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

doi:10.1186/gb-2007-8-5-r75

Genome Biology
Volume 8
Issue 5

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Brody T
Rasband W
Baler K
Kuzin A
Kundu M
Odenwald WF

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Rasband W
Baler K
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Kundu M
Odenwald WF
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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

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

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

author email corresponding author email

Genome Biology 2007, 8:R75doi:10.1186/gb-2007-8-5-r75


Published:	9 May 2007

Subject areas: Bioinformatics, Molecular biology, Genome studies

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.