And Then There was Y

The Y chromosome gets no respect.

Nicole Johnston(njohnston@the-scientist.com)
Sep 25, 2005
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Courtesy of Flashback Imaging

The Y chromosome gets no respect. Regarded as a genetic junkyard with little to offer but sex, genomes have commonly rolled off the presses without a nod to Y. Then there's the matter of decay. Without a recombination partner, genetic insults whittle away the already diminutive Y, suggesting the chromosome's, and by extension man's, eventual extinction.

But this issue's Hot Papers refute the entrenched view of the Y chromosome. One showcases its sequence,1 and the other sizes up the male chromosome across humans and other primates.2 The emerging picture turns out to be not so bleak for the fate of man. The studies reveal a crafty recombination method, ensuring Y's survival for generations. Recent work making comparisons with the completed chimpanzee genome has increased the clarity of the Y portrait, but also left a few new questions.3

AN IMPERFECT PAIR

X and Y are believed to have arisen from a common autosomal pair that gradually diverged because of progressively impaired X-Y recombination. Y literally ended up with the short end of the genetic stick. Although some X-Y crossing over occurs during male meiosis, 95% of the Y chromosome is on its own, having no partner with which to recombine. Consequently, Y lost much of its size compared to the X chromosome. The genes on the Y chromosome were thought to rot over time without a backup copy or the ability to swap out through meiosis.

In 2003, geneticist David Page and colleagues at the Whitehead Institute for Biomedical Research in Cambridge, Mass., and at Washington University in St. Louis, described, for the first time, the sequence of the male-specific region of the Y chromosome (MSY), which distinguishes the sexes and accounts for 95% of the chromosome's length.1 "This was the first time that any Y chromosome was sequenced," says coauthor Steve Rozen, a Whitehead Institute geneticist.

Data derived from the Science Watch/Hot Papers database and the Web of Science (Thomson Scientific, Philadelphia) show that Hot Papers are cited 50 to 100 times more often than the average paper of the same type and age.

"The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes," Skaletsky H, Nature , 2003 Vol 423, 825-37 (cited in 181 papers, Hist Cite Analysis)"Abundant gene conversion between arms of palindromes in human and ape Y chromosomes," Rozen S, Nature , 2003 Vol 423, 873-6 (cited in 60 papers, Hist Cite Analysis)

When the Drosophila melanogaster genome was sequenced in 2000, the Y chromosome was left out. The human genome sequence, drafted in 2001, similarly made little mention of Y. "It was thought to be so devoid of biological interest as not to be worthy of serious study," says Page. One of the gross oversights of the genomic revolution, he says, is that "it was thought to be completely understandable and excusable to declare a genome complete without sequencing the Y."

Sequencing any human chromosome is a difficult task, but Y proved to be a different creature altogether, requiring Herculean efforts to decipher its unusual code. The Human Genome Project was designed for autosomes, with the X chromosome limping behind, explains Hunt Willard, a genomicist at Duke University, who wrote an accompanying commentary for both papers.4 With Y, they had to come up with new approaches to map and sequence its DNA. The methods used to decode most genomes were just not going to work with Y's duplicated and inverted genome, says Willard.

"The Y chromosome is like a jigsaw puzzle where most of the pieces are a blue sky without many clouds," says coauthor Richard Wilson, a geneticist at Washington University.

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.

<p>A MAN, A PLAN, A PALINDROME:</p>

© 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.