Evolutionarily Conserved Role of Intragenic DNA Methylation in Regulating Alternative Promoters

While the methylation of DNA in 5a promoters suppresses gene expression, the role of DNA methylation in gene bodies is unclear1-5. To investigate the role of intragenic methylation, we generated a map of DNA methylation from human brain tissue encompassing 24.7 million of the 28 million CpG sites. From the dense, high-resolution coverage of CpG islands, the majority of methylated CpG islands were revealed to be in intragenic and intergenic regions, while less than 3% of CpG islands in 5a promoters were methylated. The CpG islands in all three locations overlapped with RNA markers of transcription initiation, and unmethylated CpG islands also overlapped significantly with trimethylation of H3K4, a histone modification enriched at active promoters. The general and CpG-island-specific patterns of methylation are conserved in mouse tissues. An in-depth investigation of the human SHANK3 locus7,8 and its mouse homologue demonstrated that this tissue-specific DNA methylation does indeed regulate intragenic promoter activity in vitro and in vivo. These methylation-regulated, alternative transcripts are expressed in a tissue and cell type-specific manner, and are expressed differentially within a single cell type from distinct brain regions. These results support a major role for intragenic methylation in regulating cell context-specific alternative promoters in gene bodies.