Saturday, June 16, 2007

Dissecting the regulatory differences between human and chimp   posted by p-ter @ 6/16/2007 04:08:00 PM

Many evolutionary biologists are content to focus on large-scale trends in evolution-- they debate whether protein-coding or regulatory changes are more important in adaptive evolution, or look to compare the numbers of genes undergoing selection in different lineages. To each their own, of course, but I find those sorts of questions unsatisfying (for the moment), because ultimately, they cannot be answered without a molecular, reductionist approach. That is, the major breakthroughs in evolutionary biology will be in identifying specific molecular changes that have occurred during evolution and characterizing their phenotypic effects.

Case in point: the study of gene expression differences between humans and chimps. There have been a number of studies on the general trends in gene expression evolution between the two species. Some tissues are more constrained, some tissues less so. This is of interest, of course, but what we (I?) really want to know is: which specific genes are differentially regulated in humans as compared to chimps, in which tissues, when in development, and what specific genetic changes cause this differentil expression? The large-scale evolutionary trends will become apparent once this (extremely difficult) question is answered.

It's because of the apparent intractability of this question that people tend to shy away from it. However, that's starting to change. Last year, using a painstakingly constructed multi-species microarray (as opposed to the human specific one used-- to study both humans and chimps-- in previous studies), Yoav Gilad identified specific genes in the liver (chosen because of its relative homogeneity) that have undergone human specific regulatory changes.

Now, he's looking for the specific polymorphisms underlying these changes. A recently published pilot study explains the approach:
Most phenotypic differences between human and chimpanzee are likely to result from differences in gene regulation, rather than changes to protein coding regions. To date, however, only a handful of human-chimpanzee nucleotide differences leading to changes in gene regulation are known. In order to identify differences in regulatory elements between human and chimpanzee, we focused on ten genes that were previously found to be differentially expressed between the two species. We then designed reporter gene assays for the putative human and chimpanzee promoters of the ten genes. Of seven promoters that we found to be active in human liver cell lines, human and chimpanzee promoters had significantly different activity in four cases, three of which recapitulated the gene expression difference seen in the microarray experiment. For these three genes, we were therefore able to demonstrate that a change in cis influences expression differences between humans and chimpanzees. Moreover, using site directed mutagenesis on one construct, the promoter for the DDA3 gene, we were able to identify three nucleotides that together lead to a cis regulatory difference between the species. High-throughput application of this approach will provide a map of regulatory element differences between humans and our close evolutionary relatives.
Something to look forward to...

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