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cis-Decoder discovers constellations of conserved DNA sequences shared among tissue-specific enhancers

Thomas Brody1*, Wayne Rasband2, Kevin Baler2, Alexander Kuzin1, Mukta Kundu1 and Ward F Odenwald1*

Author Affiliations

1 Neural Cell-Fate Determinants Section, NINDS, NIH, Bethesda, MD, 20892, USA

2 Office of Scientific Director, IRP, NIMH, NIH, Bethesda, MD, 20892, USA

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Genome Biology 2007, 8:R75  doi:10.1186/gb-2007-8-5-r75

Published: 9 May 2007


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.