Schlafen-11 and -9 are innate immune sensors for intracellular single-stranded DNA

Nucleic acids are major structures detected by the innate immune system. Although intracellular single-stranded DNA (ssDNA) is accumulated during pathogen infection or pathogenesis, it remains unclear whether and how intracellular ssDNA stimulates the immune system. We report that intracellular ssDNA triggers cytokine expression and cell death in a CGT motif-dependent manner. Through a genome-wide CRISPRLCas9 screen, we identified Schlafen-11 (SLFN11), which is essential for the response to endogenous and pathogen ssDNA. SLFN11 directly binds ssDNA containing CGT motifs and translocates to the cytoplasm upon ssDNA recognition. The mice deficient in SLFN9, the homologue of SLFN11, were resistant to CGT ssDNA-induced inflammation, acute hepatitis and septic shock. This study establishes CGT ssDNA and SLFN11/9 as a novel type of immunostimulatory nucleic acids and pattern recognition receptors, respectively. One-sentence summaries single-stranded DNA inside cells can awaken Schlafens with a CGT motif to trigger cytokine expression and lytic cell death.