And Then There was Y

REGIONAL DIFFERENCES

That's not to say that Y is featureless. The sequence revealed a mosaic of highly condensed, transcriptionally inert heterochromatic sequences, as well as three classes of transcriptionally active euchromatic sequences: X-transposed, X-degenerate, and ampliconic DNA. The euchromatic regions included at least 27 distinct proteins or protein families. The X-degenerate and ampliconic regions are largest and contain the most genes.

X-transposed DNA is the youngest class with 99% identity to the X-chromosome, reflecting a relatively recent transposition event. The X-degenerate and ampliconic classes are older, having evolved in parallel over an estimated 300 million years.

X-degenerate DNA is a genetic fossil of sorts, containing pseudogenes once identical to their X counterpart, reflecting their shared autosomal ancestry. Functional genes contained in these regions generally reflect cellular housekeeping functions.

The ampliconic regions, however, revealed the most astonishing surprises. "It was originally thought the Y chromosome would be junky, chaotically organized, with extra copies of genes reflecting ineffective natural selection," says Rozen. Instead, they found eight massive palindromes – mirror-image pairs that share greater than 99.9% sequence identity arm-to-arm and separated by a unique, nonduplicated spacer region. The palindromes account for 25% of the MSY and contain only testis-specific genes within six palindromes. The largest of these has a span of three megabases, says Page.

And it is their maintenance mechanism that refutes the notion of a decaying Y chromosome. With palindromes, the genes of the Y chromosome are in pairs as mirror-image copies, and can function as templates for repair. Their near-perfect identity stems from one copy overwriting the other copy in a process called gene conversion, explains Rozen. "It's a process that may let the testis genes in these mirror-image pairs escape degeneration in an otherwise evolutionarily hostile environment," he says.

"The Y chromosome breaks every rule that we know of in terms of inheritance," says Willard. "Usually genes are driving the story, but here the chromosome is driving the story," he explains.

MALENESS MEASURED UP

In their second Hot Paper, Page and colleagues used comparative sequencing to reveal abundant gene conversion between the arms of palindromes in both human and chimpanzee Y chromosomes.² The researchers looked for orthologs of the eight human palindromes in chimpanzees, bonobos, and gorillas. Using PCR, they amplified and sequenced palindromes from each species. The results suggest that at least six of the palindromes predate the divergence of humans and great apes.

© 2004 Nature Publishing Group

Sequence organization of the palindromic repeat, P3, is represented by the horizontal bar. The two nearly identical (99.94%) 283 kb arms are separated by a non-repeated 170 kb 'spacer.' Sequence differences numbered 1–7 are either nucleotide differences or differences in the lengths of simple tandem repeats (L, long; S, short). These slight differences allowed for assignment of BACs to the correct arm of P3. (Adapted from IHGSC, Nature, 431:931–45, 2004).

They compared nucleotide sequence for two copies of a gene – one in each palindrome arm – from 171 unrelated men, representing 42 distinct branches of Y-chromosome genealogy. In five comparatively young, closely related branches, T/T, C/T, and C/C genotypes were found within the chosen gene. The remaining 37 branches contained only C/C chromosomes. The authors conclude that the ancestral chromosome to the five younger branches underwent a C-to-T substitution in one arm leading to the C/T genotype. Descendents of this genotype underwent a gene conversion that changed it back to C/C or to T/T. From the sequence divergence between palindrome arms and the mutation rate, they were able to extrapolate the frequency at which conversion erases arm-to-arm differences. While it's unknown whether gene conversion occurs during meiosis, mitosis, or both, they estimate that roughly 600 duplicated nucleotides per newborn male may have undergone arm-to-arm conversion.

And some of the documented Y changes have clinical implications. "These two papers... had an enormous impact on our understanding of male infertility," says Sherman Silber, a fertility specialist at St. Luke's Hospital in St. Louis.

Unlike autosomes, where genes are scattered without any organization whatsoever, all spermatogenesis genes are located in these highly organized regions on the Y. In some instances during gene conversion, areas of absolute identity anneal with each other, causing the region in between to drop out. The result is a common 3.5-megabase deletion that includes 21 different spermatogenesis genes and results in severely diminished or nonexistent sperm production.

"Now we understand why male infertility is so common in humans," says Silber. The harsh reality negates many forms of fertility treatment he adds. "Of all the treatments that are available, including hormones, nothing you do will raise or lower the sperm count. There's no effect whatsoever – yet urologists are still doing the same old junk." Says Page, "That's been a very a practical clinical upshot of the sequence of the Y chromosome." His group is now focusing on completing both mouse and chimpanzee Y chromosomes.

Just recently, Page and colleagues reported new findings focused on the X-degenerate regions of the human and chimpanzee Y chromosomes, which lack palindromes and partners for gene conversion.³ Ostensibly, genes contained in these regions should be more vulnerable to decay. Instead, they found the human Y chromosome has evolved virtually unscathed over an estimated 6 million years, with no hint of decay.

The chimpanzee hasn't fared nearly as well, however. Several genes were lost to inactivating mutations, most likely due to different selective pressures stemming from chimp promiscuity and sperm competition. The authors suspect that the Y chromosome's ampliconic genes, many of which are crucial for sperm production, may be susceptible to strong selective pressures that influence its evolution. Comparing Y-chromosome variability among both chimps and humans, they suggest, could reveal if this is the case, accounting for these seemingly divergent outcomes for Y.