Are Rapidly Evolving Human Promoter Regions Due To Higher Rates Of Neutral Substitution Or Positive Selection?

Nature Genetics just published a brief correspondence on the evolution of promoter regions in the human genome. The basis of this study relies on the observation that 46% of promoter regions in the human genome have a higher number of nucleotide substitutions than corresponding introns. The authors don’t make the distinction that positive selection, relaxed constraint or mutation rate are the causes of this observation, but they suggest that they have been important to hominid evolution and the genetic diversity of humans.

If you don’t know what a promoter is, I’ll give you a quick run down. Promoters are regions of the genome that are upstream from genes. Regulatory elements such as transcription factors bind to these regions and either start the expression of the gene that is downstream or regulate expression. Any changes to these region can affect phenotypes related to the gene downstream. Between two populations with the exact same intronic sequence of a gene, a difference in the promoter region can have dramatic effects.

In this current paper, “Rapidly evolving human promoter regions,” the authors respond to a previous paper on the subject. They reanalyzed the alignments used by the previous paper. They asked whether each promoter region as a whole is evolving more rapidly than local intronic sequences. They find that almost all (569/575; 99%) of the promoter regions identified by the previous paper as containing positively selected sites have a higher average substitution rate than their paired intronic regions.

The previous authors say that positive selection is at play. They based this conclusion on positive selection on introns. But the current authors caution that promoters are unusual genomic regions, and cannot be compared to selection on introns. They simiply conclude that promoters have higher neutral substitution rates. The previous authors respond to this in this same issue of Nature Genetics. They defend that the current authors methodology “do[es] not affirm their contention that mutation is generally accelerated in primate promoters.” Either way, both teams have identified that promoter regions of the human genome are highly diversified. The reason why they are, is still unresolved, but these conclusions do fall in line with previous ones that I’ve covered here on

    Martin S Taylor, Tim Massingham, Yoshihide Hayashizaki, Piero Carninci, Nick Goldman, Colin A M Semple (2008). Rapidly evolving human promoter regions Nature Genetics, 40 (11), 1262-1263 DOI: 10.1038/ng1108-1262
    Ralph Haygood, Olivier Fedrigo, Gregory A Wray (2008). Reply to “Rapidly evolving human promoter regions” Nature Genetics, 40 (11), 1263-1264 DOI: 10.1038/ng1108-1263

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