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Old 07-08-2011, 03:50 AM   #1
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Default ChIP-Seq: Genome-wide profiling of chromatin signatures reveals epigenetic regulation

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Genome-wide profiling of chromatin signatures reveals epigenetic regulation of microRNA genes in colorectal cancer.

Cancer Res. 2011 Jul 6;

Authors: Suzuki H, Takatsuka S, Akashi H, Yamamoto E, Nojima M, Maruyama R, Kai M, Yamano HO, Sasaki Y, Tokino T, Shinomura Y, Imai K, Toyota M

Altered expression of microRNAs (miRNAs) occurs commonly in human cancer but the mechanisms are generally poorly understood. In this study, we studied the contribution of epigenetic mechanisms to miRNA dysregulation in colorectal cancer (CRC) by performing high-resolution ChIP-seq. Specifically, we conducted genome-wide profiling of trimethylated histone H3 lysine 4 (H3K4me3), trimethylated histone H3 lysine 27 (H3K27me3) and dimethylated histone H3 lysine 79 (H3K79me2) in CRC cell lines. Combining miRNA expression profiles with chromatin signatures enabled us to predict the active promoters of 233 miRNAs encoded in174 putative primary transcription units. By then comparing miRNA expression and histone modification before and after DNA demethylation, we identified 47 miRNAs encoded in 37 primary transcription units as potential targets of epigenetic silencing. The promoters of 22 transcription units were associated with CpG islands (CGIs), all of which were hypermethylated in CRC cells. DNA demethylation led to increased H3K4me3 marking at silenced miRNA genes, whereas no restoration of H3K79me2 was detected in CGI methylated miRNA genes. DNA demethylation also led to upregulation of H3K4me3 and H3K27me3 in a number of CGI-methylated miRNA genes. Among the miRNAs we found to be dysregulated, many of which are implicated in human cancer, miR-1-1 was methylated frequently in early and advanced CRC where it may act as a tumor suppressor. Our findings offer insight into the association between chromatin signatures and miRNA dysregulation in cancer, and they also suggest that miRNA re-expression may contribute to the effects of epigenetic therapy.

PMID: 21734013 [PubMed - as supplied by publisher]

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