Department of Biosystems Science, Graduate University for Advanced Studies, Hayama, Kanagawa, Japan
Paralogous gene pairs on the mammalian sex chromosomes can provide useful information on the tempo and mode of X-Y differentiation. Recently, Lahn and Page (1999)
reported intriguing results on the chromosomal locations and synonymous sequence divergences (ks with multiple-hit correction) of 19 pairs of X-Y-paralogous cDNA sequences in humans or squirrel monkeys. It was found that there are four distinct groups (strata) of the gene pairs in terms of the ks value. Of these, seven belong to stratum 4, and the X paralogs are clustered in a single chromosomal region which is adjacent to the pseudoautosomal boundary in the short arm of chromosome X. In contrast, the seven Y paralogs are scattered on chromosome Y, presumably owing to frequent chromosomal rearrangements. Together with similar observations on strata 1, 2, and 3, it was hypothesized that X-Y-chromosomal differentiation was initiated one stratum at a time and that stratum 1 was the first to embark on the differentiation and stratum 4 was the most recent. Lahn and Page (1999)
invoked chromosomal inversions as the most likely cause for formation of these strata by suppressing sex-chromosomal recombination.
Bengtsson and Goodfellow (1987)
argued that X-Y differentiation had occurred only after X-Y recombination ceased and that the most likely mechanism of suppressing recombination was chromosomal inversions. Navarro et al. (1997)
theoretically demonstrated that there should be a strong reduction in recombination in the proximal zone of an inverted region owing to the production of unbalanced gametes. Here we report that the junction between stratum 3 (ks =
30%) and stratum 4 (ks =
10%) in the human and the chimpanzee resides in the second intron of the amelogenin gene, arguing that this junction cannot be a direct breakpoint of any chromosomal inversion. We also make a similar comparison of amelogenin genes in other mammals and show that formation of stratum 4 is specific to mammalian orders.
Eutherian mammals generally possess a pair of amelogenin genes on the X and Y chromosomes (e.g., Lau et al. 1989
; Nakahori, Takenaka, and Nakagome 1991
; Salido, Yen, and Koprivnikar 1992
) which are designated AMGX and AMGY, respectively. In humans, the AMGX locus is oriented from the centromere to the telomere. Among the seven loci examined for stratum 4, the AMGX locus is most proximal and nearest to stratum 3. We retrieved two human BAC clone sequences which contained AMGX (AC002366) and AMGY (AC013412) and also determined the genomic DNA sequences of the chimpanzee homologs (data will be presented elsewhere). Quite unexpectedly, it turns out that the upstream region from intron 2 exhibits 25% sequence differences per silent site (ps without multiple-hit corrections), the same level as the corrected ks value of 30% in stratum 3 (fig. 1
). In sharp contrast, the region downstream of intron 2 exhibits ps = 10%, as in intron 3 (Huang et al. 1997
) as well as the six other paralogous gene pairs belonging to stratum 4 (Lahn and Page 1999
). The same pattern and degree of sequence differences were also found in the comparison between the chimpanzee AMGX and AMGY. These findings convincingly indicate that the junction between strata 3 and 4 arranged side by side on chromosome X occurs in the middle of the human and chimpanzee AMGX locus.
|
As argued by Bengtsson and Goodfellow (1987)
and by Lahn and Page (1999)
, X-Y differentiation may result from suppression of X-Y recombination mediated through chromosomal inversions. Also, this process may be a common, irreversible evolutionary step in mammals (Jegalian and Page 1998
). However, the deposit of stratum 4 in mammals cannot be easily explained as a direct consequence of a single chromosomal inversion for two reasons. First, if the junction between strata 3 and 4 is a breakpoint of a chromosomal inversion, the amelogenin gene on chromosome X or Y should have been disrupted, suggesting that any such inversion, if present, must have occurred somewhere else. Second, the initiation of stratum 4 differentiation is generally mammalian-order-specific, but the junctions between strata 3 and 4 are almost identical, at least between humans and cattle. This finding can be explained by a single inversion that might occur in the common ancestor of humans and cattle. However, since pigs and horses are more closely related to cattle than to humans (Goodman, Czelusniak, and Beeber 1985
) and the inversion is likely to be shared by all four mammalian species, it is difficult to account for the observed large differences in the ks or ps value among mammalian AMGX and AMGY paralogs.
Nonetheless, it is still conceivable that independent chromosomal inversions, particularly on chromosome Y, were responsible for differential initiations of recombination suppression in mammals. Although such inversions must have occurred in regions other than the amelogenin locus itself, they could happen to suppress recombination around the locus. According to Navarro et al. (1997)
, the proximal region of chromosomal inversions is expected to undergo a strong reduction in recombination. Recombination appears to be a complex event involving a number of enzymes and proteins, and the event is initiated by the specific binding of one of these proteins to the DNA molecule of the chromosome (Klein and Takahata 1990
). If this interaction is highly specific, recombination would be initiated only in limited regions of a chromosome. While the molecular mechanism of recombination is still poorly understood, it is tempting to conclude that the upstream region of the amelogenin locus may contain a sequence or structural signal responsible for initiating or suppressing recombination, thereby repeatedly triggering subsequent X-Y differentiation in different mammals.
Acknowledgements
We thank two anonymous reviewers for their constructive criticism on an early version of this paper. This work was supported in part by Monkasho grant 12304046 to N.T.
Footnotes
Stephen Palumbi, Reviewing Editor
1 Keywords: recombination
chromosomal inversion
nucleotide differences
BAC clone
evolutionary strata
2 Address for correspondence and reprints: Naoyuki Takahata, Department
of Biosystems Science, Graduate University for Advanced Studies,
Hayama, Kanagawa 240-0193, Japan. takahata{at}soken.ac.jp
.
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