription, Genetic / Q000235:genetics; D015293:Transducin
D004251:DNA Transposable Elements; D022041:Euchromatin; D006570:Heterochromatin; C485612:TBL1Y protein, human; D015293:Transducin