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 charact...

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Detalles Bibliográficos
Autores principales: Brody, Thomas, Rasband, Wayne, Baler, Kevin, Kuzin, Alexander, Kundu, Mukta, Odenwald, Ward F
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2007
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1929141/
https://www.ncbi.nlm.nih.gov/pubmed/17490485
http://dx.doi.org/10.1186/gb-2007-8-5-r75
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author Brody, Thomas
Rasband, Wayne
Baler, Kevin
Kuzin, Alexander
Kundu, Mukta
Odenwald, Ward F
author_facet Brody, Thomas
Rasband, Wayne
Baler, Kevin
Kuzin, Alexander
Kundu, Mukta
Odenwald, Ward F
author_sort Brody, Thomas
collection PubMed
description 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.
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spelling pubmed-19291412007-07-21 cis-Decoder discovers constellations of conserved DNA sequences shared among tissue-specific enhancers Brody, Thomas Rasband, Wayne Baler, Kevin Kuzin, Alexander Kundu, Mukta Odenwald, Ward F Genome Biol Method 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. BioMed Central 2007 2007-05-09 /pmc/articles/PMC1929141/ /pubmed/17490485 http://dx.doi.org/10.1186/gb-2007-8-5-r75 Text en Copyright © 2007 Brody et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Method
Brody, Thomas
Rasband, Wayne
Baler, Kevin
Kuzin, Alexander
Kundu, Mukta
Odenwald, Ward F
cis-Decoder discovers constellations of conserved DNA sequences shared among tissue-specific enhancers
title cis-Decoder discovers constellations of conserved DNA sequences shared among tissue-specific enhancers
title_full cis-Decoder discovers constellations of conserved DNA sequences shared among tissue-specific enhancers
title_fullStr cis-Decoder discovers constellations of conserved DNA sequences shared among tissue-specific enhancers
title_full_unstemmed cis-Decoder discovers constellations of conserved DNA sequences shared among tissue-specific enhancers
title_short cis-Decoder discovers constellations of conserved DNA sequences shared among tissue-specific enhancers
title_sort cis-decoder discovers constellations of conserved dna sequences shared among tissue-specific enhancers
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1929141/
https://www.ncbi.nlm.nih.gov/pubmed/17490485
http://dx.doi.org/10.1186/gb-2007-8-5-r75
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