title: cis-Decoder discovers constellations of conserved DNA sequences shared among tissue-specific enhancers.
abstract: 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.
authors.affiliation: Neural Cell-Fate Determinants Section, NINDS, NIH, Bethesda, MD 20892, USA. brodyt@ninds.nih.gov
authors.forename: Thomas
authors.initials: T
authors.lastname: Brody
authors.forename: Wayne
authors.initials: W
authors.lastname: Rasband
authors.forename: Kevin
authors.initials: K
authors.lastname: Baler
authors.forename: Alexander
authors.initials: A
authors.lastname: Kuzin
authors.forename: Mukta
authors.initials: M
authors.lastname: Kundu
authors.forename: Ward F
authors.initials: WF
authors.lastname: Odenwald
mesh_terms: 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