Psoralen mapping reveals a bacterial genome supercoiling landscape dominated by transcription

DNA supercoiling is a key regulator of all DNA metabolic processes including replication, transcription, and recombination, yet a reliable genomic assay for supercoiling is lacking. Here we present a robust and flexible method (Psora-Seq) to measure whole-genome supercoiling at 1 kb resolution. Using this tool in Escherichia coli, we observe a supercoiling landscape dominated by transcription. RNA polymerase complexes generated supercoiling twin-domains that span 25 kilobases in each direction - an order of magnitude farther than previous measurements in any organism. Thus, ribosomal and many other highly expressed genes strongly affect the topology of about 40 neighboring genes each, creating highly integrated gene circuits. Genomic patterns of supercoiling revealed by Psora-Seq could be aptly predicted from modeling based on gene expression levels alone, indicating that transcription is the major determinant of chromosome supercoiling. Large-scale supercoiling patterns were highly symmetrical between left and right chromosome arms (replichores), indicating that DNA replication also strongly influences supercoiling. Skew in the axis of symmetry from the natural ori-ter axis supports previous indications that the rightward replication fork is delayed several minutes after initiation.

DNA超螺旋 (DNA supercoiling) 是调控所有DNA代谢过程的关键因子，涵盖复制、转录与重组等核心生理过程，但目前仍缺乏适用于超螺旋检测的可靠基因组检测分析手段 (genomic assay)。本研究报道了一种稳健灵活的检测方法（Psora-Seq），可实现1千碱基（kb）分辨率下的全基因组超螺旋水平定量。将该方法应用于大肠杆菌（Escherichia coli）后，我们观测到以转录主导的超螺旋基因组景观：RNA聚合酶复合物 (RNA polymerase complexes) 可产生向两侧各延伸25千碱基的超螺旋双结构域 (twin-domains)，其跨度较此前所有生物体中的测量结果高出一个数量级。研究表明，核糖体基因及众多其他高表达基因，会分别对约40个邻近基因的染色质拓扑结构产生显著调控作用，进而构建出高度整合的基因回路。Psora-Seq所揭示的基因组超螺旋模式，仅通过基于基因表达水平的建模即可精准预测，这证实转录是染色体超螺旋的主要决定因素。染色体左右臂（复制臂，replichores）间的大规模超螺旋模式呈现高度对称性，提示DNA复制同样对超螺旋具有显著调控作用。该对称轴线偏离天然的复制起点-终点（ori-ter）轴，这一结果印证了此前的研究结论，即右向复制叉 (replication fork) 在复制起始后会被延迟数分钟。