Deciphering the dual effects of transcription on DNA replication elongation by replication-associated Micro-C

The encounters between transcription and DNA replication may remodel replication dynamics, yet the coordination of these two essential processes remains elusive. Here, we developed a replication-associated Micro-C (Repli-MiC) method to map replication fountains, which are dynamic chromatin-interaction structures induced by coupled replication forks, at nucleosome resolution in mammalian cells. We implemented a reinforcement-learning-based computational framework to enable unbiased and quantitative characterization of replication fountains, thereby allowing precise assessment of how transcription influences sister-fork elongation. With this integrated platform, we found that co-directional transcription induces a bias in the speed of sister replication forks toward the transcriptional orientation without compromising fork coupling, which is further enhanced upon depletion of DNA Topoisomerase I (TOP1). Conversely, head-on transcription potentially impairs fork elongation to weaken replication fountains. This study provides a comprehensive assay for profiling the entire DNA-replication elongation process and sheds light on the dual roles of transcription in modulating fork elongation.