Abstract 996: MBD-capture coupled with next generation sequencing elucidates genome-wide crosstalk between epigenetic marks and its role in cancer

Abstract

Abstract Aberrations in DNA methylation are a hallmark of cancer, and these epigenetic changes lead to tumor suppressor gene silencing by hypermethylation, global genomic hypomethylation, and genomic instabilities. Post-translational histone modifications are important epigenetic marks that have been implicated in regulating DNA methylation patterning. Several known histone marks, including methylation of histone H3 at lysines 4 and 27 and monoubiquitylation of histone H2A (H3K4me, H3K27me, and H2Aub, respectively), are believed to differentially regulate DNA methyltransferase activity on DNA. The histone mark H3K4me is associated with gene activation, and H3K27me and H2Aub are associated with loci of transcriptional repression and DNA methylation, especially at hypermethylated genes in cancer. Recent studies have examined the genome-wide distribution of these histone modifications or have studied how their distribution relates to DNA methylation within specific loci, but these studies have not ascribed specific roles to these histone modifications in DNA methylation patterning, nor do we understand why only subsets of genes throughout the genome become hypermethylated in cancer. This poster demonstrates how the histone marks H3K4me, H3K27me, and H2Aub affect genome-wide DNA methylation patterning and transcriptional regulation, and we highlight several epigenetic targets of H3K27me and H2Aub epigenetic repression that participate in the pathogenesis of cancer. We have used siRNA transfection in NCCIT human embryonic carcinoma cells to target critical subunits of the complexes that establish each of these histone modifications. Through these siRNA treatments, we assessed the roles of each mark in establishing DNA methylation patterns throughout the genome and how these patterns relate to genome-wide gene expression. The effects of histone mark deficiency were analyzed by an assay that isolates methylated-CpG-containing DNA (MBD-capture) coupled to massively parallel DNA sequencing to identify sequences with altered methylation patterns. These sequencing results were correlated with patterns of gene expression determined by expression microarray analysis to identify gene targets whose epigenetic misregulation results in alterations in gene expression. In total, this poster demonstrates how histone modifications contribute to the control of the human DNA methylome and postulates how these marks exert downstream effects toward the pathogenesis of cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 996. doi:1538-7445.AM2012-996