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Cell. 2015 Jul 2;162(1):108-19. doi: 10.1016/j.cell.2015.05.048. Epub 2015 Jun 25.

Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C.

Author information

1
Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
2
School of Computer Science and Engineering, The Hebrew University, Jerusalem 91904, Israel; Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel.
3
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.
4
Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA. Electronic address: oliver.rando@umassmed.edu.

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.

PMID:
26119342
PMCID:
PMC4509605
DOI:
10.1016/j.cell.2015.05.048
[Indexed for MEDLINE]
Free PMC Article
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