Shelterin-like proteins and Yku inhibit nucleolytic processing of S. cerevisiae telomeres

Background: Eukaryotic cells distinguish their chromosome ends from accidental DNA double-strand breaks (DSBs) by packaging them into protective structures called telomeres that prevent DNA repair/recombination activities. Here we investigate the role of key telomeric proteins in protecting budding yeast telomeres from degradation. Principal findings: We show that the S. cerevisiae shelterin-like proteins Rif1, Rif2 and Rap1 inhibit nucleolytic processing at both de novo and native telomeres during G1 and G2 cell cycle phases, with Rif2 and Rap1 showing the strongest effects. Also Yku prevents telomere resection in G1, independently of its role in non-homologous end joining. Yku and the shelterin-like proteins have additive effects in inhibiting DNA degradation at G1 de novo telomeres, with a major role for Yku in preventing initiation, whereas Rif1, Rif2 and Rap1 act primarily by limiting extensive resection. In fact, exonucleolytic degradation of de novo telomeres is more efficient in yku70Δ than in rif2Δ G1 cells, but generation of ssDNA in Yku-lacking cells is limited to DNA regions close to the telomere tip. This limited processing is due to the inhibitory action of Rap1, Rif1 and Rif2, as their inactivation allows extensive telomere resection not only in wild type but also in yku70Δ G1 cells. Finally, Rap1 and Rif2 prevent telomere degradation by inhibiting MRX access to telomeres, which are also protected from the Exo1 nuclease by Yku. Conclusions: Thus, chromosome end degradation is controlled by telomeric proteins that specifically inhibit the action of different nucleases.