The churning grounds of the chimp genome
Posted: Thursday, September 25, 2003
by Laura Spinney, news.bmn.com
Dresden, Germany - Preliminary analyses of the sequenced chimp genome suggest that it contains many more duplications than the human genome. One school of thought suggests these areas of duplication might drive structural variation in the primate genome.
Whereas these areas of duplication were once thought to be devoid of useful information, they could perhaps explain the differences between human and chimp, according to Evan Eichler of Case Western Reserve University in Cleveland, Ohio, one of the main proponents of this school and the researcher behind the genome comparison.
The fact that the chimp has more duplications than us could reflect the genetic bottleneck that humans went through about 200,000 years ago, coinciding with their exodus from Africa and diffusion throughout Europe and Asia, he suggested at the European Life Sciences Organization Meeting.
Lacking that bottleneck, chimps have maintained a greater genetic diversity for longer and that may have provided more opportunity for duplications to become fixed in their genome. What is not in doubt, says Eichler, is that these duplication sites are "hotspots for rapid genomic change between human and chimp".
"Imagine them as churning grounds, or blenders in the genome," he says. "There is constant change, duplication, deletion and inversion at a high frequency. And unless that load becomes too high, so that it's negative to the organism as a whole and fitness is reduced, or a change occurs that is selectively advantageous, it will continue to do this churning."
The duplications can occur within chromosomes or between chromosomes, and whereas Eichler used to think that interchromosomal duplications were the most important hotspots, he has now "shifted his guns a little bit".
Duplications within chromosomes are more randomly distributed across the chromosome than the other kind, which tend to cluster in certain regions. And they also tend to occur in the genetically active euchromatic portions of the chromosome, as opposed to the less active heterochromatic parts.
"Transcription activity is higher in those regions of the euchromatin than they are in even unique sequences of the genome," says Eichler. "So we think those are going to be the most important for new genes."
Wolfgang Enard of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, is excited about this kind of large-scale genome comparison. Last year, he and his colleagues carried out their own comparison of mRNA and protein expression patterns in blood and postmortem brain tissue taken from humans and chimps, using microarrays, to see whether the differences in body and mind that set us apart from our nearest relatives lie in patterns of gene expression.
As far as the brain is concerned, Enard says they found significantly more differences in gene expression in the regions of the human genome where Eichler finds duplications. Once the chimp's own duplications have been fully analyzed, he adds, it will be possible to say which of the gene expression differences are associated with human-specific duplications, and which with chimp-specific duplications.
For other stories from ELSO 2003, click through to BioMedNet Conference Reporter
© Elsevier Limited 2003
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