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| Status |
Public on Jun 25, 2015 |
| Title |
Mapping nucleosome resolution chromosome folding in yeast by Micro-C |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Other
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| 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 shorted 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 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.
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| Overall design |
Chromatin is fragmented by Mnase, subsequenct nucleosomal end repair, and a modified two-step method for purfiying ligation products. Using Illumina paired-end sequencing maps Micro-C library and generates nucleosome resolution contact maps.
The readme.txt file contains additional description of how each processed data file was generated.
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| Contributor(s) |
Rando OJ, Hsieh TS |
| Citation(s) |
26119342 |
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| Submission date |
Apr 17, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Xavier Darzacq |
| E-mail(s) |
darzacq@berkeley.edu
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| Phone |
510-642-0884
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| Organization name |
University of California, Berkeley
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| Department |
Molecular and Cell Biology
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| Lab |
Darzacq Lab
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| Street address |
475D Li Ka Shing Center
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| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
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| Platforms (2) |
| GPL13821 |
Illumina HiSeq 2000 (Saccharomyces cerevisiae) |
| GPL19756 |
Illumina NextSeq 500 (Saccharomyces cerevisiae) |
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| Samples (91)
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| Relations |
| BioProject |
PRJNA281500 |
| SRA |
SRP057391 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE68016_Boundary_calls_for_wild-type_yeast.xlsx |
671.2 Kb |
(ftp)(http) |
XLSX |
| GSE68016_Gene_compaction_scores_for_all_datasets_with_multiple_replicates.xlsx |
2.7 Mb |
(ftp)(http) |
XLSX |
| GSE68016_Gene_compaction_scores_for_temperature-sensitive_dataset.xlsx |
1.2 Mb |
(ftp)(http) |
XLSX |
| GSE68016_Micro-C_interactions_vs._distance_for_MNase_titrations.xlsx |
2.7 Mb |
(ftp)(http) |
XLSX |
| GSE68016_Micro-C_interactions_vs._distance_for_all_datasets.xlsx |
11.9 Mb |
(ftp)(http) |
XLSX |
| GSE68016_NDR-spanning_reads_for_all_replicates.xlsx |
2.8 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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