The histone chaperone CAF-1 maintains the stability of the ribosomal RNA gene cluster by suppressing end resection of replication-associated DNA double-strand breaks

In eukaryotes, chromatin assembly is coupled to DNA replication by the histone chaperone chromatin assembly factor-1 (CAF-1). Here, we demonstrate that CAF-1 maintains the stability of the ribosomal RNA gene (rDNA) cluster in budding yeast. Absence of CAF-1 led to homologous recombination (HR)-mediated rDNA copy number changes as well as the production of extrachromosomal rDNA circles in response to Fob1-dependent replication fork arrest at the replication fork barrier (RFB) site in the rDNA. CAF-1-mediated rDNA stabilization depends on its interaction with Proliferating Cell Nuclear Antigen. The absence of CAF-1 affected neither DNA replication fork arrest at the RFB nor subsequent DNA double-strand breaks (DSBs) but led to an increased frequency of DSB end resection, which initiates HR. Absence of CAF-1 caused the derepression of transcription of noncoding RNA from the regulatory promoter E-pro located near the RFB, which contributed to enhanced DSB end resection. Moreover, its absence led to the generation of longer Okazaki fragments, which is indicative of lower nucleosome density in the rDNA. Taken together, our findings suggest that CAF-1-mediated chromatin assembly facilitates silencing of transcription from E-pro and proper nucleosome deposition behind replication forks, leading to the restriction of DSB end resection and subsequent rearrangement-prone DSB repair.