Transcription near arrested DNA replication forks triggers ribosomal DNA copy number changes

Abstract

DNA copy number changes as a consequence of chromosomal structural rearrangements or the production of extrachromosomal circular DNA. Here, we demonstrate that the histone deacetylase Sir2 maintains the copy number of budding yeast ribosomal RNA gene (rDNA) by suppressing the initiation of homologous recombination (HR)-mediated repair of DNA double-strand breaks (DSBs) that are formed upon DNA replication fork arrest in the rDNA. Sir2 represses the transcription from the regulatory promoter E-pro, which is located near the fork arresting site. When Sir2 is absent, transcription is stimulated by E-pro but terminated by arrested replication forks. This transcription-replication collision enhances DSB formation and induces DSB end resection and HR-mediated repair that is prone to chromosomal rDNA copy number changes and the production of extrachromosomal rDNA circles. Therefore, repression of transcription near arrested replication forks is critical for the maintenance of genome stability by directing DSB repair into the HR-independent, rearrangement-free pathway.