The telomeric CTC1/STN1/TEN1 (CST) complex has recently been implicated in promoting replication recovery under replications stress at genomic regions, yet its precise role is unclear. Here we report that STN1 is enriched at GC-rich repetitive sequences genome-wide in response to hydroxyurea (HU)-induced replication stress. STN1 deficiency exacerbates fragility of these sequences under replication stress, resulting in chromosome fragmentation. We find that upon fork stalling, CST proteins form distinct nuclear foci that colocalize with RAD51. Furthermore, replication stress induces physical association between CST with RAD51 in an ATR-dependent manner. Strikingly, CST deficiency diminishes HU-induced RAD51 foci formation and reduces RAD51 recruitment to telomeres and non-telomeric GC-rich fragile sequences. Collectively, our findings establish that CST promotes RAD51 recruitment to GC-rich repetitive sequences in response to replication stress to facilitate replication restart, thereby providing insights into the mechanism underlying genome stability maintenance.

C. performed experiments and analyzed data. MC analyzed all ChIP-seq sequences, obtained metaphase FISH data, performed IF experiments and data analysis, assembled figures. Q.Z. obtained RAD51 ChIP results, performed qPCR and data analysis, participated in IF and figure assembly. OS obtained STN1 ChIP results. M.F.M. contributed to the initial conception of the project, gave technical advice, and performed initial ChIP-seq analysis, initial motif discovery experiments, and oncomine Stn1 expression analysis. Q.Z., P.J., C.H., and X.D. contributed to co-IP analysis. L.W. processed ChIP-seq reads. P.Y. directed ChIP-seq reads processing study. W.C. conceived the project, directed the study, participated in cell line establishment, FISH, IF, co-IP experiment execution, and wrote the manuscript.

Degradation and collapse of stalled replication forks are main sources of genomic instability, yet the molecular mechanisms for protecting forks from degradation/collapse are not well understood. Here, we report that human CST (CTC1‐STN1‐TEN1) proteins, which form a single‐stranded DNA‐binding complex, localize at stalled forks and protect stalled forks from degradation by the MRE11 nuclease. CST deficiency increases MRE11 binding to stalled forks, leading to nascent‐strand degradation at reversed forks and ssDNA accumulation. In addition, purified CST complex binds to 5’ DNA overhangs and directly blocks MRE11 degradation in vitro, and the DNA‐binding ability of CST is required for blocking MRE11‐mediated nascent‐strand degradation. Our results suggest that CST inhibits MRE11 binding to reversed forks, thus antagonizing excessive nascent‐strand degradation. Finally, we uncover that CST complex inactivation exacerbates genome instability in BRCA2 deficient cells. Collectively, our findings identify the CST complex as an important fork protector that preserves genome integrity under replication perturbation.