Cell type–specific DNA methylation at intragenic CpG islands in the immune system

TLDR

Human and mouse genomes contain a comparable number of CpG islands, about half of which lie away from annotated promoters yet often exhibit promoter‑like characteristics. To determine the role of CGI methylation in cell differentiation, we analyzed DNA methylation across a comprehensive CGI set in mouse hematopoietic lineage cells. Using a method that can detect roughly one‑third of genomic CpGs in the methylated state, we examined methylation patterns and found that large gene expression differences were accompanied by surprisingly few DNA methylation changes. We observed extensive DNA methylation differences between hematopoietic cells and brain, with intragenic CGIs showing methylation changes that correlate with gene silencing and a repressive chromatin state, indicating that intragenic CGIs act as regulatory sites early in lineage specification while methylation changes play a minor role in late differentiation.

Abstract

Human and mouse genomes contain a similar number of CpG islands (CGIs), which are discrete CpG-rich DNA sequences associated with transcription start sites. In both species, ∼50% of all CGIs are remote from annotated promoters but, nevertheless, often have promoter-like features. To determine the role of CGI methylation in cell differentiation, we analyzed DNA methylation at a comprehensive CGI set in cells of the mouse hematopoietic lineage. Using a method that potentially detects ∼33% of genomic CpGs in the methylated state, we found that large differences in gene expression were accompanied by surprisingly few DNA methylation changes. There were, however, many DNA methylation differences between hematopoietic cells and a distantly related tissue, brain. Altered DNA methylation in the immune system occurred predominantly at CGIs within gene bodies, which have the properties of cell type–restricted promoters, but infrequently at annotated gene promoters or CGI flanking sequences (CGI “shores”). Unexpectedly, elevated intragenic CGI methylation correlated with silencing of the associated gene. Differentially methylated intragenic CGIs tended to lack H3K4me3 and associate with a transcriptionally repressive environment regardless of methylation state. Our results indicate that DNA methylation changes play a relatively minor role in the late stages of differentiation and suggest that intragenic CGIs represent regulatory sites of differential gene expression during the early stages of lineage specification.