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

Abstract

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 RNA^3,4, the physiological role of the Ku-RNA interaction in otherwise wild-type cells remains unclear. Notably, Ku is dispensable for mouse development^5,6 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 DNA^2,8. 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.