Genome-wide profiling of DNA repair identifies higher-order coordination in single cells

Abstract Accurate repair of DNA damage is critical for maintenance of genomic integrity and cellular survival. Because damage occurs non-uniformly across the genome, single-cell resolution is required for proper interrogation, but sensitive detection has remained challenging. Here, we present genome-wide binding profiles of DNA double-strand break repair proteins in single cells, allowing for the study of heterogeneity in genomic damage locations and associated repair features. By unbiasedly detecting repair-enriched segments, we find that repair proteins often occupy entire topologically associating domains and mimic variability in chromatin loop anchoring. Genomic loci that form damage-specific 3D contacts show multi-way repair coordination in individual cells that becomes stronger according to the number of interaction partners. These findings advance our understanding of genome stability in the context of nuclear organization.