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| Status |
Public on Oct 23, 2019 |
| Title |
DNaseI hypersensitivity mapping/DNaseI high-throughput sequencing (DHS-Seq) in Saccharomyces cerevisiae |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
We report the application of DHS-Seq and digital genomic footprinting to study chromatin changes and transcription factor-DNA binding upon long-term Hsp90 depletion utilizing the temperature-sensitive allele G170D. By generating about 86 and 85.6 million reads for wild type and mutant, we were able to reconstitute the chromatin accessibility and the transcription factor-DNA binding maps under regular conditions and under conditions where Hsp90 was long-term inactivated. We find that there is a global reduction of transcription factor binding sites with concurrent loss of open chromatin upon Hsp90 inactivation. This data was used in conjunction with our previous work involving DHS-Seq studies and short-term Hsp90 depletion (GEO GSE88875) to distinguish the affected transcription factor networks and the chromatin changes upon short- and long-term Hsp90 depletion. We identified two different modes of Hsp90 operation on transcription factor activities – short-term inactivation of Hsp90 altered transcription factor DNA binding activities, whereas long-term Hsp90 inactivation affected the steady-state levels of transcription factors. Overall, this study shows that Hsp90 regulates multiple transcription factor protein families and modulates chromatin architecture on a genome-wide scale.
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| Overall design |
DHS-Seq for WT and the Hsp90 temperature-sensitive strain with allele G170D.
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| Contributor(s) |
Gvozdenov Z, Freeman BC |
| Citation(s) |
31628945 |
| Submission date |
Oct 22, 2019 |
| Last update date |
Jan 22, 2020 |
| Contact name |
Zlata Gvozdenov |
| Organization name |
Harvard Medical School
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| Department |
BCMP
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| Street address |
240 Longwood Ave
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platforms (1) |
| GPL13821 |
Illumina HiSeq 2000 (Saccharomyces cerevisiae) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA578940 |
| SRA |
SRP226650 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE139268_RAW.tar |
92.0 Mb |
(http)(custom) |
TAR (of BED, BIGWIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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