An ATM-PPM1D circuit controls the processing and restart of DNA replication forks

Abstract In response to DNA replication stress, DNA damage signaling kinases inhibit origin firing, stabilize replication forks, and reduce DNA synthesis to preserve genomic integrity, yet the mechanisms governing replication stress recovery, particularly stalled fork restart, remain poorly understood. Here, we identify the oncogenic phosphatase PPM1D/WIP1 as a regulator of replication fork restart. During recovery from replication stress, PPM1D prevents excessive MRE11- and DNA2-dependent nucleolytic degradation of stalled forks. Loss of PPM1D function leads to defects in RAD51 recruitment to chromatin and impairs RAD51-dependent fork restart. Phosphoproteomic analysis reveals that PPM1D regulates a network of ATM substrates, several of which are phosphorylated at an S/T-Q-(E/D) n motif. Strikingly, ATM inhibition suppresses the deleterious effects of PPM1D loss at replication forks, enabling timely fork restart. The dominant effect of ATM hyper-signaling in suppressing fork restart occurs, in part, through the excessive engagement of 53BP1 and consequent RAD51 antagonization. Together, these findings reveal a novel ATM signaling mode responding to fork stalling and establish PPM1D’s role in restraining ATM signaling to facilitate proper fork restart.