Cohesin guides homology search during DNA repair via 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 non-homologous bases remains unclear. Here, we introduce sister-pore-C, a high-resolution method for mapping intra- and trans-molecular interactions in replicated chromosomes. We show that DSBs reshape chromosome architecture by recruiting two functionally distinct pools of cohesin. Loop-forming cohesin accumulates across a megabase-scale domain to control homology sampling within topologically associating domains (TADs) surrounding the break site, while cohesive cohesin concentrates at the break site to tether broken ends to the sister chromatid. This dual mechanism restricts the homology search space, highlighting how chromosome conformation helps preserve genomic integrity.