RNA 5-methylcytosine marks mitochondrial double-stranded RNAs for degradation and cytosolic release

Mitochondria are essential regulators of innate immunity. They generate long mitochondrial double-stranded RNAs (mt-dsRNAs) and release them into the cytosol to trigger an immune response under pathological stress conditions. Yet the regulation of these self-immunogenic RNAs remains largely unknown. Here, we employ CRISPR screening on mitochondrial RNA (mtRNA)-binding proteins and identify NOP2/Sun RNA methyltransferase 4 (NSUN4) as a key regulator of mt-dsRNA expression in human cells. We find that NSUN4 induces 5-methylcytosine (m5C) modification on mtRNAs, especially on the termini of light-strand long noncoding RNAs. These m5C-modified RNAs are recognized by complement C1q-binding protein (C1QBP), which recruits polyribonucleotide nucleotidyltransferase to facilitate RNA turnover. Suppression of NSUN4 or C1QBP results in increased mt-dsRNA expression, while C1QBP deficiency also leads to increased cytosolic mt-dsRNAs and subsequent immune activation. Collectively, our study unveils the mechanism underlying the selective degradation of light-strand mtRNAs and establishes a molecular mark for mtRNA decay and cytosolic release. [Display omitted] •CRISPR screening of mt-RBPs reveals key regulators of mt-dsRNA expression•NSUN4 installs m5C RNA modification on mitochondrial mRNAs and lncRNAs•C1QBP recognizes m5C-modified mitochondrial RNAs and recruits PNPT1•m5C modification marks the mitochondrial RNAs for decay and cytosolic release Through CRISPR screening of 89 mitochondrial RBPs, Kim et al. find that NSUN4 downregulates mitochondrial dsRNA expression by installing 5-methylcytosine modification on light-strand RNAs. The modified RNAs are recognized by C1QBP, which recruits PNPT1 to facilitate RNA turnover, and are released to the cytosol, where they activate the immune response.