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BioMed Research International
Volume 2013 (2013), Article ID 709042, 6 pages
http://dx.doi.org/10.1155/2013/709042
Research Article

CpGislandEVO: A Database and Genome Browser for Comparative Evolutionary Genomics of CpG Islands

1Departamento de Genética, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
2Laboratório de Bioinformática, Instituto de Biotecnología, Centro de Investigación Biomédica, 18100 Granada, Spain

Received 20 April 2013; Revised 12 July 2013; Accepted 19 August 2013

Academic Editor: Stephan Koblmüller

Copyright © 2013 Guillermo Barturen et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Hypomethylated, CpG-rich DNA segments (CpG islands, CGIs) are epigenome markers involved in key biological processes. Aberrant methylation is implicated in the appearance of several disorders as cancer, immunodeficiency, or centromere instability. Furthermore, methylation differences at promoter regions between human and chimpanzee strongly associate with genes involved in neurological/psychological disorders and cancers. Therefore, the evolutionary comparative analyses of CGIs can provide insights on the functional role of these epigenome markers in both health and disease. Given the lack of specific tools, we developed CpGislandEVO. Briefly, we first compile a database of statistically significant CGIs for the best assembled mammalian genome sequences available to date. Second, by means of a coupled browser front-end, we focus on the CGIs overlapping orthologous genes extracted from OrthoDB, thus ensuring the comparison between CGIs located on truly homologous genome segments. This allows comparing the main compositional features between homologous CGIs. Finally, to facilitate nucleotide comparisons, we lifted genome coordinates between assemblies from different species, which enables the analysis of sequence divergence by direct count of nucleotide substitutions and indels occurring between homologous CGIs. The resulting CpGislandEVO database, linking together CGIs and single-cytosine DNA methylation data from several mammalian species, is freely available at our website.