Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Selective Mediator-dependence of cell type-specifying transcription [ChIP-seq]

ABSTRACT: The Mediator complex directs signals from DNA-binding transcription factors to RNA polymerase (Pol) II. Despite this pivotal position, mechanistic understanding of Mediator in human cells remains incomplete. Here, we quantified Mediator-controlled Pol II kinetics by coupling rapid subunit degradation with orthogonal experimental readouts. Consistent with a model of condensate-driven transcription initiation, large clusters of hypo-phosphorylated Pol II rapidly disassembled upon Mediator degradation. This was accompanied by a selective and pronounced disruption of cell type-specifying transcriptional circuits, whose constituent genes featured exceptionally high rates of Pol II turnover. Notably, transcriptional output of most other genes was largely unaffected by acute Mediator ablation. Maintenance of transcriptional activity at these genes was linked to an unexpected, CDK9-dependent compensatory feedback loop that elevated Pol II pause release rates genome-wide. Collectively, our work positions human Mediator as a globally acting coactivator that selectively safeguards the functionality of cell type-specifying transcriptional networks.

ORGANISM(S): Homo sapiens

PROVIDER: GSE139467 | GEO | 2020/05/11

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Mechanistic basis for selective Mediator-dependence of cell type-specifying transcription

Project description:The Mediator complex routes signals from DNA-binding transcription factors to RNA polymerase (Pol) II. Despite its pivotal position, mechanistic understanding of Mediator in human cells remains incomplete. Here, we quantified Mediator-controlled Pol II kinetics by coupling rapid subunit degradation with orthogonal experimental readouts. Consistent with a model of condensate-driven transcription initiation, large clusters of hypo-phosphorylated Pol II rapidly disassembled upon Mediator degradation. This was accompanied by a selective and pronounced disruption of cell type-specifying transcriptional circuits, whose constituent genes featured exceptionally high rates of Pol II turnover. Remarkably, transcriptional output of most other genes was largely unaffected by acute Mediator ablation. Maintenance of transcriptional activity at these genes was linked to an unexpected, CDK9-dependent compensatory feedback loop that elevated Pol II pause release rates genome-wide. Collectively, our work positions human Mediator as a globally acting coactivator that selectively safeguards the functionality of cell type-specifying transcriptional networks.

2021-09-08 | PXD017611 | Pride

Selective Mediator-dependence of cell type-specifying transcription [HiChIP]

Project description:The Mediator complex directs signals from DNA-binding transcription factors to RNA polymerase (Pol) II. Despite this pivotal position, mechanistic understanding of Mediator in human cells remains incomplete. Here, we quantified Mediator-controlled Pol II kinetics by coupling rapid subunit degradation with orthogonal experimental readouts. Consistent with a model of condensate-driven transcription initiation, large clusters of hypo-phosphorylated Pol II rapidly disassembled upon Mediator degradation. This was accompanied by a selective and pronounced disruption of cell type-specifying transcriptional circuits, whose constituent genes featured exceptionally high rates of Pol II turnover. Notably, transcriptional output of most other genes was largely unaffected by acute Mediator ablation. Maintenance of transcriptional activity at these genes was linked to an unexpected, CDK9-dependent compensatory feedback loop that elevated Pol II pause release rates genome-wide. Collectively, our work positions human Mediator as a globally acting coactivator that selectively safeguards the functionality of cell type-specifying transcriptional networks.

2020-05-11 | GSE139466 | GEO

Selective Mediator-dependence of cell type-specifying transcription [TT-seq]

2020-05-11 | GSE139463 | GEO

Selective Mediator-dependence of cell type-specifying transcription [PRO-seq]

2020-05-11 | GSE139462 | GEO

Selective Mediator-dependence of cell type-specifying transcription [Quant-Seq]

2020-05-11 | GSE139461 | GEO

Selective Mediator-dependence of cell type-specifying transcription [4C-seq]

2020-05-11 | GSE139464 | GEO

The RNA Polymerase II factor RPAP1 is critical for Mediator-driven transcription and cell identity

Project description:The RNA Polymerase II Associated Protein 1 (RPAP1) is conserved across metazoa and critical for stem cell differentiation in plants, however, very little is known about its mechanism of action or its role in mammalian cells. Here, we report that RPAP1 is essential for the expression of lineage specifying factors and for viability. Accordingly, inhibition of RPAP1 triggers somatic cell de-differentiation and facilitates reprogramming into pluripotent stem cells. Conversely, interfering with RPAP1 in ES cells severely impairs their differentiation capacity. Mechanistically, we show that RPAP1 is essential for the interaction between Pol II and Mediator, as well as for the recruitment of important regulators, such as the Mediator-specific Pol II factor POLR2M/Gdown1 and the CTD phosphatase RPAP2. In agreement, depletion of RPAP1 disturbs the loading of Pol II and Pol II Ser5 phosphorylation levels and impairs expression of super-enhancer-driven genes. We conclude that Mediator-RPAP1-Pol II is an ancient module, conserved from plants to mammals, critical for establishing and maintaining cell identity.

2018-01-10 | PXD007114 | Pride

CDK7 kinase activity promotes RNA polymerase II promoter escape by facilitating initiation factor release

Project description:Cyclin-dependent kinase 7 (CDK7), part of the general transcription factor TFIIH, promotes gene transcription by phosphorylating the C-terminal domain of RNA polymerase II (RNA Pol II). Here, we combine rapid CDK7 kinase inhibition with multi-omics analysis to unravel the direct functions of CDK7 in human cells. CDK7 inhibition causes RNA Pol II retention at promoters, leading to decreased RNA Pol II initiation and immediate global downregulation of transcript synthesis. Elongation, termination, and recruitment of co-transcriptional factors are not directly affected. Although RNA Pol II, initiation factors, and Mediator accumulate at promoters, RNA Pol II complexes can also proceed into gene bodies without promoter-proximal pausing while retaining initiation factors and Mediator. Further downstream, RNA Pol II phosphorylation increases and initiation factors and Mediator are released, allowing recruitment of elongation factors and an increase in RNA Pol II elongation velocity. Collectively, CDK7 kinase activity promotes the release of initiation factors and Mediator from RNA Pol II, facilitating RNA Pol II escape from the promoter.

2024-05-31 | PXD037842 | Pride

Selective Mediator dependence of cell-type-specifying transcription

Project description:Selective Mediator dependence of cell-type-specifying transcription

| PRJNA579913 | ENA

Evidence that Mediator is essential for Pol II transcription but not a required component of the preinitiation complex in vivo

Project description:Mediator, a transcriptional co-activator complex, is recruited to enhancers by DNA-binding activators via its tail module, and it interacts with RNA polymerase (Pol) II as part of the preinitiation complex (PIC) via its head module. Although Mediator has been described as a general transcription factor, it is unclear if it is essential for Pol II transcription and/or is a required component of the PIC in vivo. We comprehensively analyze this issue by measuring Pol II transcription upon rapid depletion of individual or multiple Mediator subunits from the nucleus. Depletion of individual subunits, even those essential for cell growth, causes a general but only modest decrease in Pol II transcription. Transcriptional effects are stronger on SAGA-dependent genes as opposed to TFIID-dependent genes. Thus, Mediator modules that associate either with the enhancer or with the core promoter confer partial transcriptional activity. Furthermore, Pol II transcription can occur when Mediator is not detected at core promoters. In contrast, simultaneous depletion of all Mediator modules causes a drastic decrease in Pol II transcription that is roughly comparable to the effect observed upon anchor-away-mediated depletion of Pol II or TBP. These results provide strong evidence that Mediator is essential for Pol II transcription in vivo, but that it is not a required component of the PIC.

2017-07-13 | GSE93190 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data