Ancient maps showed the known world in colourful detail, beyond the edges of which lay vast expanses of terra incognita. Much creative thought went into portraying this unexplored territory, often featuring nasty-looking serpents and dragons. Only when Magellan managed to circumnavigate the globe did it become apparent that the unknown was in fact navigable, and that the serpents and dragons, if not illusory, could at least be tamed. The human genome has its terra incognita too, some of it known, much of it subject to alternating angst and fascination by genome biologists, and all of it to be avoided if possible — until now. On pages 825 and 873 of this issue1, 2, a group of modern-day Magellans describe how they sailed headlong into the frothy seas of duplicated, inverted and otherwise troublesome sequences on the human Y chromosome. They have emerged safely on the other side, with tales to tell.
Because of its distinctive role in sex determination, the Y chromosome has long attracted special attention from geneticists, evolutionary biologists and even the lay public. It is known to consist of regions of DNA that show quite distinctive genetic behaviour and genomic characteristics. The two human sex chromosomes, X and Y (Fig. 1), originated a few hundred million years ago from the same ancestral autosome — a non-sex chromosome — during the evolution of sex determination3. They then diverged in sequence over the succeeding aeons. Nowadays, there are relatively short regions at either end of the Y chromosome that are still identical to the corresponding regions of the X chromosome, reflecting the frequent exchange of DNA between these regions ('recombination') that occurs during sperm production4. But more than 95% of the modern-day Y chromosome is male-specific, consisting of some 23 million base pairs (Mb) of euchromatin — the part of our genome containing most of the genes — and a variable amount of heterochromatin, consisting of highly repetitive DNA and often dismissed as non-functional. Now, in an accomplishment that can only be described as heroic, Skaletsky et al.1 report the complete sequence of the 23-Mb euchromatic segment, which they designate the MSY, for 'male-specific region of the Y'.
Figure 1: Male make-up.
The human X (left) and Y chromosomes, magnified about 10,000 times.
High resolution image and legend (110K)Prioritization in the Human Genome Project had led to the heterochromatic regions of the Y and other chromosomes being set aside to be dealt with later, if ever. But there was reason to hope that the euchromatin of the Y chromosome would present no more difficult a sequencing challenge than that found elsewhere in the genome. That supposition could not have been more wrong. As Skaletsky et al. report, the MSY is a mosaic of complex and interrelated sequences that made this one of the most problematic regions of the human genome thus far to be successfully sequenced and assembled.
For instance, about 10–15% of the MSY consists of stretches of sequence that moved there from the X chromosome within only the past few million years. These stretches are still 99% identical to their X-chromosome counterparts and are dominated by a high proportion of interspersed repetitive sequences, with only two genes. A further 20% of the MSY consists of a class of sequences ('X-degenerate' sequences1) that are more distantly related to the X chromosome, reflecting their more ancient common origin. And the remainder comprises a web of Y-specific repetitive sequences that make up a series of palindromes — sequences that read the same on both strands of the DNA double helix, with two 'arms' stretching out from a central point of mirrored symmetry. These palindromes come in a range of sizes, up to almost 3 Mb in length, with more than 99.9% identity between the two arms of each palindrome.
The repetitive sequences, particularly the palindromes, caused some difficulties for sequence assemblers. Genome-sequencing projects involve fragmenting the genome in question into small, overlapping pieces, sequencing them, and then using computer algorithms to put the pieces together in the correct order. There are various ways of doing this; assembling the MSY's palindromes (and discriminating between their arms) required an iterative mapping and sequencing process more reminiscent of the knowledge-based mapping approaches of the early days of the Human Genome Project than the high-throughput assemblies that have emerged for most of the genome5, 6. This strategy was aided by the fact that the sequence came from a single Y chromosome, so Skaletsky et al. knew that minor sequence variations must have come from duplicated copies on the same chromosome, rather than from different Y chromosomes. Although necessarily more painstaking, this overall approach provides a model for how researchers might attack at least some of the troublesome areas of the rest of the genome — such as blocks of repetitive heterochromatin and the hundreds of regions of substantial sequence duplication7 — where standard assembly programs can be fooled.
This is not just a celebratory tale of a successful sequencing journey, however. Along the way, Skaletsky et al. picked up artefacts of Y-chromosome antiquity, dating as far back as 300 million years, that allow a glimpse into the evolutionary strategies that the Y chromosome has used to survive.
For instance, from the degree and patterns of divergence of the genes found on both sex chromosomes, the authors provide evidence for the stepwise decay of the Y chromosome over time and define changes in both Y-chromosome organization and gene content and expression. Unlike the regions at the ends, most of the lengths of the sex chromosomes do not exchange sequence during sperm production, and Skaletsky et al. point to two consequences of this suppression of recombination. First, selection occurred on the Y chromosome for a group of testis-specific genes that the authors argue may have enhanced male fertility. Most of these genes are found within the palindromes, showing why it can be important to sequence such difficult regions. Second, as X–Y recombination became suppressed during evolution, an alternative mechanism had to emerge to maintain the sequence and function of the remaining Y-chromosome genes and to prevent the accumulation of inactivating mutations and the ultimate demise of the chromosome8.
To gain insight into this alternative mechanism, Rozen et al.2 examined the hypothesis that X–Y recombination has been replaced by extensive, ongoing recombination between the arms of the MSY palindromes — where the sequence on one arm of the palindrome alters or 'converts' the sequence on the other. To test the predictions of this model, the authors sequenced one particular palindrome-embedded gene from Y chromosomes from around the world, representing the full tree of the previously established Y-chromosome genealogy9. They found several instances where the sequence of the copy of the gene on one arm of the palindrome had altered the sequence of the other arm's copy. From this, they calculate that as many as 600 base pairs (from the 5.4 Mb contained in MSY palindromes) must be converted in each newborn male in the human population.
These data also indicate that gene conversion in general may be more common than previously suspected, especially in other palindromic and duplicated regions around the genome7. This supports a more dynamic view of genome change, in which, even within a single generation, not only does the occasional mutation occur (there are estimated to be as many as 100–200 new base-pair changes in each person), but also perhaps thousands of gene-conversion events.
The tales told by these Magellans of the genome hold two lessons for those who might question the wisdom of such exploration. First, even the most repetitive and seemingly impenetrable stretches of the genome hold secrets that justify the effort. Second, each chromosome has its own story to tell, quite apart from the story of the genome as a whole. Although the sex chromosomes provide the strongest case for a special relationship between genome organization and the unique biology of a chromosome10, 11, the other chromosomes shouldn't feel left out. Each is the product of hundreds of millions of years of evolution, shaped by processes that have rearranged and exchanged sequences, contributed to the formation of new species, given birth to new genes and gene families, and provided the basis for a range of genetically determined or genomically influenced traits. Piecing together these events remains a worthwhile challenge, for among the flotsam and jetsam of each chromosome lie clues to our history.
