We describe a Hi-C-based method, Micro-C, in which micrococcal nuclease is used instead of restriction enzymes to fragment chromatin, enabling nucleosome resolution chromosome folding maps. Analysis of Micro-C maps for budding yeast reveals abundant self-associating domains similar to those reported in other species, but not previously observed in yeast. These structures, far shorter than topologically associating domains in mammals, typically encompass one to five genes in yeast. Strong boundaries between self-associating domains occur at promoters of highly transcribed genes and regions of rapid histone turnover that are typically bound by the RSC chromatin-remodeling complex. Investigation of chromosome folding in mutants confirms roles for RSC, “gene looping” factor Ssu72, Mediator, H3K56 acetyltransferase Rtt109, and the N-terminal tail of H4 in folding of the yeast genome. This approach provides detailed structural maps of a eukaryotic genome, and our findings provide insights into the machinery underlying chromosome compaction.
Hsieh, T.H., Weiner, A., Lajoie, B., Dekker, J., Friedman, N., and Rando, O.J. (2015). Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C. Cell 162, 108-119.
Chromosome conformation capture (3C) has revolutionized the ways in which the conformation of chromatin and its relationship to other molecular functions can be studied. 3C-based techniques are used to determine the spatial arrangement of chromosomes in organisms ranging from bacteria to humans. In particular, they can be applied to the study of chromosome folding and organization in model organisms with small genomes and for which powerful genetic tools exist, such as budding yeast. Studies in yeast allow the mechanisms that establish or maintain chromatin structure to be analyzed at very high resolution with relatively low cost, and further our understanding of these fundamental processes in higher eukaryotes as well. Here we provide an overview of chromatin structure and introduce methods for performing 3C, with a focus on studies in budding yeast. Variations of the basic 3C approach (e.g., 3C-PCR, 5C, and Hi-C) can be used according to the scope and goals of a given experiment.
Belton, J.M., and Dekker, J. (2015a). Chromosome Conformation Capture (3C) in Budding Yeast. Cold Spring Harbor protocols 2015, pdb prot085175.
Belton, J.M., and Dekker, J. (2015b). Chromosome Conformation Capture Carbon Copy (5C) in Budding Yeast. Cold Spring Harbor protocols 2015, pdb prot085191.
Belton, J.M., and Dekker, J. (2015c). Hi-C in Budding Yeast. Cold Spring Harbor protocols 2015, pdb prot085209.
Belton, J.M., and Dekker, J. (2015d). Measuring Chromatin Structure in Budding Yeast. Cold Spring Harbor protocols 2015, pdb top077552.
Belton, J.M., and Dekker, J. (2015e). Randomized ligation control for chromosome conformation capture. Cold Spring Harbor protocols 2015, pdb prot085183.