A slippery boundary.

T he 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 (2), and remained active on both sex chromosomes. Iwase et al. (1) show that sequences from a variety of mammals in this region form a monophyletic clade for the X chromosome and a distinct monophyletic clade for the Y chromosome, suggesting that mammalian species have diversified since this region became a nonrecombining part of the sex chromosomes. This is so because the tree indicates that comparisons among mammals in genes on the nonrecombining Y chromosome indicate greater similarity than any comparison between the X and Y chromosomes. As one moves rightwards in Fig. 1, the genealogy changes, such that some Xand Ylinked genes are closest neighbors on the tree. In this region, the divergence between the X and Y chromosomes drops from 30% to 10%, and this drop occurs at a transposable element insertion into the second intron of amelogenin. Because of this relatively lower X–Y divergence, Iwase et al. propose that the 3 region of amelogenin used to freely recombine between the X and Y, but later the PAB moved to the right, leaving all of amelogenin in the nonrecombining region where it is today. To date the time of movement of the pseudoautosomal boundary, Iwase et al. (1) make use of the X vs. Y divergence, and arrive at an estimate of 27–70 million years ago. This is after the mammalian radiation, implying that there may have been more than one change in the pseudoautosomal boundary. Consistent with this, the location of the PAB, and gene content of nonrecombining vs. pseudoautosomal regions, are widely different among mammals (3). These results beg the question what exactly defines the PAB? It is a rather remarkable phenomenon that a pair of chromosomes can freely recombine up to this point, and then beyond this point recombination is absolutely prohibited. It seems to be a common feature of the PAB that a transposable element has inserted there. Although it is plausible that a transposable element insertion could disrupt pairing, and that once pairing is disrupted so is recombination, this is not a very satisfying answer because transposable elements insert in autosomes all of the time, and chromosome pairing and recombination is disrupted in only a minor and local way. It may be useful to consider that it is not only recombination that breaks at the PAB, but that well before recombination occurs, the pairing between the X and Y chromosomes may change drastically at the PAB. In particular, the PAB almost certainly marks the end of the region of synapsis between the sex chromosomes, a condition necessary for normal recombination. Despite our ignorance of what exactly are the features that make a particular part of a chromosome become a PAB, the sequence analysis of Iwase et al. (1) does demonstrate very clearly that it does not require anything particularly unusual. The fact that different mammals have such a diversity of PABs, and that they have moved more than once in our evolutionary history, suggests that there is a large component of chance in the setting of the PAB boundary. This chance aspect leaves open the possibility that it is determined by some form of chromatin remodeling, determined by the proteins