DNMT3B-Mediated Gene Body Methylation Suppresses Aberrant Transcription

DNA methylation of promoter CpG dinucleotides is associated with suppression of gene expression, but the role of DNA methylation in the gene body is not fully understood. To investigate the effects of gene body methylation, Neri and colleagues generated Dnmt3b^−/− mouse embryonic stem cell lines, as DNMT3B is the DNA methyltransferase responsible for de novo DNA methylation in the gene body. DNMT3B bound preferentially to highly expressed genes marked by trimethylation of histone 3 at lysine 36 (H3K36me3), and Dnmt3b loss resulted in a global reduction in DNA methylation on exons and introns. Further, RNA sequencing revealed that Dnmt3b deletion increased the number of transcripts that started from the second exon onward, suggesting an increase in transcription starting within the gene body. Consistent with these findings, Dnmt3b^−/− cells had increased binding of RNA polymerase II (Pol II) at intragenic regions, especially the introns and exons of highly expressed genes, suggesting that DNMT3B may suppress Pol II binding downstream of canonical promoters and thereby prevent the initiation of spurious intragenic transcription. The intragenic transcription start sites were associated with H3K36me3, which was required to recruit DNMT3B to the gene body to suppress spurious intragenic transcription initiation. Moreover, the catalytic activity of DNMT3B was needed to block spurious transcription, indicating that DNMT3B-mediated DNA methylation was essential to block transcription from cryptic intragenic sites. A fraction of the spurious transcripts in Dnmt3b^−/− cell were degraded by the RNA exosome complex, but other transcripts produced from intragenic cryptic start sites were capped, polyadenylated, and translated into aberrant proteins. Together, these findings elucidate a role for gene body DNA methylation in suppressing the initiation of aberrant intergenic transcription. Further, tumors often exhibit intragenic DNA hypomethylation or SETD2 mutations that lead to gene body hypomethylation, suggesting that this epigenetic mechanism may promote the expression of abnormal transcripts in cancer.

Neri F, Rapelli S, Krepelova A, Incarnato D, Parlato C, Basile G, et al. Intragenic DNA methylation prevents spurious transcription initiation. Nature 2017;543:72–7.