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MBE Advance Access published online on May 9, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn110
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© The Author 2008. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

DNA METHYLATION AND STRUCTURAL AND FUNCTIONAL BIMODALITY OF VERTEBRATE PROMOTERS

Navin Elango and Soojin V. Yi*

School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332, USA

* Corresponding author: Soojin Yi (soojinyi{at}gatech.edu). Phone: 404-385-6084, Fax: 404-894-2295

Received for publication April 24, 2008. Accepted for publication April 29, 2008.

Human promoters divide into two classes, the low CpG (LCG) and the high CpG (HCG), based on their CpG dinucleotide content. The LCG class of promoters is hyper-methylated and is associated with tissue-specific genes, while the HCG class is hypo-methylated and associated with broadly-expressed genes. By analyzing several chordate genomes separated for hundreds of millions of years, here we show that the divide between low CpG and high CpG promoters is conserved in several distantly related vertebrate taxa (including human, chicken, frog, lizard, and fish), but not in close invertebrate outgroups (sea squirts). Furthermore, LCG and HCG promoters are distinctively associated with tissue-specific and broadly expressed genes in these distantly related vertebrate taxa. Our results indicate that the function of DNA methylation on gene expression is conserved across these vertebrate taxa and suggest that the two classes of promoters have evolved early in vertebrate evolution, as a consequence of the advent of global DNA methylation.

Key Words: DNA methylation • promoter • expression • genome evolution • vertebrates


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