The repair of DNA double-strand breaks (DSBs) is essential for safeguarding genome integrity. When a DSB forms, the PI3K-related ATM kinase rapidly triggers the establishment of megabase-sized, chromatin domains decorated with phosphorylated histone H2AX (γH2AX), which act as seeds for the formation of DNA-damage response foci¹. It is unclear how these foci are rapidly assembled to establish a ‘repair-prone’ environment within the nucleus. Topologically associating domains are a key feature of 3D genome organization that compartmentalize transcription and replication, but little is known about their contribution to DNA repair processes^2,3. Here we show that topologically associating domains are functional units of the DNA damage response, and are instrumental for the correct establishment of γH2AX–53BP1 chromatin domains in a manner that involves one-sided cohesin-mediated loop extrusion on both sides of the DSB. We propose a model in which H2AX-containing nucleosomes are rapidly phosphorylated as they actively pass by DSB-anchored cohesin. Our work highlights the importance of chromosome conformation in the maintenance of genome integrity and demonstrates the establishment of a chromatin modification by loop extrusion.

DNA 双链断裂 (DSB) 的修复对于保护基因组完整性至关重要。当 DSB 形成时，与 PI3K 相关的 ATM 激酶会迅速触发由磷酸化组蛋白 H2AX (γH2AX) 修饰的兆碱基大小的染色质结构域的建立，这些结构域充当形成 DNA 损伤反应灶¹的种子。目前尚不清楚这些病灶如何快速组装以在细胞核内建立“易于修复”的环境。拓扑关联结构域是 3D 基因组组织的一个关键特征，可划分转录和复制，但对其对 DNA 修复过程的贡献知之甚少^2,3. 在这里，我们表明拓扑关联结构域是 DNA 损伤反应的功能单元，并且有助于正确建立 γH2AX-53BP1 染色质结构域，其方式涉及 DSB 两侧的单侧黏连蛋白介导的环挤出。我们提出了一个模型，其中含有 H2AX 的核小体在通过 DSB 锚定的黏连蛋白主动通过时被快速磷酸化。我们的工作强调了染色体构象在维持基因组完整性中的重要性，并证明了通过环挤压建立染色质修饰。