Loop-extruding Smc5/6 organizes transcription-induced positive DNA supercoils [ChIP-seq]

The Structural Maintenance of Chromosome (SMC) protein complexes cohesin, condensin and the Smc5/6 complex (Smc5/6) are essential for chromosome function. At the molecular level, these complexes fold DNA by loop extrusion. Accordingly, cohesin creates chromosome loops in interphase, and condensin compacts mitotic chromosomes. However, the role of Smc5/6’s recently discovered DNA loop extrusion activity is unknown. Here, we uncover that Smc5/6 controls the spatial organization of supercoiled chromosomal regions. The results show that Smc5/6 associates with transcription-induced positively supercoiled chromosomal DNA at cohesin-dependent chromosome loop boundaries. Mechanistically, single-molecule imaging reveals that dimers of Smc5/6 specifically recognize the tip of positively supercoiled DNA plectonemes, and efficiently initiates loop extrusion to gather the supercoiled DNA into a large plectonemic loop. Finally, Hi-C analysis shows that Smc5/6 links chromosomal regions containing transcription-induced positive supercoiling in cis. Altogether, our findings indicate that Smc5/6 controls the three-dimensional organization of chromosomes by recognizing and initiating loop extrusion on positively supercoiled DNA.染色体结构维持蛋白复合物（Structural Maintenance of Chromosome，SMC）包含黏连蛋白（cohesin）、凝缩蛋白（condensin）以及Smc5/6复合物（Smc5/6），这类复合物对染色体功能至关重要。在分子层面，这类复合物通过环挤压（loop extrusion）实现DNA的折叠。具体而言，黏连蛋白可在细胞间期形成染色体环，而凝缩蛋白则介导有丝分裂染色体的凝缩。然而，Smc5/6新近被发现的DNA环挤压活性，其对应的生物学功能仍未明确。本研究揭示，Smc5/6可调控超螺旋染色体区域的空间组织。实验结果表明，Smc5/6可结合于黏连蛋白依赖性染色体环边界处、由转录诱导产生的正超螺旋染色体DNA。机制层面，单分子成像研究显示，Smc5/6二聚体可特异性识别正超螺旋DNA缠结环的顶端，并高效启动环挤压过程，将超螺旋DNA聚集为大型缠结环。最后，Hi-C分析结果显示，Smc5/6可在顺式层面连接含有转录诱导正超螺旋的染色体区域。综上，本研究结果表明，Smc5/6可通过识别正超螺旋DNA并启动环挤压过程，调控染色体的三维组织架构。