TONSOKU prevents the formation of large tandem duplications induced by replication stress

Copy number variation (CNV) plays fundamental roles in the modulation of agronomic traits and tumorigenesis. However, the molecular mechanisms giving rise to CNVs remain to be fully elucidated. Here we characterize the mutational consequences associated with the loss of the conserved DNA repair protein TONSOKU (TSK/TONSL), which is required to resolve impaired replication forks. Using Arabidopsis thaliana as a model, we show that tsk mutants accumulate large, heritable tandem duplications within their genomes that are created by DNA Polymerase theta. We link these duplications to late replicating heterochromatic regions enriched in sources of replication stress, and show that the stochastic developmental phenotypes observed in tsk mutants result from activation of the DNA damage response. Thus, we describe a previously uncharacterized source of large tandem duplications relevant to understanding genome stability in diverse eukaryotes and in disease contexts.