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The Y chromosome is a sex chromosomefound in several vertebrates and mammals, including humans. In addition to 22 pairs of autosomes, the human males have one X chromosome and one Y chromosome. In these organisms, the presence or absence of the Y chromosome determines the development of male traits.


Around 300 million years ago, the two sex chromosomes diverged from two identical autosomal chromosomes. Over time, the Y chromosome has lost most of its genes, shrinking in size. Today, only a small part of the Y chromosome shares sequence similarity with the X chromosome. A large scientific study on Y chromosomes in eight mammals, including monkeys, mice, rats, bulls, opossums, chimpanzees, and humans, showed 18 highly similar regions on Y chromosomes. The fact that these regions are retained in all these mammals, despite losing a large portion of Y chromosomes during evolution, shows that the genes on Y chromosomes are vital for the survival of these mammals.


The mammalian Y chromosome has three major regions. The pseudoautosomal regions on the Y chromosome share homology with the X chromosome and can undergo meiotic recombination. Thus, genes present in the pseudoautosomal regions are inherited in an autosomal rather than a sex-linked fashion. The second region is a euchromatin region designated as a Male-specific Y chromosome region or MSY. It spans 23 Mb in length and has few protein-coding genes, such as the SRY gene, a master regulator of maleness and the ZFY gene required for spermatogenesis. The third region is a heterochromatin region that contains several repetitive sequences.

Mutations and their effects

Deletions in the MSY region of the Y chromosome affect sperm development and cause male sterility. For example, deletions in the AZF gene on the long arm of the Y chromosome lead to a condition called azoospermia, where spermatozoa are not found in male ejaculate. In addition, deletions in specific regions of MSY are associated with testicular germ cell tumors (TGCTs).

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