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| Status |
Public on Jan 16, 2019 |
| Title |
Contrasting roles of the RSC and ISW1/CHD1 chromatin remodelers in RNA polymerase II elongation and termination |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Most yeast genes have a nucleosome-depleted region (NDR) at the promoter and an array of regularly spaced nucleosomes phased relative to the transcription start site. We have examined the interplay between RSC (a conserved essential SWI/SNF-type complex that determines NDR size) and the ISW1, CHD1 and ISW2 nucleosome spacing enzymes in chromatin organization and transcription, using isogenic strains lacking all combinations of these enzymes. The contributions of these remodelers to chromatin organization are largely combinatorial, distinct and non-redundant, supporting a model in which the +1 nucleosome is positioned by RSC and then used as a reference nucleosome by the spacing enzymes. Defective chromatin organization correlates with altered RNA polymerase II (Pol II) distribution. RSC-depleted cells exhibit low levels of elongating Pol II and high levels of terminating Pol II, consistent with defects in both termination and initiation, suggesting that RSC facilitates both. Cells lacking both ISW1 and CHD1 show the opposite Pol II distribution, suggesting elongation and termination defects. These cells have extremely disrupted chromatin, with high levels of close-packed di-nucleosomes near the 5’-ends of genes. We propose that ISW1 and CHD1 facilitate Pol II elongation by separating close-packed nucleosomes and by eliminating long linkers to prevent cryptic initiation.
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| Overall design |
MNase-seq data from two biological replicate experiments (one experiment with 2 levels of MNase digestion, the other with one level of digestion): MNase digestion of nuclei from wild type (WT) and isw1∆ chd1∆ double mutant cells
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| Contributor(s) |
Ocampo J, Chereji RV, Eriksson PR, Clark DJ |
| Citation(s) |
30683752 |
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| Submission date |
Jul 23, 2018 |
| Last update date |
Apr 17, 2019 |
| Contact name |
Razvan V. Chereji |
| E-mail(s) |
razvan.chereji@nih.gov
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| Phone |
301-435-8670
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| Organization name |
National Institutes of Health
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| Department |
NICHD
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| Lab |
David J. Clark Lab
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| Street address |
6 Center Drive, Room 2A14
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| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platforms (1) |
| GPL13821 |
Illumina HiSeq 2000 (Saccharomyces cerevisiae) |
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| Samples (6)
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| GSM3302136 |
Wild type cells, 200U MNase, Experiment 1 |
| GSM3302137 |
Wild type cells, 25U MNase, Experiment 2 |
| GSM3302138 |
Wild type cells, 50U MNase, Experiment 2 |
| GSM3302139 |
isw1∆ chd1∆ cells, 50U MNase, Experiment 1 |
| GSM3302140 |
isw1∆ chd1∆ cells, 25U MNase, Experiment 2 |
| GSM3302141 |
isw1∆ chd1∆ cells, 50U MNase, Experiment 2 |
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| Relations |
| BioProject |
PRJNA482377 |
| SRA |
SRP154867 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE117514_RAW.tar |
277.9 Mb |
(http)(custom) |
TAR (of TDF) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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