THE ROLE OF CIS- AND TRANS-ACTING FACTORS IN REGULATION OF DNA METHYLATION

Abstract

High level DNA methylation of promoter CpG islands (CGIs) represses gene expression. However, low-level CGI methylation is currently not distinguished from complete absence of methylation in the literature. Here we show that very low levels of methylation or methylation seeds (1-20%) on promoter CGIs is present in 5-20% of human genes and negatively correlates with gene expression in all tissues examined. In vitro, seeding directly represses reporter gene expression, an effect mediated by methyl-CpG-binding proteins as transient knockdown of MBD4 reverses this repression. In vivo, seeded genes are enriched for polycomb occupancy but seeding can also occur in H3K4me3 occupied promoters, where it also correlates with gene repression independently of Polycomb repressive complex binding. Seeded CGIs in normal WBCs are 19 fold and 65 fold more likely to gain hypermethylation in Acute Myelogenous Leukemia and Myelodysplastic Syndrome patients respectively, compared to unmethylated CGIs (i.e. those with <1% methylation). This study reveals a novel epigenetic mechanism of tissue specific methylation seeds that have strong effects on gene expression in healthy tissues, possess unique histone status, and predispose to gain of methylation in leukemias more so than previously known factors. In the second part, we analyzed the role of chromodomain protein CHD7 in CpG island methylator phenotype (CIMP) Colorectal Cancers (CRCs). Analysis of CHD7 target genes identified that frequently methylated genes in CIMP-positive CRCs have significantly higher enrichment of CHD7 occupancy in mouse neural stem cells and are among genes regulated by CHD7 in mouse embryonic stem cells. This study provides evidence for a causal link between CHD7 mutations in CRCs and the CIMP phenotype.