The c-Myc oncoprotein regulates transcription of genes that are associated with cell growth, proliferation and apoptosis. c-Myc levels are modulated by ubiquitin/proteasome-mediated degradation. Proteasome inhibition leads to c-Myc accumulation within nucleoli, indicating that c-Myc might have a nucleolar function. Here we show that the proteins c-Myc and Max interact in nucleoli and are associated with ribosomal DNA. This association is increased upon activation of quiescent cells and is followed by recruitment of the Myc cofactor TRRAP, enhanced histone acetylation, recruitment of RNA polymerase I (Pol I), and activation of rDNA transcription. Using small interfering RNAs (siRNAs) against c-Myc and an inhibitor of Myc-Max interactions, we demonstrate that c-Myc is required for activating rDNA transcription in response to mitogenic signals. Furthermore, using the ligand-activated MycER (ER, oestrogen receptor) system, we show that c-Myc can activate Pol I transcription in the absence of Pol II transcription. These results suggest that c-Myc coordinates the activity of all three nuclear RNA polymerases, and thereby plays a key role in regulating ribosome biogenesis and cell growth.

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).

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