Laffitte, A.; Lin, D.; Tian, Y. J.; Liu, N.; Lusk, C. P.; Mochrie, S.; King, M. C.

While homologous recombination (HR) is often considered to be an error-free DNA repair mechanism in mitotically growing cells, the ultimate fidelity of this pathway depends on the ability of the cell to engage the ideal template, the replicated sister chromatid. This is particularly challenging during repair of repetitive regions of the genome 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 the 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 homeologous repeat-encoding sequences. In addition, the LINC complex component Kms1, which we have previously shown associates with persistent DNA double-strand breaks that move to the nuclear periphery, also antagonizes both intragenic and intergenic recombination at the flocculin genes. Loss of Kms1 also enhances use of microhomology-mediated end-joining (MMEJ). Our observations suggest that S. pombe leverages nuclear compartmentalization to maintain the stability of repetitive genic regions through a constitutive tethering mechanism at the nuclear periphery. Moreover, association of DSBs with Kms1-containing LINC complexes enforces stringency to both attenuate the use of microhomology that drives mutagenic end-joining or selecting the correct template for HR.