Comprehensive analysis of the base composition around the transcription start site in Metazoa.docVIP

BMC Genomics BioMedCentral Research article Open Access Comprehensive analysis of the base composition around the transcription start site in Metazoa Stein Aerts*1, Gert Thijs1, Michal Dabrowski2, Yves Moreau1,3 and Bart De Moor1 Address: 1Department of Electrical Engineering (ESAT-SCD), Katholieke Universiteit Leuven, Belgium, 2Laboratory of Transcription Regulation, Nencki Institute, Warsaw, Poland and 3On leave at Center for Biological Sequence Analysis, BioCentrum, Technical University of Denmark, Lyngby, Denmark Email: Stein Aerts* - stein.aerts@esat.kuleuven.ac.be; Gert Thijs - gert.thijs@esat.kuleuven.ac.be; Michal Dabrowski - m.dabrowski@.pl; Yves Moreau - yves.moreau@esat.kuleuven.ac.be; Bart De Moor - bart.demoor@esat.kuleuven.ac.be * Corresponding author Published: 01 June 2004 Received: 27 January 2004 Accepted: 01 June 2004 BMC Genomics 2004, 5:34 This article is available from: /1471-2164/5/34 ? 2004 Aerts et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the articles original URL. Abstract Background: The transcription start site of a metazoan gene remains poorly understood, mostly because there is no clear signal present in all genes. Now that several sequenced metazoan genomes have been annotated, we have been able to compare the base composition around the transcription start site for all annotated genes across multiple genomes. Results: The most prominent feature in the base compositions is a significant local variation in G+C content over a large region around the transcription start site. The change is present in all animal phyla but the extent of variation is different between distinct classes of vertebrates, and the shape of the variation is completely different between vertebrates and arthropods. Furthermore, the height of the vari