Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach.docVIP

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Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach.doc

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Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach

Open Access Me od 2005ElementoVolumthe 6,andIssuTavazoiee 2, Article R18 Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach Olivier Elemento and Saeed Tavazoie Address: Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA. Correspondence: Saeed Tavazoie. E-mail: tavazoie@ Published: 26 January 2005 Received: 1 September 2004 Revised: 29 October 2004 Accepted: 3 December 2004 Genome Biology 2005, 6:R18 The electronic version of this article is the complete one and can be found online at /2005/6/2/R18 ? 2005 Elemento and Tavazoie; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Genome-widertoeprqyuTierhleeemaaleiugntnhtsmo,rdiscoveryemsndatnse.syIcotrsifbawepofhapilconservedpihcoawsthieoornfwutlsoaupregulatoryprappirrriossaioncfhgycfeooarelementsnstdiscoveringsse,rwvaotrimon, falicegloballyrsosasnldarmgconservedaemphmyalolsg,eyniregulatoryeltdicsdaislatargnecelementsensu.m/bper betweenof knowntwoandgenomesnovel puthattativdoese regunotla- Abstract We describe a powerful new approach for discovering globally conserved regulatory elements between two genomes. The method is fast, simple and comprehensive, without requiring alignments. Its application to pairs of yeasts, worms, flies and mammals yields a large number of known and novel putative regulatory elements. Many of these are validated by independent biological observations, have spatial and/or orientation biases, are co-conserved with other elements and show surprising conservation across large phylogenetic distances. Background have so far relied mostly on detecting locally conserved motifs within global alignments of o