{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE328nnn/GSE328746/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Genomics"],"species":["Saccharomyces cerevisiae"],"gds_type":["Genome binding/occupancy profiling by high throughput sequencing"],"full_dataset_link":["https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE328746"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"The balance between R-loop levels and RNAPII occupancy dictates Transcription-Replication Conflict occurrence","description":"Maintaining genome integrity requires the precise coordination of replication and transcription. While R-loops are known to cause transcription-replication conflicts (TRCs), the precise nature of the barrier, whether it is the RNA:DNA hybrid itself, the stalled RNA Polymerase II (RNAPII), or a combination of both, remains elusive. Using live-cell imaging to monitor a single R-loop prone locus in real time, we demonstrate that wild-type replisomes traverse R-loops with high efficiency. Conversely, depleting R-loop processing factors, such as Rnase H enzymes or Mph1 and Sen1 helicases triggers replication fork stalling, particularly in head-on orientation. Paradoxically, we discover that R-loops serve a critical regulatory function by suppressing excessive RNAPII occupancy. In an RNAPII mutant with high DNA affinity, the enzymatic removal of R-loops leads to a pile-up of RNAPII molecules, creating a barrier to replication, more severe than the R-loops themselves. Our findings reveal a dual nature of R-loops: while they can be obstacles, they also serve as a physiological buffer that prevents the formation of high-density RNAPII “trains”. These findings establish that the precise regulation of both R-loop levels and RNAPII density is critical for preventing harmful TRCs and maintaining genome stability.","dates":{"publication":"2026/04/29"},"accession":"GSE328746","cross_references":{"GSM":["GSM9688509","GSM9688498","GSM9688511","GSM9688500","GSM9688510","GSM9688499","GSM9688502","GSM9688512","GSM9688501","GSM9688504","GSM9688503","GSM9688506","GSM9688505","GSM9688508","GSM9688507"],"GPL":["34739"],"GSE":["328746"],"taxon":["Saccharomyces cerevisiae"]}}