Transcription onset of genes critical in liver carcinogenesis is epigenetically regulated by methylated DNA-binding protein MBD2

Abstract

We previously delineated genes whose promoters are hypomethylated and induced in hepatocellular carcinoma (HCC) patients. The purpose of this study was to establish the players that regulate these genes in liver cancer cells. We performed chromatin immunoprecipitation with methyl-CpG-binding domain protein 2 (MBD2), RNA polymerase II (RNA pol II), CCAAT/enhancer-binding protein alpha (CEBPA) antibodies and methylated DNA immunoprecipitation in HepG2 liver cancer cells treated with scrambled small interfering RNA (siRNA) and siRNA to MBD2 or CEBPA. We then hybridized DNA to microarrays spanning the entire coding sequences, introns and regulatory regions of several hundred HCC-hypomethylated genes. These analyses reveal that MBD2 binds a significant fraction of the hypomethylated genes, determines RNA pol II binding and DNA methylation state. MBD2 binding can result in promoter activation and hypomethylation or in repression. In activated target genes, MBD2 colocalizes with the transcription factor CEBPA, and MBD2 binding at these positions is reduced upon CEBPA depletion. Significant fraction of MBD2 effects on DNA methylation and transcription appears to be indirect since changes occur upon MBD2 depletion in genes where no MBD2 binding was detected. Our study delineates the rules governing the interaction of MBD2 with its targets and the consequences to RNA pol II binding and DNA methylation states. This has important implications for understanding the role of DNA methylation in cancer and targeting DNA methylation proteins in cancer therapy.

Anticancer Natural Compounds as Epigenetic Modulators of Gene Expression

“…Modulation of DNA methylation patterns by retinoic acid can contribute to its anti-proliferative, and pro-apoptotic actions observed in leukemia, breast, prostate, pancreatic, and head and neck cancers [323-331]. Treatment of human MCF-7 breast cancer cells with retinoid acid reduced promoter methylation and increased in the expression of RARβ2 and PTEN tumor suppressor genes, as well as inhibited breast cancer growth [84, 186, 332, 333]. Genome-wide analysis of the potential effects of all-trans retinoid acids on gene methylation and expression in neuroblastoma revealed that retinoic acid compounds reduced the expression of methyltransferases, DNMT1 and DNMT3B, while induced the expression of microRNAs targeting these DNMT proteins [334, 335].…”

Stilbenoid‐Mediated Epigenetic Activation of Semaphorin 3A in Breast Cancer Cells Involves Changes in Dynamic Interactions of DNA with DNMT3A and NF1C Transcription Factor

“…It occurs mostly within tumor suppressor genes (TSGs) leading to their silencing, which can participate in tumor formation. In contrast, promoters of certain genes functionally linked to processes accelerating carcinogenesis become hypomethylated, which leads to their upregulation and contributes to cancer . Thus, reversing alterations in DNA methylation constitutes an excellent anti‐cancer approach.…”

Genome-Wide Binding of MBD2 Reveals Strong Preference for Highly Methylated Loci

“…Since promoter hyper-methylation is a well-known hallmark of cancer, several studies linked MBD2 function to epigenetic regulation of genes critical during carcinogenesis [18], [19], however, most of these studies looked at a limited number of target genes. Recent studies challenged the model of MBD2 as a predominantly promoter-proximal repressor suggesting that binding could also regulate activity of target genes [20].…”