Liao Qin, Brandão Hugo B, Ren Zhongqing, Wang Xindan
Department of Biology, Indiana University, Bloomington, IN, USA.
Illumina Inc., San Diego, CA, USA.
Nat Commun. 2025 Aug 4;16(1):7151. doi: 10.1038/s41467-025-62596-y.
Structural maintenance of chromosomes (SMC) complexes organize genomes by extruding DNA loops, while replisomes duplicate entire chromosomes. These essential molecular machines must collide frequently in every cell cycle, yet how such collisions are resolved in vivo remains poorly understood. Taking advantage of the ability to load SMC complexes at defined sites in the Bacillus subtilis genome, we engineered head-on and head-to-tail collisions between SMC complexes and the replisome. Replisome progression was monitored by genome-wide marker frequency analysis, and SMC translocation was monitored by time-resolved ChIP-seq and Hi-C. We found that SMC complexes do not impede replisome progression. By contrast, replisomes restrict SMC translocation regardless of collision orientations. Combining experimental data with simulations, we determined that SMC complexes are blocked by the replisome and then released from the chromosome. Occasionally, SMC complexes can bypass the replisome and continue translocating. Our findings establish that the replisome is a barrier to SMC-mediated DNA-loop extrusion in vivo, with implications for processes such as chromosome segregation, DNA repair, and gene regulation that require dynamic chromosome organization in all organisms.
染色体结构维持（SMC）复合体通过挤压DNA环来组织基因组，而复制体则复制整个染色体。这些重要的分子机器在每个细胞周期中必定频繁碰撞，然而在体内如何解决这种碰撞仍知之甚少。利用在枯草芽孢杆菌基因组特定位点加载SMC复合体的能力，我们设计了SMC复合体与复制体之间的迎面碰撞和头尾碰撞。通过全基因组标记频率分析监测复制体的进展，通过时间分辨染色质免疫沉淀测序（ChIP-seq）和高通量染色体构象捕获技术（Hi-C）监测SMC的易位。我们发现SMC复合体不会阻碍复制体的进展。相比之下，无论碰撞方向如何，复制体都会限制SMC的易位。将实验数据与模拟相结合，我们确定SMC复合体被复制体阻断，然后从染色体上释放。偶尔，SMC复合体可以绕过复制体并继续易位。我们的研究结果表明，复制体是体内SMC介导的DNA环挤压的障碍，这对染色体分离、DNA修复和基因调控等过程具有影响，而这些过程在所有生物体中都需要动态的染色体组织。
