Senataxin promotes recombination fidelity during antigen receptor gene diversification

Immunoglobulin (Ig) and T cell receptor (TCR) V(D)J gene recombination relies on non-homologous end-joining (NHEJ), which repairs DNA double-strand breaks (DSBs) introduced by the RAG1/2 nuclease complex. Functional redundancies exist between NHEJ and the ATM kinase-dependent chromatin DSB response, likely masking the activity of additional factors. Here, we performed targeted CRISPR/Cas9 knockout screens (+/- ATM kinase inhibition) in pro-B cells and identified Senataxin (SETX) as a novel player in V(D)J recombination. We show that SETX supports V(D)J recombination, particularly when the ATM kinase is inhibited or in an XLF-deficient background. Furthermore, we show that SETX suppresses the formation of aberrant coding end-to-signal end hybrid joints during V(D)J recombination, both in vitro and in vivo. Finally, SETX prevents the aberrant joining of AID-induced DNA ends during class switch recombination (CSR). Overall, our work reveals an important role for SETX in promoting recombination fidelity and suppressing genome instability during antigen receptor gene diversification.