Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisonsReport as inadecuate

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Genome Biology

, 8:R1

First Online: 03 January 2007Received: 02 September 2006Revised: 15 November 2006Accepted: 03 January 2007


BackgroundGenomic comparisons between human and distant, non-primate mammals are commonly used to identify cis-regulatory elements based on constrained sequence evolution. However, these methods fail to detect functional elements that are too weakly conserved among mammals to distinguish them from non-functional DNA.

ResultsTo evaluate a strategy for large scale genome annotation that is complementary to the commonly used distal species comparisons, we explored the potential of deep intra-primate sequence comparisons. We sequenced the orthologs of 558 kb of human genomic sequence, covering multiple loci involved in cholesterol homeostasis, in 6 non-human primates. Our analysis identified six non-coding DNA elements displaying significant conservation among primates but undetectable in more distant comparisons. In vitro and in vivo tests revealed that at least three of these six elements have regulatory function. Notably, the mouse orthologs of these three functional human sequences had regulatory activity despite their lack of significant sequence conservation, indicating that they are ancestral mammalian cis-regulatory elements. These regulatory elements could be detected even in a smaller set of three primate species including human, rhesus and marmoset.

ConclusionWe have demonstrated that intra-primate sequence comparisons can be used to identify functional modules in large genomic regions, including cis-regulatory elements that are not detectable through comparison with non-mammalian genomes. With the available human and rhesus genomes and that of marmoset, which is being actively sequenced, this strategy can be extended to the whole genome in the near future.

Electronic supplementary materialThe online version of this article doi:10.1186-gb-2007-8-1-r1 contains supplementary material, which is available to authorized users.

Qian-fei Wang, Shyam Prabhakar contributed equally to this work.

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Author: Qian-fei Wang - Shyam Prabhakar - Sumita Chanan - Jan-Fang Cheng - Edward M Rubin - Dario Boffelli


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