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| Status |
Public on Mar 01, 2013 |
| Title |
Dynamics of yeast ISWI and CHD chromatin remodeler genomic association (part 1) |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Chromatin remodelers influence genetic processes by altering nucleosome occupancy, positioning, and composition. In vitro, yeast ISWI and CHD remodelers require > 20 bp of extranucleosomal DNA for remodeling, but linker DNA in S. cerevisiae averages < 20 bp. To resolve this paradox, we have mapped the genomic distributions of the yeast Isw1, Isw2, and Chd1 remodelers at base-pair resolution. Surprisingly, remodelers are highly enriched at promoter nucleosome depleted regions (5' NDRs), where they bind to regions of extended linker DNA. Remodelers are also enriched in the bodies of genes displaying high nucleosome turnover. We hypothesize that remodelers bind but do not act at 5' NDRs, remaining in physical proximity to gene bodies, where they act on regions of transient nucleosome depletion following transcriptional elongation.
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| Overall design |
We have analyzed the dynamics of yeast ISWI and CHD chromatin remodeler genomic association at base-pair resolution using native chromatin immunoprecipitation followed by sequencing (N-ChIP-seq).
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| Contributor(s) |
Zentner GE, Henikoff S |
| Citation(s) |
23468649 |
| |
| Submission date |
Jul 17, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Jorja Henikoff |
| E-mail(s) |
[email protected]
|
| Phone |
206-667-4850
|
| Organization name |
Fred Hutchinson Cancer Research Center
|
| Department |
Basic Sciences
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| Lab |
Henikoff
|
| Street address |
1100 Fairview AV N, A1-162
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109-1024 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL13821 |
Illumina HiSeq 2000 (Saccharomyces cerevisiae) |
|
| Samples (7)
|
| GSM968685 |
Isw1 K227R N-ChIP-seq 2.5' MNase (Isw1 K227R FLAG IP 20120410 2) |
| GSM968686 |
Isw2 K215R N-ChIP-seq 2.5' MNase (K215R Flag 20111207 4) |
| GSM968687 |
Chd1 K407R N-ChIP-seq 2.5' MNase (K407R Chd1 FLAG 20120606 2) |
| GSM968688 |
Chd1 K407R input 2.5' MNase (K407R Chd1 input 20120606 1) |
| GSM968689 |
Chd1 WT N-ChIP-seq 2.5' MNase (WT Chd1 FLAG 20120606 2) |
| GSM968690 |
Chd1 WT input 2.5' MNase (WT Chd1 input 20120606 1) |
| GSM968691 |
Isw2 WT N-ChIP-seq 2.5' MNase (WT Flag 20111207 3) |
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| This SubSeries is part of SuperSeries: |
| GSE39331 |
Dynamics of yeast ISWI and CHD chromatin remodeler genomic association |
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| Relations |
| BioProject |
PRJNA170934 |
| SRA |
SRP014442 |
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