The three-dimensional organization of chromosomes guides genome function from gene expression to DNA repair and recombination. This organization can be modeled from genome-wide chromosome conformation data. To reveal features from dynamic or transient events that are only visible in a fraction of cells at any given moment, we develop quantitative and real time image analysis methods.
Motion of single DNA loci in yeast is compatible with highly flexible chromatin fiber. Based on measured dynamic parameters we propose biophysical models of yeast chromatin behavior which could explain altered motion in response to transcription and DNA breakage.
Geometrical analysis and mathematical polymer modeling of 3D measurements of 3 distinct labeled DNA loci in living cells, revealed that conformation of yeast chromosome III is mating type specific. S cerevisiae switch mating type by gene conversion between the MAT locus and either of two silent loci (HML or HMR) on opposite ends of chromosome III. MATa cells choose HMLα as a template, while MATα cells use HMRa, providing a paradigm for long-range interactions between distant loci and donor selection during homologous recombination mediated DNA repair. We confirmed and extended our findings by Hi-C and 5C to show that, in non-switching strains, deletion of a 2.15 kb intergenic region, comprising the recombination enhancer (RE), abolished the mating type-dependent conformation. Hence, the RE induces conformational changes in both mating types in the absence of mating type switching.