Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons.
BACKGROUND
Genomic 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.


RESULTS
To 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.


CONCLUSIONS
We 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.
Wang
Qian-fei
QF
Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA. qwang2@medicine.bsd.uchicago.edu
Prabhakar
Shyam
S
Chanan
Sumita
S
Cheng
Jan-Fang
JF
Rubin
Edward M
EM
Boffelli
Dario
D
D000818:Animals; D001483:Base Sequence; D017124:Conserved Sequence; D021901:DNA, Intergenic / Q000235:genetics; D019143:Evolution, Molecular; D016678:Genome; D000882:Haplorhini / Q000235:genetics; D008322:Mammals / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D011323:Primates / Q000235:genetics*; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity; D051780:Sterol Regulatory Element Binding Protein 1 / Q000235:genetics
D021901:DNA, Intergenic; D051780:Sterol Regulatory Element Binding Protein 1