CG dinucleotide clustering is a species-specific property of the genome

Glass, J. L. et al. (2007) CG dinucleotide clustering is a species-specific property of the genome. Nucleic Acids Research, 35(20), pp. 6798-6807. (doi: 10.1093/nar/gkm489)

Abstract

Cytosines at cytosine-guanine (CG) dinucleotides are the near-exclusive target of DNA methyltransferases in mammalian genomes. Spontaneous deamination of methylcytosine to thymine makes methylated cytosines unusually susceptible to mutation and consequent depletion. The loci where CG dinucleotides remain relatively enriched, presumably due to their unmethylated status during the germ cell cycle, have been referred to as CpG islands. Currently, CpG islands are solely defined by base compositional criteria, allowing annotation of any sequenced genome. Using a novel bioinformatic approach, we show that CG clusters can be identified as an inherent property of genomic sequence without imposing a base compositional a priori assumption. We also show that the CG clusters co-localize in the human genome with hypomethylated loci and annotated transcription start sites to a greater extent than annotations produced by prior CpG island definitions. Moreover, this new approach allows CG clusters to be identified in a species-specific manner, revealing a degree of orthologous conservation that is not revealed by current base compositional approaches. Finally, our approach is able to identify methylating genomes (such as Takifugu rubripes) that lack CG clustering entirely, in which it is inappropriate to annotate CpG islands or CG clusters.

• Item Type: Articles
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Olivier, Dr Emmanuel
• Authors: Glass, J. L., Thompson, R. F., Khulan, B., Figueroa, M. E., Olivier, E. N., Oakley, E. J., Van Zant, G., Bouhassira, E. E., Melnick, A., Golden, A., Fazzari, M. J., and Greally, J. M.
• College/School: College of Medical Veterinary and Life Sciences > School of Cardiovascular & Metabolic Health
• Journal Name: Nucleic Acids Research
• Publisher: Oxford University Press
• ISSN: 0305-1048
• ISSN (Online): 1362-4962
• Copyright Holders: Copyright © 2007 The Authors
• First Published: First published in Nucleic Acids Research 35(20):6798-6807
• Publisher Policy: Reproduced under a Creative Commons License

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