Essential Roles for Polymerase θ-Mediated End Joining in the Repair of Chromosome Breaks

DNA polymerase theta (Pol θ)-mediated end joining (TMEJ) has been implicated in the repair of chromosome breaks, but its cellular mechanism and role relative to canonical repair pathways are poorly understood. We show that it accounts for most repairs associated with microhomologies and is made efficient by coupling a microhomology search to removal of non-homologous tails and microhomology-primed synthesis across broken ends. In contrast to non-homologous end joining (NHEJ), TMEJ efficiently repairs end structures expected after aborted homology-directed repair (5′ to 3′ resected ends) or replication fork collapse. It typically does not compete with canonical repair pathways but, in NHEJ-deficient cells, is engaged more frequently and protects against translocation. Cell viability is also severely impaired upon combined deficiency in Pol θ and a factor that antagonizes end resection (Ku or 53BP1). TMEJ thus helps to sustain cell viability and genome stability by rescuing chromosome break repair when resection is misregulated or NHEJ is compromised. [Display omitted] •Pol θ directs end joining by coupling a microhomology search to synthesis across ends•Pol θ-mediated end joining is critical when either canonical repair pathway fails•Pol θ is also essential when cells aberrantly regulate resection of chromosome breaks•Pol θ-dependent repair can both suppress and promote genome instability Wyatt et al. show that Polymerase θ accounts for most microhomology-dependent chromosome break repair and outline a mechanism that makes this pathway efficient and flexible. They define biologically relevant substrates, determine that it is essential in cells that inappropriately regulate resection, and show that it can both positively and negatively affect genome stability.