Mrc1-Dependent Chromatin Compaction Represses DNA Double-Stranded Break Repair by Homologous Recombination Upon Replication Stress

Abstract

The coordination of DNA replication and repair is critical for the maintenance of genome stability. It has been shown that the Mrc1-mediated S phase checkpoint inhibits DNA double-stranded break (DSB) repair through homologous recombination (HR). How the replication checkpoint inhibits HR remains only partially understood. Here we show that replication stress induces the suppression of both Sgs1/Dna2- and Exo1-mediated resection pathways in an Mrc1-dependent manner. As a result, the loading of the single-stranded DNA binding factor replication protein A (RPA) and Rad51 and DSB repair by HR were severely impaired under replication stress. Notably, the deletion of MRC1 partially restored the recruitment of resection enzymes, DSB end resection, and the loading of RPA and Rad51. The role of Mrc1 in inhibiting DSB end resection is independent of Csm3, Tof1, or Ctf4. Mechanistically, we reveal that replication stress induces global chromatin compaction in a manner partially dependent on Mrc1, and this chromatin compaction limits the access of chromatin remodeling factors and HR proteins, leading to the suppression of HR. Our study reveals a critical role of the Mrc1-dependent chromatin structure change in coordinating DNA replication and recombination under replication stress.

Genetic requirements for repair of lesions caused by single genomic ribonucleotides in S phase

“…2A ). Indeed, Mrc1 can differentially regulate resection and HDR at DSBs 41 and it was recently demonstrated that this involves changes in chromatin compaction 42 . Further support that the repair of rNMP-derived lesions is coupled to alterations of chromatin was shown in a recent study in human cells 43 .…”

Genetic requirements for repair of lesions caused by single genomic ribonucleotides in S phase

“…This hypothesis is supported by the fact that deletion of the fork protection protein and damage checkpoint mediator MRC1 can rescue the sensitivity of rtt101 Δ cells to genotoxic agents (Buser et al, 2016) as well as to accumulation of rNMPs ( Figure 2A ). Indeed, Mrc1 can differentially regulate resection and HDR at DSBs (Alabert et al, 2009) and it was recently demonstrated that this involves changes in chromatin compaction (Xing et al, 2021). Further support that the repair of rNMP-derived lesions is coupled to alterations of chromatin was shown in a recent study in human cells (Nakamura et al, 2021).…”