Epigenetic Drugs Promote Transcription from Cryptic Start Sites

Epigenetic inhibitors targeting DNA methyltransferases (DNMTi) or histone deacetylases (HDACi) are used to treat several hematopoietic malignancies, but their mechanisms of action have not been fully elucidated. Brocks, Schmidt, Daskalakis, and colleagues found that HDACi promoted expression of DAPK1, which is normally epigenetically silenced by CpG-island hypermethylation, from noncanonical intronic transcription start sites (TSS), and performed global mapping of DNMTi- and HDACi-induced transcriptomic and epigenomic changes using cap analysis of gene expression to determine if the aberrant activation of cryptic TSSs was a global phenomenon. Indeed, treatment with DNMTi, HDACi, or the combination triggered global alterations in TSS usage with induction of de novo transcription from nonannotated TSSs, which were termed treatment-induced nonannotated TSSs (TINAT). Overall, approximately 60% of TINATs were located in intergenic regions and approximately 20% occurred in intronic regions, but the transcripts were generally not expressed under normal conditions; 50%–60% of TINATs generated spliced transcripts, 30% of which were spliced into protein-coding exons. Protein-coding TINAT–exon fusion transcripts were predicted including in-frame isoforms that may produce original, truncated, or chimeric transcripts, and out-of-frame transcripts expected to give rise to novel peptides. Existence of a number of predicted transcripts was experimentally validated, and several were linked to abnormal functions including suppression of cell growth or immunogenic activity. Both DNMTi and HDACi activated nearly identical TINATs, but acted via distinct mechanisms. HDACi resulted in a rapid increase in histone tail acetylation (H2AK9ac, H3K14ac, and H3K23ac), whereas DNMTi promoted DNA hypomethylation and enrichment of classic promoter histone marks. The large majority (more than 80%) of TINATs were associated with long terminal repeats (LTR), especially those of the ERV9/LTR12 family, which are normally epigenetically silenced. These findings reveal a previously undescribed mechanism of action for epigenetic therapies in inducing de novo transcription of LTRs instead of altering canonical gene expression.

Brocks D, Schmidt CR, Daskalakis M, Jang HS, Shah NM, Li D, et al. DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats. Nat Genet 2017 Jun 12 [Epub ahead of print].