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| Status |
Public on Jul 16, 2019 |
| Title |
Selective Disruption of Core Regulatory Transcription [ChIP-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Activation of identity determining transcription factors (TFs), or core regulatory TFs, is governed by cell-type specific enhancers, an important subset of these being super enhancers (SEs). This mechanism is distinct from constitutive expression of housekeeping genes. The characterization of drug-like small molecules to selectively inhibit core regulatory circuitry is of high interest for treatment of cancers, which are addicted to core regulatory TF function at SEs. Surprisingly, we find histone deacetylases (HDAC) to be an indispensable component of SE-driven transcription. While histone acetylation is a marker for active genes, over accumulation of acetylation selectively halts core regulatory transcription. We show this conundrum may in part be explained by a SE-specific need for resetting histones to maintain SE boundaries, to facilitate enhancer-promoter looping and high levels of transcription.
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| Overall design |
Genome-wide profiles for histone marks, chromatin remodelers, ATAC, transcription factors, coactivators, RNA Polymerase and architectural proteins in Rhabdomyosarcoma (RMS) cell lines before and after HDAC inhibition
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| Contributor(s) |
Gryder BE, Wen X, Khan J |
| Citation(s) |
31285436, 32744500, 34836971 |
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| Submission date |
Jun 27, 2018 |
| Last update date |
Dec 15, 2021 |
| Contact name |
Javed Khan |
| E-mail(s) |
khanjav@mail.nih.gov
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| Phone |
2407606135
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| Organization name |
NCI, NIH
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| Department |
Genetics Branch
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| Lab |
Javed Khan
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| Street address |
37 Convent Dr.
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (48)
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| This SubSeries is part of SuperSeries: |
| GSE120771 |
Selective Disruption of Core Regulatory Transcription |
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| Relations |
| BioProject |
PRJNA478223 |
| SRA |
SRP151465 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE116344_RAW.tar |
10.8 Mb |
(http)(custom) |
TAR (of BED) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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