Transcription-Replication Conflict Shapes DNA Break Dynamics.

Double strand breaks (DSBs) originating from transcription and replication conflict (TRC) sites are prone to rearrangements. Through the application of a capture-ligation assay on mouse neural progenitor cells experiencing replication stress, we unveiled that interactions between transcription and replication fork architecture dictate DSB location and orientation. Specifically, telomere-to-centromere forks generate telomere-connected DSBs, while centromere-to-telomere forks lead to centromere-connected DSBs in genomes that replicate during median and late stages. This pattern, however, reverses in early-replicating DNA. Mapping nascent RNA and RNA polymerase activity revealed that head-to-head interactions between replication and transcription machineries elevate DSBs by 30% compared to co-directional interactions. By deleting promoter elements in the moderately transcribed