Replication–Transcription Conflicts: A Perpetual War on the Chromosome

DNA replication and transcription occur in all living cells across all domains of life. Both essential processes occur simultaneously on the same template, leading to conflicts between the macromolecular machines that perform these functions. Numerous studies over the past few decades demonstrate that this is an inevitable problem in both prokaryotic and eukaryotic cells. We have learned that conflicts lead to replication fork reversal, breaks in the DNA, R-loop formation, topological stress, and mutagenesis, and they can ultimately impact evolution. Recent studies have also provided insight into the various mechanisms that mitigate, resolve, and allow tolerance of conflicts and how conflicts result in divergent pathological consequences across divergent species. In this review, we summarize current knowledge regarding the outcomes of encounters between replication and transcription machineries and explore how these clashes are dealt with across species.