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

Abstract

Summary 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, while 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.

Donor Preference Meets Heterochromatin: Moonlighting Activities of a Recombinational Enhancer in Saccharomyces cerevisiae

“…In comparison to a cells, a cells show more frequent interactions between the left arm of chromosome III, which contains HML and the RE, and a region on the right arm that extends from the centromere to the MAT locus. Upon deletion of the right portion of the RE locus, chromosome III adopts a configuration that is indistinguishable between the two mating types (Belton et al 2015). This configuration is distinct from that of both MATa RE cells and MATa RE cells, suggesting that the RE regulates chromosome folding in both mating types.…”

“…One noteworthy difference between a cells and a cells is the spatial conformation of chromosome III (Belton et al 2015;Lassadi et al 2015). In comparison to a cells, a cells show more frequent interactions between the left arm of chromosome III, which contains HML and the RE, and a region on the right arm that extends from the centromere to the MAT locus.…”

“…In addition, a cells transcribe multiple RNA species from the central and right portions of the RE (Szeto et al 1997;Ercan et al 2005). A recent study shows that the conformation of chromosome III differs between a and a cells, and that this difference depends on the right portion of the RE, but not on the left portion containing the minimal RE (Belton et al 2015). Given that the right portion makes only a small contribution to the effect on recombination, the RE is roughly divisible into two subregions with separate functions.…”

“…In budding yeast, a 2-kbp region referred to as the recombination enhancer (RE) acts in cis to promote the use of sites located throughout the left arm of chromosome III as donor templates during mating-type interconversion (Wu and Haber 1996). Through a separate, unknown mechanism, the RE also regulates the spatial conformation of chromosome III (Belton et al 2015). Hence, this extraordinary locus is enriched for features that mediate long-range effects.…”

“…Given that a cells and a cells show similar patterns of DNase-I sensitivity throughout this chromosome arm, the RE does not dramatically alter the local chromatin structure (Ercan and Simpson 2004). Remarkably, the RE does effect a change in the higher-order folding of chromosome III; however, this function is genetically separable from the recombination function (Belton et al 2015;Lassadi et al 2015). The mechanism by which the RE acts at a distance remains unresolved.…”