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Bioinformatic interrogation of expression array data to identify nutritionally regulated genes potentially modulated by DNA methylation

Lookup NU author(s): Dr Jill McKay, Professor Dianne Ford, Professor Caroline Relton, Professor John Mathers


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DNA methylation occurs at CpG dinucleotide sites within the genome and is recognised as one of the mechanisms involved in regulation of gene expression. CpG sites are relatively underrepresented in the mammalian genome, but occur densely in regions called CpG islands (CGIs). CGIs located in the promoters of genes inhibit transcription when methylated by impeding transcription factor binding. Due to the malleable nature of DNA methylation, environmental factors are able to influence promoter CGI methylation patterns and thus influence gene expression. Recent studies have provided evidence that nutrition (and other environmental exposures) can cause altered CGI methylation but, with a few exceptions, the genes influenced by these exposures remain largely unknown. Here we describe a novel bioinformatics approach for the analysis of gene expression microarray data designed to identify regulatory sites within promoters of differentially expressed genes that may be influenced by changes in DNA methylation.

Publication metadata

Author(s): Mckay JA, Adriaens ME, Ford D, Relton CL, Evelo CTA, Mathers JC

Publication type: Article

Publication status: Published

Journal: Genes & Nutrition

Year: 2008

Volume: 3

Issue: 3-4

Pages: 167-171

ISSN (print): 1555-8932

ISSN (electronic): 1865-3499

Publisher: Springer


DOI: 10.1007/s12263-008-0095-0


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