Morao Ana Karina, Chervova Almira, Zhao Yuya, Ercan Sevinc, Cecere Germano
Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, UMR 3738, CNRS, Paris 75015, France.
Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA.
bioRxiv. 2025 Jan 3:2025.01.03.631213. doi: 10.1101/2025.01.03.631213.
Transcription introduces torsional stress in the DNA fiber causing it to transition from a relaxed to a supercoiled state that can propagate across several kilobases and modulate the binding and activity of DNA-associated proteins. As a result, transcription at one locus has the potential to impact nearby transcription events. In this study, we asked how DNA supercoiling affects histone modifications and transcription of neighboring genes in the multicellular eukaryote . We acutely depleted the two major topoisomerases and measured nascent transcription by Global Run-on sequencing (GRO-seq), RNA Polymerase II occupancy by ChIP-seq, gene expression by RNA-seq and four transcription-associated histone modifications by Cut & Tag. Depletion of topoisomerases I and II led to genome-wide changes in transcription dynamics, with minor disruptions to the histone modification landscape. Our results showed that topoisomerase I is required for transcription elongation and is partially redundant with topoisomerase II. Analysis of transcription changes with respect to neighboring genes suggest that negative supercoiling promotes the transcription of genes with a divergent neighbor and positive supercoiling suppresses transcription of convergent genes. Additionally, topoisomerase depletion caused coordinated changes in the expression of divergent gene pairs, suggesting that negative supercoiling drives their synchronized expression. Conversely, the coordinated expression of convergent genes was disrupted, suggesting that excessive positive supercoiling inhibits transcription. Overall, our data supports a model in which DNA supercoiling generated by transcription at one site propagates along the eukaryotic chromatin fiber, influencing nearby transcription in an orientation-dependent manner.
转录会在DNA纤维中引入扭转应力，使其从松弛状态转变为超螺旋状态，这种状态可以跨越几千个碱基对进行传播，并调节与DNA相关蛋白的结合和活性。因此，一个位点的转录有可能影响附近的转录事件。在本研究中，我们探究了DNA超螺旋如何影响多细胞真核生物中组蛋白修饰和邻近基因的转录。我们急性耗尽了两种主要的拓扑异构酶，并通过全局运行测序（GRO-seq）测量新生转录，通过染色质免疫沉淀测序（ChIP-seq）测量RNA聚合酶II的占有率，通过RNA测序（RNA-seq）测量基因表达，并通过切割与标签（Cut & Tag）测量四种与转录相关的组蛋白修饰。拓扑异构酶I和II的耗尽导致全基因组转录动力学发生变化，对组蛋白修饰格局的干扰较小。我们的结果表明，拓扑异构酶I是转录延伸所必需的，并且与拓扑异构酶II部分冗余。对邻近基因转录变化的分析表明，负超螺旋促进具有发散型邻近基因的转录，而正超螺旋抑制汇聚型基因的转录。此外，拓扑异构酶的耗尽导致发散型基因对的表达发生协同变化，表明负超螺旋驱动它们的同步表达。相反，汇聚型基因的协同表达被破坏，表明过多的正超螺旋抑制转录。总体而言，我们的数据支持一种模型，即一个位点转录产生的DNA超螺旋沿着真核染色质纤维传播，以方向依赖的方式影响附近的转录。
