Ataxin‐3 consolidates the MDC1‐dependent DNA double‐strand break response by counteracting the SUMO‐targeted ubiquitin ligase RNF4

The SUMO‐targeted ubiquitin ligase RNF4 functions at the crossroads of the SUMO and ubiquitin systems. Here, we report that the deubiquitylation enzyme (DUB) ataxin‐3 counteracts RNF4 activity during the DNA double‐strand break (DSB) response. We find that ataxin‐3 negatively regulates ubiquitylation of the checkpoint mediator MDC1, a known RNF4 substrate. Loss of ataxin‐3 markedly decreases the chromatin dwell time of MDC1 at DSBs, which can be fully reversed by co‐depletion of RNF4. Ataxin‐3 is recruited to DSBs in a SUMOylation‐dependent fashion, and in vitro it directly interacts with and is stimulated by recombinant SUMO, defining a SUMO‐dependent mechanism for DUB activity toward MDC1. Loss of ataxin‐3 results in reduced DNA damage‐induced ubiquitylation due to impaired MDC1‐dependent recruitment of the ubiquitin ligases RNF8 and RNF168, and reduced recruitment of 53BP1 and BRCA1. Finally, ataxin‐3 is required for efficient MDC1‐dependent DSB repair by non‐homologous end‐joining and homologous recombination. Consequently, loss of ataxin‐3 sensitizes cells to ionizing radiation and poly(ADP‐ribose) polymerase inhibitor. We propose that the opposing activities of RNF4 and ataxin‐3 consolidate robust MDC1‐dependent signaling and repair of DSBs.