Multiple strategies to resolve the conflict between replication and transcription in mammalian cells

RNA polymerase II (Pol II) and the replisome use the same DNA template during the S phase. How these two machineries pass each other is a quintessential biological question. In this study, we demonstrated that the de novo transcriptomes of G1- and S-phase mouse embryonic fibroblasts (MEFs) showed extensive overlap. Pol II density decreased somewhat in the S-phase-enriched MEFs according to ChIP-seq. Based on long-read sequencing, a minor fraction of replication forks showed codirectional bias. A quarter of the forks were aborted near the Pol II-dense transcription start site (TSS), but the majority of forks could still pass it. The speed of the passing forks was slower if their progressing tips were closer to the TSS, suggesting that the passing was not uneventful. Paradoxically, the forks tended to travel faster in regions with more Pol IIs, likely due to greater negative supercoiling. These observations are based on cell population studies. Nevertheless, they suggest that mammalian cells rely on multiple mechanisms to resolve or mitigate the transcription-replication conflict, but these mechanisms operate with limited capacity. The majority of the forks can pass Pol IIs unscathed, albeit with some difficulty, suggesting the existence of a so-far unidentified, highly efficient conflict-resolution mechanism.