R-loop processing via REXO4-RNaseH1–mediated endo- and exo-cleavage coupling mode prevents genome instability and antitumor immunity

R-loop metabolism is closely associated with genome stability and tumors. Here, we identify an exonuclease REXO4, which collaborates with RNaseH1 endonuclease to degrade R-loops in an “endo/exo-cleavage coupling” manner. Specifically, REXO4 directly degrades the RNA strand in R-loops from the end or internal nick through its 3′-5′ exonuclease activity and stimulates RNaseH1 endonuclease activity. The genome-wide R-loop regions regulated by REXO4 highly overlap with those regulated by RNaseH1, and REXO4 overexpression counteracts genome-wide R-loop accumulation caused by RNaseH1 deficiency. Furthermore, REXO4-deficient tumors display elevated R-loop mutation burden, and tumor patient-derived mutations in REXO4 enzymatic region all impair R-loop cleavage activity. Besides, we identify a compound 17 (named REXO4-IN-17) capable of inhibiting REXO4 nuclease activity. Interfering with REXO4 increases the sensitivity of tumor cells to alkylating and G4 stabilizing chemotherapeutic drugs and activates cGAS-mediated antitumor immunity. Therefore, our study proposes an endo/exo-cleavage coupling the R-loop processing model, which provides additional insights into the link between R-loop–associated genome instability, antitumor immunity, and tumors.