Brendan Maher in Nature:
The mammalian Y chromosome has long been thought of as a sort of genomic wasteland, usually shrinking over the course of evolution and largely bereft of pertinent information. Page’s work has helped to change perceptions of the Y chromosome by revealing that it contains remarkable patterns of repeating sequences that appear dozens to hundreds of times1, 2. But the structure of these sequences and precise measures of how often they repeat have been difficult to determine. Standard sequencing technologies often cannot distinguish between long stretches of genetic code that differ by a single DNA ‘letter’. Page and his collaborators avoided this problem by using what he calls ‘super-resolution’ sequencing (a technique better known as single-haplotype iterative mapping and sequencing, or SHIMS), which can detect such minute variation between lengthy segments of DNA.
The team sequenced many large, continuous stretches of the Y chromosome and carefully scrutinized the areas that looked as if they overlapped. They found that repeating structures make up about 24% of the accessible DNA in the human Y chromosome, and 44% of that of the bull. And in the Y chromosome of the mouse, which is much larger than that of a human, repeating structures make up almost 90% of accessible DNA. The intricate patterns, which often contain palindromes — sequence that reads the same in forward and reverse order — carry three families of protein-coding genes. What the genes are doing — and how they got there — remains a mystery, however.