Y Chromosome


The Y chromosome has a key role in human sex determination and carries the male sex‐determining gene, SRY. As a consequence of this function, it has unique genetic properties such as a large region that is haploid and escapes meiotic recombination, and unique physical properties such as low gene but high repeated sequence density. The sequence of the euchromatic half of the chromosome has been determined in one individual, and this is accelerating systematic studies of both sequence and structural variation in the population and their phenotypic consequences.

Keywords: Y chromosomal structure; male sex determination; SRY; male fertility; AZF

Figure 1.

The Y chromosome. Coordinates (left) are from Ensembl release 44 (April 2007). (a) Inheritance patterns; PAR, pseudoautosomal region. (b) Major cytogenetic divisions. (c) Genetic functions discussed in this article. AZF localizations are based on molecular mapping of deletions. (d) Banding pattern. Note that bands are only located approximately on the molecular map. (e) Genes relevant to the genetic functions discussed, identified by molecular methods. (f) Copy‐number variable regions found as polymorphisms in the population, with the genes or other sequences they contain indicated. (g) Inversion polymorphisms; the ‘+’ indicates that a complex set of inversions are found in the AZFc region.



Akkari Y, Lawce H, Kelson S et al. (2005) Y chromosome heterochromatin of differing lengths in two cell populations of the same individual. Prenatal Diagnosis 25: 304–306.

Babcock M, Yatsenko S, Stankiewicz P et al. (2007) AT‐rich repeats associated with chromosome 22q11.2 rearrangement disorders shape human genome architecture on Yq12. Genome Research 17: 451–460.

Hurles ME and Tyler‐Smith C (2006) Y‐chromosomal rearrangements and azoospermia. In: Lupski JR and Stankiewicz P (eds), Genomic Disorders: The Genomic Basis of Disease, pp. 273–288. Totowa, NJ: Humana Press.

Jehan Z, Vallinayagam S, Tiwari S et al. (2007) Novel noncoding RNA from human Y distal heterochromatic block (Yq12) generates testis‐specific chimeric CDC2L2. Genome Research 17: 433–440.

Jobling MA, Lo IC, Turner DJ et al. (2007) Structural variation on the short arm of the human Y chromosome: recurrent multigene deletions encompassing Amelogenin Y. Human Molecular Genetics 16: 307–316.

Kirsch S, Weiss B, Miner TL et al. (2005) Interchromosomal segmental duplications of the pericentromeric region on the human Y chromosome. Genome Research 15: 195–204.

Lahn BT and Page DC (1997) Functional coherence of the human Y chromosome. Science 278: 675–680.

Mathias N, Bayes M and Tyler‐Smith C (1994) Highly informative compound haplotypes for the human Y chromosome. Human Molecular Genetics 3: 115–123.

Polanco JC and Koopman P (2007) Sry and the hesitant beginnings of male development. Developmental Biology 302: 13–24.

Repping S, van Daalen SK, Brown LG et al. (2006) High mutation rates have driven extensive structural polymorphism among human Y chromosomes. Nature Genetics 38: 463–467.

Sinclair AH, Berta P, Palmer MS et al. (1990) A gene from the human sex‐determining region encodes a protein with homology to a conserved DNA‐binding motif. Nature 346: 240–244.

Skaletsky H, Kuroda‐Kawaguchi T, Minx PJ et al. (2003) The male‐specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 423: 825–837.

Tiepolo L and Zuffardi O (1976) Localization of factors controlling spermatogenesis in the nonfluorescent portion of the human Y chromosome long arm. Human Genetics 34: 119–124.

Tyler‐Smith C, Gimelli G, Giglio S et al. (1999) Transmission of a fully functional human neocentromere through three generations. American Journal of Human Genetics 64: 1440–1444.

Vogt PH, Edelmann A, Kirsch S et al. (1996) Human Y chromosome azoospermia factors (AZF) mapped to different subregions in Yq11. Human Molecular Genetics 5: 933–943.

Further Reading

Carvalho CMB and Santos FR (2005) Human Y‐chromosome variation and male dysfunction. Journal of Molecular and Genetic Medicine 1: 63–75.

Jobling MA and Tyler‐Smith C (2003) The human Y chromosome: an evolutionary marker comes of age. Nature Reviews Genetics 4: 598–612.

Lahn BT, Pearson NM and Jegalian K (2001) The human Y chromosome, in the light of evolution. Nature Reviews Genetics 2: 207–216.

Page DC (2004) 2003 Curt Stern Award address, on low expectation exceeded; or, the genomic salvation of the Y chromosome. American Journal of Human Genetics 74: 399–402.

Ross MT, Bentley DR and Tyler‐Smith C (2006) The sequences of the human sex chromosomes. Current Opinion in Genetics and Development 16: 213–218.

Willard HF (2005) Tales of the Y chromosome. Nature 434: 267–268.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Tyler‐Smith, Chris(Dec 2007) Y Chromosome. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0005796.pub2]