The balance between R-loops and RNAPII occupancy determines the outcome of transcription-replication conflicts

About the speaker:

Ioannis is a postdoctoral researcher in Stephen Hamperl’s laboratory. Since his PhD, his research has focused on understanding how cells coordinate transcription and replication. To address this, he has developed and applied advanced real-time microscopy techniques to dissect how cells manage the simultaneous occurrence of both processes without compromising genome stability.

Summary:

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 in yeast to monitor a single R-loop prone locus in real time, we demonstrate that wild-type replisomes traverse R-loop enriched transcription units with high efficiency. We find that while R-loops initially repress transcription, replisome passage prompts a robust recovery of transcription activity. Indeed, we discover that R-loops serve a critical regulatory function by suppressing excessive RNAPII occupancy. Our findings reveal a dual nature of R-loops: while they can be obstacles and repress transcription, they can 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.