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直接观察转录-复制冲突揭示了复制后 DNA:RNA 杂交体。

Direct visualization of transcription-replication conflicts reveals post-replicative DNA:RNA hybrids.

机构信息

Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland.

Vanderbilt University School of Medicine, Nashville, TN, USA.

出版信息

Nat Struct Mol Biol. 2023 Mar;30(3):348-359. doi: 10.1038/s41594-023-00928-6. Epub 2023 Mar 2.

DOI:10.1038/s41594-023-00928-6
PMID:36864174
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10023573/
Abstract

Transcription-replication collisions (TRCs) are crucial determinants of genome instability. R-loops were linked to head-on TRCs and proposed to obstruct replication fork progression. The underlying mechanisms, however, remained elusive due to the lack of direct visualization and of non-ambiguous research tools. Here, we ascertained the stability of estrogen-induced R-loops on the human genome, visualized them directly by electron microscopy (EM), and measured R-loop frequency and size at the single-molecule level. Combining EM and immuno-labeling on locus-specific head-on TRCs in bacteria, we observed the frequent accumulation of DNA:RNA hybrids behind replication forks. These post-replicative structures are linked to fork slowing and reversal across conflict regions and are distinct from physiological DNA:RNA hybrids at Okazaki fragments. Comet assays on nascent DNA revealed a marked delay in nascent DNA maturation in multiple conditions previously linked to R-loop accumulation. Altogether, our findings suggest that TRC-associated replication interference entails transactions that follow initial R-loop bypass by the replication fork.

摘要

转录-复制碰撞（TRCs）是基因组不稳定性的关键决定因素。R 环与正面 TRCs 有关，并被提议阻碍复制叉的推进。然而，由于缺乏直接可视化和非模糊研究工具，其潜在机制仍然难以捉摸。在这里，我们确定了雌激素诱导的 R 环在人类基因组上的稳定性，通过电子显微镜（EM）直接对其进行可视化，并在单分子水平上测量 R 环的频率和大小。通过 EM 和细菌中特定基因座的正面 TRC 上的免疫标记相结合，我们观察到复制叉后面经常积累 DNA：RNA 杂交体。这些复制后结构与冲突区域的叉减速和反转有关，与冈崎片段上的生理 DNA：RNA 杂交体不同。对新生 DNA 的彗星分析表明，在以前与 R 环积累相关的多种条件下，新生 DNA 成熟明显延迟。总的来说，我们的发现表明，与 TRC 相关的复制干扰需要复制叉初始绕过 R 环后进行的交易。

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2
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3
Topological stress is responsible for the detrimental outcomes of head-on replication-transcription conflicts.
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Res Sq. 2025 Jul 3:rs.3.rs-6080272. doi: 10.21203/rs.3.rs-6080272/v1.
4
DNA polymerase α/primase extraction from chromatin by VCP/p97 restricts ATR activation during unperturbed DNA replication.通过VCP/p97从染色质中提取DNA聚合酶α/引发酶可在正常DNA复制过程中限制ATR激活。
Nat Commun. 2025 Jul 1;16(1):5706. doi: 10.1038/s41467-025-60077-w.
5
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