title: Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C.
abstract: 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.
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
authors.forename: Tsung-Han S
authors.initials: TH
authors.lastname: Hsieh
authors.affiliation: School of Computer Science and Engineering, The Hebrew University, Jerusalem 91904, Israel; Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel.
authors.forename: Assaf
authors.initials: A
authors.lastname: Weiner
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
authors.forename: Bryan
authors.initials: B
authors.lastname: Lajoie
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
authors.forename: Job
authors.initials: J
authors.lastname: Dekker
authors.affiliation: School of Computer Science and Engineering, The Hebrew University, Jerusalem 91904, Israel; Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel.
authors.forename: Nir
authors.initials: N
authors.lastname: Friedman
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA. Electronic address: oliver.rando@umassmed.edu.
authors.forename: Oliver J
authors.initials: OJ
authors.lastname: Rando
mesh_terms: D001671:Biochemistry / Q000379:methods*; D015825:Chromosomes, Fungal / Q000737:chemistry*; D009707:Nucleosomes / Q000737:chemistry*; D012441:Saccharomyces cerevisiae / Q000737:chemistry* / Q000235:genetics
chemical_list: D009707:Nucleosomes