DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats

Abstract

Several mechanisms of action have been proposed for DNA methyltransferase and histone deacetylase inhibitors (DNMTi and HDACi); mainly based on candidate gene approaches. However, less is known about their genome-wide transcriptional and epigenomic consequences. By mapping global transcription start site (TSS) and chromatin dynamics, we observed the cryptic transcription of thousands of treatment-induced non-annotated TSSs (TINATs) following DNMTi and/or HDACi treatment. The resulting transcripts frequently splice into protein-coding exons and encode truncated or chimeric open reading frames translated into products with predicted abnormal or immunogenic functions. TINAT transcription after DNMTi coincided with DNA hypomethylation and gain in classical promoter histone marks, while HDACi specifically induced a subset of TINATs in association with H2AK9ac, H3K14ac, and H3K23ac. Despite this mechanistic difference, both inhibitors convergently induced transcription from identical sites since we found TINATs to be encoded in solitary long-terminal repeats of the LTR12 family, epigenetically repressed in virtually all normal cells. In contrast to genetic mutations, epigenetic changes are potentially reversible, which is deeming them an attractive target for cancer treatment. Inhibitors directed against DNA methyltransferases (DNMTi) and histone deacetylases (HDACi) are used for the treatment of several haematopoietic malignancies1,2. However, despite their clinical use for several years, there is still a lack of knowledge regarding the mode of action3. Two previous studies on DNMTi in cancer cell lines reported the up-regulation of double stranded RNA (dsRNA) molecules originating from codogenic endogenous retroviruses (ERV) followed by an interferon response and the induction of viral defense genes4,5. However, it remains unclear how other classes of epigenetic drugs integrate into these findings and whether there are additional effects, potentially missed by candidate gene approaches. Here, we globally mapped DNMTi and HDACi-induced transcriptomic and epigenomic changes by using whole-genome profiling technologies (Supplementary Fig. 1 and Supplementary Table 1) and show that the vast majority of TSSs that transcriptionally responded towards epigenetic modulation were cryptic, currently non-annotated TSSs encoded in solitary long-terminal repeats (LTRs).

Virulence‐ and signaling‐associated genes display a preference for long 3′UTRs during rice infection and metabolic stress in the rice blast fungus

“…We noted that PASs often locate to intergenic regions with homology to transposable elements (TEs). In humans, it is common to find nonannotated transcription start sites (TSS) in their long terminal repeats (LTRs) modulated by epigenetic mechanisms (Brocks et al ., ). In our experiments, this type of epigenetic regulation can be responsible for the distinct expression of orphan PASs observed in M. oryzae TEs under different nutritional conditions.…”

Endogenous retroviruses are a source of enhancers with oncogenic potential in acute myeloid leukaemia

“…DNase hypersensitivity is associated with both active gene promoters and distal enhancers. LTR12C elements, for example, were previously shown to frequently act as alternative gene promoters in different cell types, including hepatocellular carcinoma (Hashimoto et al, 2015) and cell lines treated with DNMT and HDAC inhibitors (Brocks et al, 2017). In contrast, LTR5_Hs (HERV-K) elements appear to mainly act as distal enhancer elements in embryonic carcinoma cells and embryonic stem cells (Fuentes et al, 2018;Pontis et al, 2019).…”

Colorectal cancer: epigenetic alterations and their clinical implications

“…In addition, it has been reported that treatment of epithelial cancer cell lines (including CRC cells) with demethylating agents, namely 5-azacitidine, leads to a significant enrichment of immunomodulatory pathways (interferon signaling, antigen processing and presentation, and cytokines/chemokines) (97). Lately, Brocks et al (98) demonstrated the genome-wide transcriptional and epigenomic consequences of DNA methyltransferases inhibitors (DNMTi) and histone deacetylase inhibitors (HDACi): cryptic transcription of thousands of treatment-induced non-annotated transcriptional start sites (TINATs) may contribute to cancer immunogenicity due to novel translated potential antigenic proteins.…”