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.
Highlights
Maintenance of genome stability relies on checkpoint signaling pathways that perceive DNA damage or replication stress to initiate a cellular response that coordinates DNA replication, repair with the cell cycle progression
We showed that the Mrc1-dependent replication stress signaling plays a critical role in repressing the 5′-end resection of the HO endonuclease-induced double-stranded break (DSB) and homologous recombination (HR) repair
Previous studies have revealed that resection of 5′-ends of DSBs is inhibited upon HU treatment that causes replication stress by reducing the dNTP level (Alabert et al, 2009; Barlow and Rothstein, 2009)
Summary
Maintenance of genome stability relies on checkpoint signaling pathways that perceive DNA damage or replication stress to initiate a cellular response that coordinates DNA replication, repair with the cell cycle progression. During the S phase, cells are vulnerable since the progression of replication forks can be impeded by numerous physical, chemical, or genetic perturbations, such as the hard-to-replicate regions, natural pausing sites, chromatinbound proteins, secondary DNA structures, active transcription, or DNA replication inhibitors (Giannattasio and Branzei, 2017; Pardo et al, 2017). These barriers can cause the uncoupling of DNA helicase and replicative polymerases or between leading or lagging strand synthesis, leading to the accumulation of single-stranded DNA (ssDNA) (Garcia-Rodriguez et al, 2018). Activation of the replication checkpoint turns on a cassette of events, leading to stabilization of stalled forks, suppression of late fired origins, induction of DNA damage response genes, upregulation of dNTP pools, and arrest of the cell cycle (Pardo et al, 2017)
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