Understanding The Repair Mechanisms at Ionizing Radiation-induced Damage in The Human Genome

Ionizing radiation (IR) such as X-rays induce damage clusters in the genome that include DNA double-strand breaks (DSB) with unligatable dirty ends, along with more frequent oxidized bases and single-strand breaks (SSB). While nonhomologous end joining and homologous recombination are major DSB repair pathways which have been extensively characterized over the past decades, contribution of error-prone alternative end joining (Alt-EJ) at X-ray-induced DNA damage is poorly characterized and underestimated. Moreover, how repair of oxidative base lesions and DSB are coordinated at damage clusters is an important unanswered question. I used recircularization of linearized plasmid reporters to monitor repair of DSBs with 3P-blocked termini, which mimic X-ray-induced strand breaks, both in cell and in vitro, with repair complexes and measured relative efficiency of NHEJ vs. Alt-EJ based on sequence analysis of the joint site. Although NHEJ was the predominant pathway for DSB repair, Alt-EJ was significantly enhanced in pre-irradiated cells. This stimulation was dependent on XRCC1 phosphorylation by casein kinase 2 (CK2) that enhanced the interaction of XRCC1 with the end resection enzymes Mre11 and CtIP. The XRCC1 immunocomplex isolated from U2OS cells had Alt-EJ activity in vitro; this activity was significantly higher in the immunocomplex from pre-irradiated cells. Our studies thus suggest that activation of Alt-EJ proficient repair complexes after irradiation in surviving cells could contribute to radioresistance and could be therapeutically targeted. In a separate study, we showed that there is a hierarchy in repair of DSBs by NHEJ followed by base excision repair of oxidized bases at IR-induced damage clusters, coordinated by scaffold attachment factor-A (SAF-A), that is crucial to maintain genomic integrity.