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| Status |
Public on Mar 01, 2013 |
| Title |
Dynamics of yeast ISWI and CHD chromatin remodeler genomic association (part 2) |
| 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
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109-1024 |
| Country |
USA |
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| Platforms (1) |
| GPL13821 |
Illumina HiSeq 2000 (Saccharomyces cerevisiae) |
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| Samples (11)
|
| GSM968692 |
Isw1 WT N-ChIP-seq 2.5' MNase (1.25 IP 20120410 6) |
| GSM968693 |
Isw1 WT input 2.5' MNase (1.25 input 20120410 7) |
| GSM968694 |
Chd1 WT N-ChIP-seq 10' MNase (Chd1FLAG 20120223 7) |
| GSM968695 |
Chd1 WT input 10' MNase (Chd1IN 20120223 6) |
| GSM968696 |
Isw1 WT N-ChIP-seq 10' MNase (Isw1FLAG 20120223 3) |
| GSM968697 |
Isw1 WT input 10' MNase (Isw1IN 20120223 2) |
| GSM968698 |
Isw1 K227R input 2.5' MNase (Isw1 K227R input 20120410 3) |
| GSM968699 |
Isw2 WT N ChIP-seq 10' MNase (Isw2FLAG 20120223 5) |
| GSM968700 |
Isw2 WT input 10' MNase (Isw2IN 20120223 4) |
| GSM968701 |
Isw2 K215R input 2.5' MNase (K215Rinp 20111207 6) |
| GSM968702 |
Isw2 WT input 2.5' MNase (WT inp 20111207 5) |
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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 |
PRJNA170935 |
| SRA |
SRP071614 |
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