Chromatin-associated circRNA ciCRLF3(2) regulates cell differentiation blockage via activating non-homologous end joining-based DNA repair.

DNA damage response (DDR) is a complicated network that responds to DNA lesions to prevent their accumulation; a defective DDR is one hallmark of cancer. Although targeting DDR pathways has been considered as a therapeutic approach, DDR inhibitors have also been reported ineffective for treating some low mutation burden cancers, such as Mixed-lineage leukemia (MLL)-rearranged (MLL-r) leukemia, a clinically fatal and refractory malignancy. Exploring the roles and mechanisms of DDR pathways in these low mutation burden cancers may help understand the chromatin biology and develop therapeutic strategies. Here, we identified a set of DDR-related chromatin-associated circular RNAs (cacircRNAs) that regulate DNA repair via the non-homologous end joining (NHEJ) pathway, which is vital for meeting the high DNA repair demands during the progression of MLL-r leukemia. Among these cacircRNAs, we identified ciCRLF3(2) as a previously unknown component of the NHEJ complex. We showed that ciCRLF3(2) recruits NHEJ regulators to DNA lesions, supporting abundant DNA repair in leukemia cells. ciCRLF3(2) abundance is abnormally upregulated in MLL-r leukemia and indicates a poor prognosis. Targeting ciCRLF3(2) suppressed NHEJ-mediated DNA repair, leading to DNA damage and broad anti-cancer effects in vitro and in vivo. A patient-derived xenograft model of MLL-r leukemia further indicated that ciCRLF3(2) depletion can decrease the leukemic burden. These findings demonstrate the function of cacircRNAs in DDR and chromatin biology and reveal a new avenue for developing strategies to treat low mutation burden cancers, such as MLL-r leukemia.