Mapping nucleosome resolution chromosome folding in yeast by Micro-C

By Tsung-Han S. Hsieh, A. Weiner, B. Lajoie, Job Dekker, Nir Friedman, Oliver J. Rando. Cell, 2015

666 citations recorded by the source corpus.

SUMMARY 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.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/65248ca1a2333ef2c553252fbc296a2b171e1812

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

1. Bing Ren
2. Anthony D. Schmitt
3. Ming Hu
4. Job Dekker
5. B. Lajoie
6. J. Wysocka
7. Yawen Bai
8. Bing-Rui Zhou

In Plant Science

1. Bing Ren
2. Ming Hu
3. Anthony D. Schmitt
4. Job Dekker
5. B. Lajoie
6. J. Wysocka
7. H. K. Long
8. Edith Heard

Citations in the corpus

• Topological polymorphism of nucleosome fibers and folding of chromatin (2021, background): “Several distinct arrangements of nucleosomes were detected, two of which were denoted as IN-IN and OUT-OUT orientations (14), or ‘‘inward’’ and ‘‘outward’’ interactions of nucleosomes (17).”
• Local states of chromatin compaction at transcription start sites control transcription levels (2021, methodology): “A derivative of the chromosome conformation capture (3C) method also revealed that motifs consisting of 3 - 4 nucleosomes were commonly formed in budding yeast ( 27 ).”
• Genome-wide mapping and analysis of chromosome architecture (2016, methodology): “Similarly, micrococcal nuclease (MNase) has been used to fragment chromatin before proximity ligation in yeast nuclei, helping to achieve nucleosome-level resolution of chromatin organization 50 .”
• Revisit of reconstituted 30-nm nucleosome arrays reveals an ensemble of dynamic structures (2018, background): “A number of studies have failed to reveal long regularly folded 30-nm fibers, including those using cryo-EM tomography [21], small angle X-ray [13], Micro-C [45], super-resolution light microscopy J Mol Biol.”
• Ever-changing landscapes: transcriptional enhancers in development and evolution (2016, background): “(E) During mitosis, TAD structure is lost. highly transcribed genes (Hsieh et al., 2015).”
• Gene regulatory network inference in the era of single-cell multi-omics (2023, background): “High-resolution Hi-C maps exist, such as Micro-C 190 , but their cost becomes prohibitive when comparing many experimental conditions.”
• HiC-Pro: an optimized and flexible pipeline for Hi-C data processing (2015, background): “HiC-Pro allows the processing of data from Hi-C protocols based on restriction enzyme or nuclease digestion such as DNase Hi-C [4] or Micro-C [16].”