Binding of MYC to nascent RNA suppresses innate immune signaling by R-loop-derived RNA-DNA hybrids [DRIPc]

In response to perturbed transcription elongation, the MYC oncoprotein multimerizes and undergoes a phase transition; the underlying mechanisms and their function are unknown. Here, we show that MYC relocalizes from its canonical location on DNA to RNA in response to the accumulation of intronic RNA. MYC directly binds RNA, which promotes its multimerization. MYC multimers concentrate the nuclear exosome, a 3'-5' RNA exonuclease, and its targeting complexes around double-stranded RNA and R-loops. RNA binding of MYC suppresses activation of the innate immune kinase TBK1. Upon MYC depletion, intron-derived dsRNAs, including RNA derived from small nucleolar RNAs, and RNA-DNA hybrids accumulate on TLR3, a pattern recognition receptor that activates TBK1. RNA binding of MYC is required to suppress the accumulation of R-loop-derived RNA-DNA hybrids on TLR3. Our data show that the phase transition of MYC is an RNA-driven stress response that suppresses the accumulation of immunogenic RNAs. Overall design: The first aim was to investigate how the treatment with CBL0137 affects R-loop levels in cells expressing oncogenic MYC levels. To investigate this, DRIPc-sequencing was performed in U2OSMYC-Tet-On cells treated with doxycycline to induce oncogenic MYC levels and CBL0137 (5 µM, 2 h) or DMSO as control. To further evaluate how MYC RNA binding affects R-loop levels and distribution, DRIPc-sequencing was performed in KPC cells depleted of endogenous MYC and exogenously expressing WT MYC or RBRIII MUT MYC. Additionally, we determined the effect of Exosc10 depletion on R-loops in KPC cells in the presence of either WTMYC or RBRIIIMUTMYC.