Abstract
3D nuclear architecture is a key factor in regulating many cellular processes. Here, based on the published haploid yeast chromosome conformation capture data, we investigated the role of chromosome organization in DNA double-strand break repair, mainly through gene conversion. By using both single-donor viability assay and two-donor competition assay, we found the repair efficiency of a homologous donor sequence is highly correlated with their reconstituted distances to the recipient DSB site, which was deduced from the Hi-C database. Such correlation still exists when the break is induced at another locus. We also demonstrated that increasing the length of homology, inserting an ectopic Recombination Enhancer (RE), slowing down resection by FUN30 deletion, and enhancing RPA protein abundance effectively increased the repair efficiency. In addition, intra-chromosomal gene conversion is more frequent than inter-chromosomal events, but it is still constrained by chromosome organization. Our data revealed the tethering of centromeres to the spindle pole body during homologous recombination process, which agrees with the RabI configuration of yeast chromosomes. The result also provided extensive data to validate the chromosome polymer folding model. Through this study, we hope to provide more insights in the structural-functional correlation in eukaryotic genomes.