Global identification of yeast chromosome interactions using Genome conformation capture

Chromosome positioning and the clustering of functionally related loci in yeast is driven by chromosomal interactions

“…Yet, there are clearly nucleolar associated sequences. 2,26,41 Therefore, excluding rDNA interactions from the model 6 causes the nucleolus to become artificially disjoint from the rest of the genome. To address these conflicting issues, we incorporated only two rDNA repeats in our models and implemented interactions between the rDNA and other loci as attractive forces toward the nucleolusnucleoplasm boundary.…”

“…Lutz R. Gehlen, 1, † Gerd Gruenert, [1][2][3] that the spatial arrangement of the genome inside the nucleus can be reconstructed by combining the entirety of chromosomal interactions measured by proximity-based ligation (e.g., genome conformation capture; GCC 2 ). Single representations of the 3-dimensional organization of the Saccharomyces cerevisiae and Schizosaccharomyces pombe genomes have been generated using empirically obtained chromosomal interaction frequencies that were converted into linear distance approximations.…”

“…Critically, the chromosomal interactions identified by proximity-based ligation are averaged across the test cell population and the subset of interactions that is present in a single cell cannot be determined. Therefore, it remained unclear: (1) how much the genome organization depends upon the specific subset of interactions that are currently present within it; and (2) what contribution the nuclear membrane and gross localization effects (e.g., centromeres, telomeres and the nucleolus) make to the overall organization.…”

“…18 So far, the existence of chromosome territories within the budding yeast nucleus is debated 20,21 although there is growing evidence of their existence. 2,6,10,12,21 Therefore, we used our model to investigate if single chromosomes assume preferred positions within the yeast nucleus.…”

“…[2][3][4][5][6] The strength of the proximity-based ligation methodologies is their ability to identify loci that are directly or indirectly (i.e., mediated by a defined or unknown complex) held close enough to be cross-linked, within a subset of the test population, at a moment in time. However, these techniques do not reveal the spatial organization of loci outside of cross-linking distance nor do they identify where a given locus is positioned within the nuclear or cellular space.…”