Abstract
Although many studies have shown that chromosomes are folded into cells in a nonrandom fashion, the functional significance of this spatial organization remains poorly understood. Combining theory and fluorescence microscopy, we demonstrate that the folded state of yeast chromosome III changes in response to a DNA double-strand break at the
MAT
locus, in agreement with previous studies. Importantly, we show that the change in the folded state of the chromosome after the break quantitatively accounts for the dynamics of homology search during DNA repair. Our study provides an example of a cell changing the folded state of one of its chromosomes in response to an internal chemical cue (DNA break), thereby affecting its function (DNA repair).
Chromosomes are folded into cells in a nonrandom fashion, with particular genetic loci occupying distinct spatial regions. This observation raises the question of whether the spatial organization of a chromosome governs its functions, such as recombination or transcription. We consider this general question in the specific context of mating-type switching in budding yeast, which is a model system for homologous recombination. Mating-type switching is induced by a DNA double-strand break (DSB) at the
MAT
locus on chromosome III, followed by homologous recombination between the cut
MAT
locus and one of two donor loci (
HML
α and
HMR
a), located on the same chromosome. Previous studies have suggested that in
MAT
a cells after the DSB is induced chromosome III undergoes refolding, which directs the
MAT
locus to recombine with
HML
α. Here, we propose a quantitative model of mating-type switching predicated on the assumption of DSB-induced chromosome refolding, which also takes into account the previously measured stochastic dynamics and polymer nature of yeast chromosomes. Using quantitative fluorescence microscopy, we measure changes in the distance between the donor (
HML
α) and
MAT
loci after the DSB and find agreement with the theory. Predictions of the theory also agree with measurements of changes in the use of
HML
α as the donor, when we perturb the refolding of chromosome III. These results establish refolding of yeast chromosome III as a key driving force in
MAT
switching and provide an example of a cell regulating the spatial organization of its chromosome so as to direct homology search during recombination.