Loop-extruding Smc5/6 organizes transcription-induced positive DNA supercoils. Jeppsson et al

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 associates with transcription-induced positively supercoiled DNA at cohesin-dependent loop boundaries on budding yeast (Saccharomyces cerevisiae) chromosomes. 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（Structural Maintenance of Chromosome, SMC）蛋白复合物包括黏连蛋白（cohesin）、凝缩蛋白（condensin）以及Smc5/6复合物（Smc5/6 complex, Smc5/6），其对于染色体功能至关重要。从分子层面来看，这类复合物通过环挤出（loop extrusion）方式折叠DNA。相应地，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新近发现的DNA环挤出活性的具体功能目前仍未明确。本研究揭示，在酿酒酵母（Saccharomyces cerevisiae）染色体的黏连蛋白依赖性环边界处，Smc5/6可结合转录诱导的正超螺旋DNA。机制层面上，单分子成像（single-molecule imaging）实验显示，Smc5/6二聚体能够特异性识别正超螺旋DNA纽结（plectonemes）的顶端，并高效启动环挤出过程，将超螺旋DNA组装为大型超螺旋环结构。最后，Hi-C分析结果表明，Smc5/6可在顺式（cis）层面连接包含转录诱导正超螺旋的染色体区域。综上，本研究结果证实，Smc5/6通过识别正超螺旋DNA并启动环挤出过程，调控染色体的三维组织结构。