Cohesin guides homology search during DNA repair using loops and sister chromatid linkages.

Accurate repair of DNA double-strand breaks (DSBs) is essential for genome stability, and defective repair underlies diseases such as cancer. Homologous recombination uses an intact homologous sequence to faithfully restore damaged DNA, yet how broken DNA ends find homologous sites in a genome containing billions of bases remains unclear. Here, we introduce sister-pore-C, a high-resolution method to map intra- and intermolecular interactions in replicated chromosomes. We show how DSBs remodel chromosome architecture using two functionally distinct pools of cohesin. Loop-extruding cohesin accumulates across megabase-scale domains surrounding DSBs to control local homology sampling, whereas cohesive cohesin concentrates at break sites to tether DNA ends to the sister chromatid. This mechanism restricts the homology-sampling space, highlighting how chromosome conformation helps to preserve genomic integrity. Editor's summary: Cells constantly face DNA damage that, if repaired incorrectly, can lead to cancer or genetic instability. Homologous recombination, one of the most accurate repair mechanisms, requires broken DNA to find a matching sequence among billions of bases. Using a powerful method to map DNA interactions inside cells, Teloni et al. uncovered how this search is guided by the protein complex cohesin. They found that cohesin acts in two ways: by forming loops that focus the search to DNA near the break and by clamping the broken end to its sister chromatid to scan the correct repair template. Marin-Gonzalez et al. found that cohesin actively reels in surrounding chromatin to help the repair protein RAD51 scan for homology. This directed, one-dimensional scanning mechanism greatly accelerates the search process. These studies reveal how cells overcome a fundamental biophysical problem in DNA repair, with implications for understanding genome instability in cancer and other diseases (see the Perspective by Hu). —Di Jiang INTRODUCTION: Accurate repair of DNA double-strand breaks (DSBs) is essential for genome stability, because errors can cause cell death or chromosomal rearrangements linked to cancer. Homologous recombination restores DNA sequences around the break by copying from an intact template, usually the sister chromatid. A key challenge has been to understand how broken DNA ends locate the correct homologous sequence within the folded genome. Although the biochemical steps of repair are well described, the contribution of nuclear architecture to the homology search process has remained unclear. RATIONALE: Cohesin, a ring-shaped protein complex, organizes chromosomes by extruding DNA loops to form topologically associating domains (TADs) and by linking sister chromatids. Both functions influence genome topology, but how this affects homology search was unknown. To address this, we developed sister-pore-C, a high-resolution method to map intra- and interchromatid contacts genome wide. Combined with targeted DSB induction and acute cohesin perturbations, this approach allowed us to determine how cohesin-mediated structures guide RAD51 filament sampling during repair. RESULTS: RAD51 filaments sampled homology primarily near DSBs and within TAD boundaries, indicating that cohesin-mediated loops control the search space. Loss of loop-extruding cohesin narrowed RAD51 distribution, whereas hyperprocessive extrusion expanded sampling but reduced its local concentration near the DNA break. Sister-pore-C revealed that DSBs remodel chromosome architecture locally, increasing looping and promoting contacts with the sister chromatid near the break. Cohesin mapping showed that loop-extruding complexes accumulate across a broad domain surrounding the DSB, whereas cohesive cohesin concentrates at the break itself, establishing distinct cis- and trans-sister architectures. Functionally, depletion of loop-extruding cohesin or excessive extrusion delayed repair, and loss of cohesion abolished repair, demonstrating that both mechanisms are essential for efficient homologous recombination. CONCLUSION: Cohesin directs homology search through a dual mechanism: A cohesive clamp tethers broken DNA ends to the sister chromatid, and loop extrusion controls sampling within the local TAD. This spatial organization narrows the search space and accelerates repair, establishing chromosome topology as an active determinant of repair efficiency. Sister-pore-C enables genome-wide mapping of intra- and intersister contacts, providing a framework with which to explore recombination architectures in other processes such as meiosis. Model of how DNA DSBs locally reorganize chromatin to facilitate homology search.: Cohesive cohesin (red) accumulates directly adjacent to the break site (green) to direct sampling toward the intact sister chromatid, whereas loop-extruding cohesin (blue) spreads across a megabase-scale domain to regulate the lateral sampling range. [ABSTRACT FROM AUTHOR]