Thursdays and Fridays are big days for science news, since Nature comes out on Thursday and Science on Friday. PNAS seems to have new articles every day. News that is embargoed can now be published. So I scan the Table of Contents for interesting articles.
This one caught me eye: Phylogenetic Shadowing of Primate Sequences to Find Functional Regions of the Human Genome. Now I have no idea what the heck ‘phylogenetic shadowing’ is. A Google search finds 4 articles, all by the current authors, so this must be a neologism and will require reading of the article to determine what it means.
Help is on the way
Luckily, there is something from Eurekalert that gives a lot more detail of the process. With the title Scientists Find That Apes and Monkeys Provide Needed Help in Understanding the Human Genome it provides a nice background. Normally, we compare genomes of animals that had a last common ancestor maybe 100 million years ago. This is because it is much more difficult to find important genes in animals that are closely related. There are not enough differences to provide us any clues as to where important genes are.
A metaphor one of the authors uses is that comparing mice and humans is like looking at a go-cart and a car. Easy to detail the differences. But comparing baboons to humans, whose genomes are 95% similar, is like looking at a sedan and a station wagon. The differences are harder to detail, they are more subtle.
Comparing multiple genomes
If you look at humans and chimps, almost everything is the same, non-essential DNA from introns and the coding sequences from exons. But these researchers found a way. They simultaneously looked at the genomes of up to 15 non-human primates. The increase in information, coupled with filtering tools, helped tremendously. Now minor differences between each of them could be used to cumulatively identify the regions that coded for protein and those that did not.
They demonstrated the usefulness of this approach by examining a gene only found in primates, apolipoprotein A. This is a gene that may have some very important ramifications in heart disease. Using any other mammal than primates would have been useless. Using phylogenetic shadowing they were able to identify the regulatory regions that control expression of this gene. So, not only did they develop a novel approach for filtering the huge amount of information found today, they used it to examine a clinically relevant protein. Nice to see the combination of novelty and relevance.
