CpG methylation recruits sequence specific transcription factors essential for tissue specific gene expression

Abstract

CG methylation is an epigenetically inherited chemical modification of DNA found in plants and animals. In mammals it is essential for accurate regulation of gene expression and normal development. Mammalian genomes are depleted for the CG dinucleotide, a result of the chemical deamination of methyl-cytosine in CG resulting in TpG. Most CG dinucleotides are methylated, but ~15% are unmethylated. Five percent of CGs cluster into ~20,000 regions termed CG islands (CGI) which are generally unmethylated. About half of CGIs are associated with housekeeping genes. In contrast, the gene body, repeats and transposable elements in which CGs are generally methylated. Unraveling the epigenetic machinery operating in normal cells is important for understanding the epigenetic aberrations that are involved in human diseases including cancer. With the advent of high-throughput sequencing technologies, it is possible to identify the CG methylation status of all 30million unique CGs in the human genome, and monitor differences in distinct cell types during differentiation and development. Here we summarize the present understanding of DNA methylation in normal cells and discuss recent observations that CG methylation can have an effect on tissue specific gene expression. We also discuss how aberrant CG methylation can lead to cancer. This article is part of a Special Issue entitled: Chromatin in time and space.

Figure 1

Frequency of CG dinucleotide across the human and drosophila genome shows the presence of CG clusters called CG Islands (CGI) only in the human genome.

Figure 2

CG methylation status of mouse promoters. Immunoprecipitated methylated DNA are hybridized to NimbleGen promoter arrays and the average methylation for each promoter is determined. Average methylation level (in log2) is plotted against number of CG dinucleotides (in log10) for each promoter. Two distinct clusters are formed, for low CG promoters, methylation increases with the CG density and they are methylated promoters while for high CG promoters, average methylation is low and are the unmethylated promoters.

Figure 3

Relative luciferase activity is measured for the 4X CRE reporter plasmid, which has no CG in backbone. Unmethylated version of the 4X-CRE is transactivated by the CREB transcription factor while methylated version of 4X-CRE is transactivated by the C/EBPα transcription factor.

Figure 4

5-azacytidine can prevent or cause tissue specific gene expression: A proposed model of methylation mediated tissue specific gene expression in normal and cancer cells. A) In normal cells low CG promoters are methylated and bound by C/EB;, while the high CG enhancers are unmethylated and activating the transcription. Demethylation by 5-azacytidine causes demethylation at the proximal promoters and inhibits binding of C/EBP and thus represses gene expression. B) In cancer cells, proximal promoters are methylated and bound by C/EB; while high CG enhancers become methylated, which causes formation of heterochromatin and thus tissue specific gene silencing. After 5- azacytidine treatment, demethylation begins stochastically at the high CG enhancers and allows transcription factor binding to activate differentiation specific genes.