Whole-genome sequencing of Schizosaccharomyces pombe strains with mutations in recombination and mating-type switching genes

Homologous recombination (HR) is generally viewed as dispensable in yeast and vertebrates, yet mounting evidence indicates that its essentiality depends on cellular context. Here, we dissect the basis of this context dependency in the two most widely used Schizosaccharomyces pombe heterothallic strains. In the homothallic h90 strain, considered wild type, mating-type switching (MTS) occurs every other cell division and requires HR to repair programmed double-strand breaks (DSBs) at the mat1 locus. We show that the heterothallic h-S strain, although frequently employed in HR-deficient backgrounds (rad51?, rad52?, rad54?), is likewise dependent on HR for viability. These mutants survive only when harboring secondary suppressor mutations that prevent mat1 DSB formation, such as smt-0, swi1?, or fml1?. By contrast, HR is dispensable in the h+N strain, where duplication of the mat2/3 region into mat1 introduces the cenH and REIII elements, which nucleate H3K9 methylation and heterochromatin spreading across the imprint site. This chromatin state blocks recruitment of the imprintosome complex, thereby preventing imprinting, DSB formation, and MTS, while also silencing nearby genes. Disruption of this heterochromatin, via deletion of cenH or essential chromatin modifiers, restores MTS in h+N cells and reinstates HR essentiality in the absence of the Clr4 methyltransferase. Collectively, these findings demonstrate that HR is indispensable for S. pombe survival due to its critical role in repairing mat1 DSBs, except when mutations or epigenetic states prevent their formation.