The LINC complex component Kms1 and CENP-B protein Cbp1 cooperate to enforce faithful homology-directed DNA repair at the nuclear periphery in S. pombe

While homologous recombination (HR) is often considered to be an error-free DNA repair mechanism, the fidelity of this pathway depends on the cell’s ability to engage the ideal template, the replicated sister chromatid. This is particularly challenging during repair of repetitive genome regions for which non-allelic sequences can errantly be used as templates. Here, we develop a model to study spontaneous DNA damage and repair that occurs at repetitive protein coding genes of the S. pombe flocculin family. We observe that genes encoding most members of this protein family constitutively reside at the nuclear periphery by virtue of their close proximity to binding sites for the CENP-B like protein, Cbp1. Tethering via Cbp1 to the nuclear periphery enhances the stability of the flocculin genes against intragenic recombination and restrains intergenic recombination between homoeologous repeat-encoding sequences. The LINC complex component Kms1 also antagonizes both intragenic and intergenic recombination at the flocculin genes as well as microhomology-mediated end-joining (MMEJ). Our observations suggest that S. pombe leverages nuclear compartmentalization to maintain the stability of repetitive genic regions at the nuclear periphery while association of DSBs with Kms1-containing LINC complexes enforces stringency to avoid mutagenic end-joining and use of the incorrect template during HR.