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Looping out of control: R-loops in transcription-replication conflict

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Abstract

Transcription-replication conflict is a major cause of replication stress that arises when replication forks collide with the transcription machinery. Replication fork stalling at sites of transcription compromises chromosome replication fidelity and can induce DNA damage with potentially deleterious consequences for genome stability and organismal health. The block to DNA replication by the transcription machinery is complex and can involve stalled or elongating RNA polymerases, promoter-bound transcription factor complexes, or DNA topology constraints. In addition, studies over the past two decades have identified co-transcriptional R-loops as a major source for impairment of DNA replication forks at active genes. However, how R-loops impede DNA replication at the molecular level is incompletely understood. Current evidence suggests that RNA:DNA hybrids, DNA secondary structures, stalled RNA polymerases, and condensed chromatin states associated with R-loops contribute to the of fork progression. Moreover, since both R-loops and replication forks are intrinsically asymmetric structures, the outcome of R-loop-replisome collisions is influenced by collision orientation. Collectively, the data suggest that the impact of R-loops on DNA replication is highly dependent on their specific structural composition. Here, we will summarize our current understanding of the molecular basis for R-loop-induced replication fork progression defects.

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Funding

Work in the Remus lab is funded by NIGMS grants R01-GM107239 and R01-GM127428, and NIH-NCI Cancer Center Support Grant P30 CA008748.

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  1. Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, 10065, USA

    Charanya Kumar & Dirk Remus

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  1. Charanya Kumar
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Charanya Kumar and Dirk Remus wrote and edited the manuscript.

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Correspondence to Dirk Remus.

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Kumar, C., Remus, D. Looping out of control: R-loops in transcription-replication conflict. Chromosoma 133, 37–56 (2024). https://doi.org/10.1007/s00412-023-00804-8

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