Either Rap1 or Cdc13 can protect telomeric single-stranded 3′ overhangs from degradation in vitro

Telomeres, the DNA-protein structures capping the ends of linear chromosomes, are important for regulating replicative senescence and maintaining genome stability. Telomeres consist of G-rich repetitive sequences that end in a G-rich single-stranded (ss) 3' overhang, which is vital for telomere function. It is largely unknown how the 3' overhang is protected against exonucleases. In budding yeast, double-stranded (ds) telomeric DNA is bound by Rap1, while ssDNA is bound by Cdc13. Here, we developed an in vitro DNA 3'end protection assay to gain mechanistic insight into how Naumovozyma castelli Cdc13 and Rap1 may protect against 3' exonucleolytic degradation by Exonuclease T. Our results show that Cdc13 protects the 3' overhang at least 5 nucleotides (nt) beyond its binding site, when bound directly adjacent to the ds-ss junction. Rap1 protects 1-2 nt of the 3' overhang when bound to dsDNA adjacent to the ds-ss junction. Remarkably, when Rap1 is bound across the ds-ss junction, the protection of the 3' overhang is extended to 6 nt. This shows that binding by either Cdc13 or Rap1 can protect telomeric overhangs from 3' exonucleolytic degradation, and suggests a new important role for Rap1 in protecting short overhangs under circumstances when Cdc13 cannot bind the telomere.