Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage 英文参考文献.docVIP

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Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage 英文参考文献.doc

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Open Access Re rch 2006SangesetVoal.lumesea7, Issue 7, Article R56 Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage Remo Sanges*, Eva Kalmar?, Pamela Claudiani*, Maria DAmato*, Ferenc Muller? and Elia Stupka* Addresses: *Telethon Institute of Genetics and Medicine, Via P. Castellino, 80131 Napoli, Italy. ?Institute of Toxicology and Genetics, Forschungzenbrum, Karlsruhe, Postfach 3640, D-76021 Karlsruhe, Germany. Correspondence: Ferenc Muller. Email: Ferenc.Mueller@itg.fzk.de. Elia Stupka. Email: elia@tigem.it Published: 19 July 2006 Received: 27 March 2006 Revised: 5 April 2006 Accepted: 27 June 2006 Genome Biology 2006, 7:R56 (doi:10.1186/gb-2006-7-7-r56) The electronic version of this article is the complete one and can be found online at /2006/7/7/R56 ? 2006 Sanges et al.; 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. uRegulatorynpdeArlgigonnme selementhnutfoflfinorgtshufflinghduolroinggouesvinovleuevolutionrtebratetion./ploci reveals that a significant proportion of conserved itcis/it-regulatory elements have Abstract Background: All vertebrates share a remarkable degree of similarity in their development as well as in the basic functions of their cells. Despite this, attempts at unearthing genome-wide regulatory elements conserved throughout the vertebrate lineage using BLAST-like approaches have thus far detected noncoding conservation in only a few hundred genes, mostly associated with regulation of transcription and development. Results: We used a unique combination of tools to obtain regional global-local alignments of orthologous loci. This approach takes into account shuffling of regulatory regions that are likely to occur over evolutionary dista