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A human B cell methylome at 100-base pair resolution

Author:
Rauch, Tibor A., Wu, Xiwei, Zhong, Xueyan, Riggs, Arthur D., Pfeifer, Gerd P.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2009 v.106 no.3 pp. 671-678
ISSN:
0027-8424
Subject:
DNA methylation, chromosomes, gene expression, genes, genomic islands, humans
Abstract:
Using a methylated-DNA enrichment technique (methylated CpG island recovery assay, MIRA) in combination with whole-genome tiling arrays, we have characterized by MIRA-chip the entire B cell "methylome" of an individual human at 100-bp resolution. We find that at the chromosome level high CpG methylation density is correlated with subtelomeric regions and Giemsa-light bands (R bands). The majority of the most highly methylated regions that could be identified on the tiling arrays were associated with genes. Approximately 10% of all promoters in B cells were found to be methylated, and this methylation correlates with low gene expression. Notably, apparent exceptions to this correlation were the result of transcription from previously unidentified, unmethylated transcription start sites, suggesting that methylation may control alternate promoter usage. Methylation of intragenic (gene body) sequences was found to correlate with increased, not decreased, transcription, and a methylated region near the 3' end was found in approximately 12% of all genes. The majority of broad regions (10-44 kb) of high methylation were at segmental duplications. Our data provide a valuable resource for the analysis of CpG methylation patterns in a differentiated human cell type and provide new clues regarding the function of mammalian DNA methylation.
Agid:
2362959