The Conformation of Yeast Chromosome III Is Mating Type Dependent and Controlled by the Recombination Enhancer

Mating-type switching in yeast occurs through gene conversion between the MAT locus and one of two silent loci (HML or HMR) on opposite ends of the chromosome. MATa cells choose HML as template, whereas MATα cells use HMR. The recombination enhancer (RE) located on the left arm regulates this process. One long-standing hypothesis is that switching is guided by mating-type-specific and possibly RE-dependent chromosome folding. Here, we use Hi-C, 5C, and live-cell imaging to characterize the conformation of chromosome III in both mating types. We discovered a mating-type-specific conformational difference in the left arm. Deletion of a 1-kb subregion within the RE, which is not necessary during switching, abolished mating-type-dependent chromosome folding. The RE is therefore a composite element with one subregion essential for donor selection during switching and a separate region involved in modulating chromosome conformation. [Display omitted] •The conformation of the left arm of yeast chromosome III is mating type specific•In MATa cells, HMLα is closer to the centromere and the MAT locus•The recombination enhancer is a functionally composite element•The right half of the RE is a cell-type-specific architectural element Yeast mating-type switching involves a mating-type-dependent selection of either the left (HML) or right silent mating-type locus (HMR) on chromosome III for gene conversion with the active MAT locus. One hypothesis has been that this involves differential folding of the chromosome. Belton et al. now show that a 1-kb cis-element located within the larger recombination enhancer determines mating-type-dependent chromosome folding so that in MATa cells HML associates with the centromere and MAT locus more frequently than in MATα cells.