TONSOKU prevents the formation of large tandem duplications and restrains ATR–WEE1 checkpoint activation

Copy number variation (CNV) plays a fundamental role in modulating plant agronomic traits and tumorigenesis in animals. While frequently linked to replication stress, the mechanisms giving rise to CNVs are not fully elucidated. Here we characterize the mutational consequences associated with losing the conserved TONSOKU (TSK/TONSL) pathway (CAF-1-H3.1-TSK), which is required to resolve impaired DNA replication forks. Using Arabidopsis thaliana, we demonstrate that tsk mutants rapidly accumulate large, heritable tandem duplications within their genomes that are consistent with DNA Polymerase θ (Pol θ) activity. These duplications are associated with late replicating heterochromatin enriched in sources of replication stress. We also show that stochastic developmental phenotypes in tsk plants are the result of the DNA Damage Response (DDR), with phenotype suppression occurring when ATR–WEE1 checkpoint signaling is removed. We thus describe a previously uncharacterized source of large tandem duplications that are relevant to understanding genome stability in diverse eukaryotes, and in disease contexts. Large tandem duplications arise in Arabidopsis genomes in the absence of the DNA repair protein TONSOKU. This is linked to the activity of Pol θ and sites of late-replicating heterochromatin. This genome instability causes developmental defects dependent on the ATR-WEE1 axis of the DNA damage response.