Transient telomere uncapping triggers telomeric and subtelomeric rearrangements

Telomeres are nucleoprotein structures that cap the extremities of eukaryotic linear chromosomes, thus preventing them from being detected as DNA damage. Telomere uncapping poses a profound threat to genome integrity, yet the immediate consequences of transient uncapping remain unclear. In Saccharomyces cerevisiae, the Cdc13-Stn1-Ten1 complex caps telomeres and limits resection, which would otherwise lead to DNA damage checkpoint activation. Here, using the temperature-sensitive cdc13-1 allele, we demonstrate that even transient telomere uncapping induces extensive genomic rearrangements within a few cell cycles, despite a functional DNA damage checkpoint. Two distinct rearrangement signatures were observed in cells surviving transient uncapping: one characterized by the reorganization and recombination of the subtelomeric region, mostly involving the Y elements, and the other exhibiting massively elongated telomeres up to 10 kb, corresponding to a [~]30-fold increase. Long-read sequencing revealed that the genomic instability was confined to the subtelomere and telomere regions, and evidenced Y' element loss/amplification, terminal duplication of chromosome ends, and telomeric-circle-driven amplification of telomere repeats. Rearrangements unfold over multiple generations and require the homologous recombination factor Rad52 and the Pol{delta} subunit Pol32, which is essential for break-induced replication. The recombination proteins Rad51 and Rad59 also contribute to the rearrangements in partially independent pathways. Remarkably, survivors with elongated telomeres demonstrate robust resistance to subsequent telomere uncapping, in a Rad52-dependent manner. Our findings provide novel insights into the consequences of transient telomere uncapping for genome stability, a process that might contribute to subtelomere and telomere dynamics and evolution.