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Status |
Public on Aug 22, 2022 |
Title |
Mediator facilitates transcription initiation at most promoters via a Tail-independent mechanism [RNA-seq] |
Organism |
Saccharomyces cerevisiae |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
Mediator (MED) is a conserved factor with important roles in basal and activated transcription. Here, we investigate the genome-wide roles of yeast MED by rapid depletion of its activator-binding domain (Tail) and monitoring changes in nascent transcription. Rapid Tail depletion surprisingly reduces transcription from only a small subset of genes. At most of these Tail-dependent genes, in unperturbed conditions, MED is detected at both the UASs and promoters. In contrast, at most Tail-independent genes, we find MED primarily at promoters but not at the UASs. These results suggest that MED Tail and activator-mediated MED recruitment regulate only a small subset of genes. Further, we define three classes of genes that differ in PIC assembly pathways and the requirements for MED Tail, SAGA, TFIID and BET factors Bdf1/2. Our combined results have broad implications for the roles of MED, other coactivators, and mechanisms of transcriptional regulation at different gene classes.
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Overall design |
Newly synthesized RNAs were labeled with 4-thioU, purified and analyzed with RNA-seq. Depletion of selected factors was achieved either thorugh targeted degradation (auxin-degron system) or gene deletion. For degron experiments, corresponding control and treatment sample files are labeled DMSO and 3IAA (3-indolacetic acid), respectively. Control samples for deletion experiments are indicated in the Methods section of the accompanying manuscript. All experiments were done in three replicates (A,B,C).
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Contributor(s) |
Warfield L, Donczew R, Mahendrawada L, Hahn S |
Citation missing |
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Submission date |
Dec 13, 2021 |
Last update date |
Nov 29, 2022 |
Contact name |
Rafal Donczew |
E-mail(s) |
Rafal-donczew@omrf.org
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Organization name |
Oklahoma Medical Research Foundation
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Department |
Cell Cycle and Cancer Biology
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Lab |
Hahn Lab
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Street address |
825 NE 13th St
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City |
Oklahoma City |
State/province |
OK |
ZIP/Postal code |
73104 |
Country |
USA |
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Platforms (1) |
GPL17342 |
Illumina HiSeq 2500 (Saccharomyces cerevisiae) |
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Samples (177)
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This SubSeries is part of SuperSeries: |
GSE190778 |
Mediator facilitates transcription initiation at most promoters via a Tail-independent mechanism |
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Relations |
BioProject |
PRJNA788465 |
SRA |
SRP350527 |