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Series GSE190777 Query DataSets for GSE190777
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
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.
 
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).
 
Contributor(s) Warfield L, Donczew R, Mahendrawada L, Hahn S
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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
Organization name Oklahoma Medical Research Foundation
Department Cell Cycle and Cancer Biology
Lab Hahn Lab
Street address 825 NE 13th St
City Oklahoma City
State/province OK
ZIP/Postal code 73104
Country USA
 
Platforms (1)
GPL17342 Illumina HiSeq 2500 (Saccharomyces cerevisiae)
Samples (177)
GSM5731443 CCL1_3IAA_A (RNA-seq)
GSM5731444 CCL1_3IAA_B (RNA-seq)
GSM5731445 CCL1_3IAA_C (RNA-seq)
This SubSeries is part of SuperSeries:
GSE190778 Mediator facilitates transcription initiation at most promoters via a Tail-independent mechanism
Relations
BioProject PRJNA788465
SRA SRP350527

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE190777_RAW.tar 7.4 Mb (http)(custom) TAR (of CSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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