TY - JOUR
T1 - Finding cis-regulatory elements using comparative genomics
T2 - Some lessons from ENCODE data
AU - King, David C.
AU - Taylor, James
AU - Zhang, Ying
AU - Cheng, Yong
AU - Lawson, Heather A.
AU - Martin, Joel
AU - Chiaromonte, Francesca
AU - Miller, Webb
AU - Hardison, Ross C.
PY - 2007/6
Y1 - 2007/6
N2 - Identification of functional genomic regions using interspecies comparison will be most effective when the full span of relationships between genomic function and evolutionary constraint are utilized. We find that sets of putative transcriptional regulatory sequences, defined by ENCODE experimental data, have a wide span of evolutionary histories, ranging from stringent constraint shown by deep phylogenetic comparisons to recent selection on lineage-specific elements. This diversity of evolutionary histories can be captured, at least in part, by the suite of available comparative genomics tools, especially after correction for regional differences in the neutral substitution rate. Putative transcriptional regulatory regions show alignability in different clades, and the genes associated with them are enriched for distinct functions. Some of the putative regulatory regions show evidence for recent selection, including a primate-specific, distal promoter that may play a novel role in regulation.
AB - Identification of functional genomic regions using interspecies comparison will be most effective when the full span of relationships between genomic function and evolutionary constraint are utilized. We find that sets of putative transcriptional regulatory sequences, defined by ENCODE experimental data, have a wide span of evolutionary histories, ranging from stringent constraint shown by deep phylogenetic comparisons to recent selection on lineage-specific elements. This diversity of evolutionary histories can be captured, at least in part, by the suite of available comparative genomics tools, especially after correction for regional differences in the neutral substitution rate. Putative transcriptional regulatory regions show alignability in different clades, and the genes associated with them are enriched for distinct functions. Some of the putative regulatory regions show evidence for recent selection, including a primate-specific, distal promoter that may play a novel role in regulation.
UR - http://www.scopus.com/inward/record.url?scp=34250358295&partnerID=8YFLogxK
U2 - 10.1101/gr.5592107
DO - 10.1101/gr.5592107
M3 - Article
C2 - 17567996
AN - SCOPUS:34250358295
SN - 1088-9051
VL - 17
SP - 775
EP - 786
JO - Genome research
JF - Genome research
IS - 6
ER -