cis-Decoder discovers constellations of conserved DNA sequences shared among tissue-specific enhancers.
A systematic approach is described for analysis of evolutionarily conserved cis-regulatory DNA using cis-Decoder, a tool for discovery of conserved sequence elements that are shared between similarly regulated enhancers. Analysis of 2,086 conserved sequence blocks (CSBs), identified from 135 characterized enhancers, reveals most CSBs consist of shorter overlapping/adjacent elements that are either enhancer type-specific or common to enhancers with divergent regulatory behaviors. Our findings suggest that enhancers employ overlapping repertoires of highly conserved core elements.
Brody
Thomas
T
Neural Cell-Fate Determinants Section, NINDS, NIH, Bethesda, MD 20892, USA. brodyt@ninds.nih.gov
Rasband
Wayne
W
Baler
Kevin
K
Kuzin
Alexander
A
Kundu
Mukta
M
Odenwald
Ward F
WF
D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D017124:Conserved Sequence; D004742:Enhancer Elements, Genetic / Q000235:genetics*; D006801:Humans; D016415:Sequence Alignment