A slippery boundary

The Y chromosome has provided one of the greatest challenges in finalizing complete mammalian genome sequences in part because of its unusual relationship with the X chromosome. Part of the Y chromosome, known as the pseudoautosomal region, must pair with the complementary region on the X chromosome and undergo recombination, so that the resulting crossovers stabilize the sex chromosomes for proper separation during meiosis. The Y chromosome also bears at least one gene that is male-determining, and this region of the Y chromosome must not recombine with the X chromosome or sterility or intersexuality may result. Apart from these two rules, the gene content of the pseudoautosomal and nonrecombing parts of the Y chromosome are subject to relatively weak evolutionary forces. Iwase et al. (1), in this issue of PNAS, describe a remarkable finding that the boundary between these two portions of the Y chromosome moved relatively recently, and that there appears to be considerable opportunity for chance to play a large role in gene content of these two very different segments of the Y chromosome.

Iwase et al. (1) make a compelling case that the pseudoautosomal boundary (PAB) previously resided in the second intron of the gene encoding amelogenin. To see how this inference could be made solely based on DNA sequence comparisons, it will help to refer to Fig. 1. Any region of the X and Y chromosomes that freely recombines would be expected to show divergence levels that are equal to the level of polymorphism on the X chromosome, or ≈1 bp per 1,000. This is the state of the current pseudoautosomal region, which falls on the right end of the diagram. The far left portion of the diagram indicates the region that has been nonrecombining. Amelogenin arrived onto the sex chromosomes ≈100 million years ago …