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| Status |
Public on Sep 29, 2021 |
| Title |
Stabilization of Pol II protein, orchestration of transcription cycles, and maintenance of enhancer landscape by general transcription regulator SPT5 [ChIP-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Transcription machinery progression is governed by multitasking regulators including SPT5, an evolutionarily conserved factor implicated in virtually all transcriptional steps from enhancer activation to termination. Yet its mechanistic understanding in human cells remains incomplete. Here we utilize rapid degradation system and reveal crucial function of SPT5 in maintaining cellular and chromatin Pol II levels. Rapid SPT5 depletion causes a pronounced reduction of paused Pol II at promoters and enhancers, distinct from NELF degradation resulting in short-distance paused Pol II redistribution. Most of genes exhibit down- but not upregulation, accompanied by greatly impaired transcription activation and altered chromatin landscape at enhancers, and severe Pol II processivity defects at gene bodies. Phosphorylation of KOWx-4/5- linker potentiates pause release and is antagonized by Integrator-PP2A (INTAC) targeting SPT5 and Pol II. Our findings position SPT5 as an essential positive regulator of global transcription by controlling cellular Pol II levels, enhancer activation and landscape, paused Pol II stability, elongation processivity and termination in human.
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| Overall design |
We performed PRO-seq, ATAC-seq, RNA-seq, ChIP-seq, or TT-seq to investigate the role of SPT5 in regulating transcription. In this study, samples for each condition were collected in biological duplicates. Cells were treated with dTAG13 for 3, 12,or 24 hours, the corresponding control cells were treated for the same duration with vehicle only (DMSO) at the same vol/vol dilution.
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| Contributor(s) |
Hu S, Peng L, Wang Z, Song A, Chen FX |
| Citation(s) |
34534457 |
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| Submission date |
Jul 26, 2021 |
| Last update date |
Sep 30, 2021 |
| Contact name |
Linna Peng |
| E-mail(s) |
[email protected]
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| Phone |
8618810567356
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| Organization name |
Fudan University
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| Street address |
Dong'an Road
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| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (28)
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| GSM5471898 |
ChIP-BRG1_DMSO-3h_SPT5-N-PURO-Fkbp12_DLD1_rep1 |
| GSM5471899 |
ChIP-BRG1_DMSO-3h_SPT5-N-PURO-Fkbp12_DLD1_rep2 |
| GSM5471900 |
ChIP-BRG1_dTAG-3h_SPT5-N-PURO-Fkbp12_DLD1_rep1 |
| GSM5471901 |
ChIP-BRG1_dTAG-3h_SPT5-N-PURO-Fkbp12_DLD1_rep2 |
| GSM5471902 |
ChIP-Flag-SPT5_DMSO-3h_SPT5-N-PURO-Fkbp12_DLD1_rep1 |
| GSM5471903 |
ChIP-Flag-SPT5_DMSO-3h_SPT5-N-PURO-Fkbp12_DLD1_rep2 |
| GSM5471904 |
ChIP-Flag-SPT5_dTAG-3h_SPT5-N-PURO-Fkbp12_DLD1_rep1 |
| GSM5471905 |
ChIP-Flag-SPT5_dTAG-3h_SPT5-N-PURO-Fkbp12_DLD1_rep2 |
| GSM5471906 |
ChIP-H3K27ac_DMSO-3h_SPT5-N-PURO-Fkbp12_DLD1_rep1 |
| GSM5471907 |
ChIP-H3K27ac_DMSO-3h_SPT5-N-PURO-Fkbp12_DLD1_rep2 |
| GSM5471908 |
ChIP-H3K27ac_dTAG-3h_SPT5-N-PURO-Fkbp12_DLD1_rep1 |
| GSM5471909 |
ChIP-H3K27ac_dTAG-3h_SPT5-N-PURO-Fkbp12_DLD1_rep2 |
| GSM5471910 |
ChIP-Input_DMSO-3h_SPT5-N-PURO-Fkbp12_DLD1_rep1 |
| GSM5471911 |
ChIP-Input_DMSO-3h_SPT5-N-PURO-Fkbp12_DLD1_rep2 |
| GSM5471912 |
ChIP-Input_dTAG-3h_SPT5-N-PURO-Fkbp12_DLD1_rep1 |
| GSM5471913 |
ChIP-Input_dTAG-3h_SPT5-N-PURO-Fkbp12_DLD1_rep2 |
| GSM5471914 |
ChIP-Med1_DMSO-3h_SPT5-N-PURO-Fkbp12_DLD1_rep1 |
| GSM5471915 |
ChIP-Med1_DMSO-3h_SPT5-N-PURO-Fkbp12_DLD1_rep2 |
| GSM5471916 |
ChIP-Med1_dTAG-3h_SPT5-N-PURO-Fkbp12_DLD1_rep1 |
| GSM5471917 |
ChIP-Med1_dTAG-3h_SPT5-N-PURO-Fkbp12_DLD1_rep2 |
| GSM5471918 |
ChIP-RPB1_DMSO-3h_SPT5-N-PURO-Fkbp12_DLD1_rep1 |
| GSM5471919 |
ChIP-RPB1_DMSO-3h_SPT5-N-PURO-Fkbp12_DLD1_rep2 |
| GSM5471920 |
ChIP-RPB1_dTAG-3h_SPT5-N-PURO-Fkbp12_DLD1_rep1 |
| GSM5471921 |
ChIP-RPB1_dTAG-3h_SPT5-N-PURO-Fkbp12_DLD1_rep2 |
| GSM5471922 |
ChIP-SPT5_DMSO-3h_SPT5-N-PURO-Fkbp12_DLD1_rep1 |
| GSM5471923 |
ChIP-SPT5_DMSO-3h_SPT5-N-PURO-Fkbp12_DLD1_rep2 |
| GSM5471924 |
ChIP-SPT5_dTAG-3h_SPT5-N-PURO-Fkbp12_DLD1_rep1 |
| GSM5471925 |
ChIP-SPT5_dTAG-3h_SPT5-N-PURO-Fkbp12_DLD1_rep2 |
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| This SubSeries is part of SuperSeries: |
| GSE180845 |
Stabilization of Pol II protein, orchestration of transcription cycles, and maintenance of enhancer landscape by general transcription regulator SPT5 |
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| Relations |
| BioProject |
PRJNA749767 |
| SRA |
SRP329917 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE180842_RAW.tar |
8.1 Gb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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