Ku limits RNA-induced innate immunity to allow Alu expansion in primates

Ku70 and Ku80 form the Ku heterodimer, a ring-shaped complex that initiates the non-homologous end-joining (NHEJ) DNA repair pathway1. Ku binds to double-stranded DNA ends and recruits other NHEJ factors, including LIG4 and DNA-PKcs. Although Ku can bind to double-stranded RNA (dsRNA)2 and trap mutated DNA-PKcs on ribosomal RNA3,4, the physiological role of the Ku–RNA interaction in otherwise wild-type cells remains unclear. Notably, Ku is dispensable for mouse development5,6 but is essential in human cells7. Despite their similar genome sizes, human cells express about 100-fold more Ku than mouse cells, suggesting that Ku has functions beyond NHEJ, possibly through a dose-sensitive interaction with dsRNA, which binds Ku 10 to 100 times more weakly than double-stranded DNA2,8. Here, Ku depletion induces profound interferon and NF-κB signalling via the dsRNA sensor MDA5–RIG-I and MAVS. Prolonged Ku degradation further activates other dsRNA sensors, especially PKR (also known as EIF2AK2) (suppressing translation) and OAS–RNaseL (cleaving ribosomal RNA), leading to growth arrest and cell death. Knockout of MAVS, RIG-I or MDA5 suppressed interferon signalling and, similarly to PKR knockout, partially rescued Ku-depleted human cells. Ku crosslinking and immunoprecipitation analyses revealed binding of Ku to diverse dsRNA molecules, predominantly stem-loops in primate-specific antisense Alu elements9 in introns and 3′ untranslated regions. Ku expression is higher in primates than in non-primate mammals and is tightly correlated with Alu expansion. Thus, Ku has a vital role in accommodating Alu expansion in primates, limiting dsRNA-induced innate immunity, which explains its high expression and essential function in human cells. Studies on the essentiality of Ku in human cells reveal that Ku interacts with diverse double-stranded RNA molecules, including antisense Alu, and enables tolerance of Alu sequence expansion in primates.