发表机构
Laboratoire Interdisciplinaire de Physique, CNRS and Université Grenoble Alpes（法国国家科学研究中心与格勒诺布尔阿尔卑斯大学跨学科物理实验室）
机构由 AI 辅助整理，请以论文原文为准。AI 中文总结
本研究通过布朗动力学模拟揭示高转录细菌基因周围DNA形成拱形条纹和束状结构域，源于聚合酶产生的超螺旋波导致DNA缠结，促进远距离片段接触。
AI 中文摘要
近期高分辨率（500 bp）Hi-C实验报告了在细菌DNA高表达位点周围具有异常模式的接触图。这些模式被描述为拱形条纹和束状结构域，延伸近100 kbp。我们采用专门设计的粗粒化模型进行了布朗动力学模拟，以合理化这些发现。该模型的主要特点是明确考虑了由易位聚合酶在其位置下游（分别上游）产生的正（分别负）超螺旋波。从模拟中计算的接触图也显示了在扭转注入速率超过阈值时出现拱形条纹和束状结构域模式。计算得到的DNA构象表明，这些模式反映了极其缠结的DNA几何结构，涉及螺旋状和环状超螺旋，且部分DNA片段同时经历这两种超螺旋。此外，位于聚合酶两侧的DNA片段系统地缠绕在另一侧的片段上，这是由扭转持续注入驱动的纯粹非平衡效应。因此，本研究揭示了对DNA位点的重复转录系统地使相距数十kbp的DNA片段接触，这可能最终有助于变构调节和长距离通讯。
英文摘要
Recent high-resolution (500 bp) Hi-C experiments reported contact maps with unusual patterns around highly expressed bacterial DNA loci. These patterns, described as arched stripes and bundled domains, extend over nearly 100 kbp. We performed Brownian Dynamics simulations with a specially designed coarse-grained model to rationalize these findings. The main feature of the model is that it takes explicitly into account the waves of positive (respectively, negative) supercoiling generated by the translocating polymerase downstream (respectively, upstream) of its position. Contact maps computed from the simulations also display the arched stripe and bundled domain patterns for above-threshold values of the rate of twist injection. Computed DNA conformations indicate that these patterns reflect an extraordinarily entangled DNA geometry, which involves both plectonemic and toroidal supercoiling, with some DNA segments experiencing both of them simultaneously. Moreover, DNA segments located on each side of the polymerase systematically wind around tracts located on the other side, which is a purely out-of-equilibrium effect driven by the continuous injection of twist. The present work therefore reveals that repeated transcription of a DNA locus systematically brings into contact DNA segments separated by several tens of kbp, which may eventually contribute to allosteric modulation and long-range communication.
Journal refMicroorganisms 14 (2026) 2162 (1-28)
DOI：10.3390/microorganisms14102162
