RNA-mediated MYC multimerization suppresses innate immune signaling [mRNA]

In response to perturbed transcription elongation or splicing, MYC proteins multimerize and undergo a phase transition; the underlying mechanisms and the biological function of this transition are poorly understood. Here, we show that MYC proteins globally bind to nascent RNA in tumor cells and relocalize from their canonical location on DNA to RNA in response to the accumulation of intronic RNA. Blocking nascent RNA degradation induces MYC multimerization and MYC multimers are hubs that concentrate the nuclear exosome, a 3'-5' RNA exonuclease, and its targeting complexes around double-stranded (ds)RNA and R-loops. MYC binds RNA directly, and RNA binding promotes MYC multimerization and the recruitment of the exosome to R-loops. RNA binding of MYC has no role in transcriptional regulation but suppresses activation of the innate immune kinase TBK1 by the TLR3 pattern recognition receptor. Upon MYC depletion, intron-derived dsRNAs, including RNA derived from several classes of repetitive elements and small nucleolar RNAs (snoRNAs), accumulate on TLR3. TLR3-bound snoRNAs recovered from MYC-depleted cells carry aberrant 3'-ends, indicating defective exosomal processing. Our data show that the phase transition of MYC is a stress response driven by its binding to RNA that suppresses the accumulation of aberrant RNAs, which would otherwise activate innate immune signaling. Overall design: To characterize the phenotypes of the MYC RBRIIIMUT, we performed mRNA-seq to compare the gene expression profile between MYC WT and the MYC RBRIIIMUT; shMYC was used as control. For this experiment, KPC cells expressing both, two doxycycline-inducible shRNAs targeting MYC as well as exogeneous, doxycycline-inducbible MYC WT or MYC RBRIIIMUT constructs or no additional exogenous construct for the shMYC condition. All cell lines were treated with doxycycline (1 µg/ml) for 48 h. For each of the conditions, 3 biological replicates have been produced.