TFIIH kinase CDK7 drives cell proliferation through a common core transcription factor network.
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ABSTRACT:
PROVIDER: PRJNA1087696 | ENA |
REPOSITORIES: ENA
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Project description:We combined cryo-EM, transcriptomics, and a clinically relevant inhibitor to define how the TFIIH-associated CDK7 kinase coordinately controls the cell cycle and RNA polymerase II (RNAPII) transcription. CDK7 inhibition rapidly blocked expression of constitutively active genes, whereas inducible genes were unaffected. Distinct sets of sequence-specific, DNA-binding transcription factors (TFs) regulate constitutive vs. inducible genes; accordingly, inducible TFs (e.g. HSF1) were refractory to CDK7 inhibition. By contrast, CDK7 was required to maintain activity of a core set of promoter-associated TFs that drive proliferative gene expression programs; these core TFs (n=78) are constitutively active in proliferating cells. Thus, a major biological function for CDK7 is regulation of TFs that drive cell proliferation, revealing an apparent universal mechanism by which CDK7 coordinates RNAPII transcription with cell cycle regulation.
2024-12-19 | GSE262536 | GEO
Project description:We combined cryo-EM, transcriptomics, and a clinically relevant inhibitor to define how the TFIIH-associated CDK7 kinase coordinately controls the cell cycle and RNA polymerase II (RNAPII) transcription. CDK7 inhibition rapidly blocked expression of constitutively active genes, whereas inducible genes were unaffected. Distinct sets of sequence-specific, DNA-binding transcription factors (TFs) regulate constitutive vs. inducible genes; accordingly, inducible TFs (e.g. HSF1) were refractory to CDK7 inhibition. By contrast, CDK7 was required to maintain activity of a core set of promoter-associated TFs that drive proliferative gene expression programs; these core TFs (n=78) are constitutively active in proliferating cells. Thus, a major biological function for CDK7 is regulation of TFs that drive cell proliferation, revealing an apparent universal mechanism by which CDK7 coordinates RNAPII transcription with cell cycle regulation.
2024-12-19 | GSE261575 | GEO
Project description:TFIIH kinase CDK7 drives cell proliferation through a common core transcription factor network
| PRJNA1092248 | ENA
Project description:CDK7 associates with the 10-subunit TFIIH complex and regulates transcription by phosphorylating the C-terminal domain (CTD) of RNA polymerase II (RNAPII). Few additional CDK7 substrates are known. Here, using the covalent inhibitor SY-351 and quantitative phosphoproteomics, we identified CDK7 kinase substrates in human cells. Among hundreds of high-confidence targets, the vast majority are unique to CDK7 (i.e. distinct from other transcription-associated kinases), with a subset that suggest novel cellular functions. Transcription-associated factors were predominant CDK7 substrates, including SF3B1, U2AF2, and other splicing components. Accordingly, widespread and diverse splicing defects, such as alternative exon inclusion and intron retention, were characterized in CDK7-inhibited cells. Combined with biochemical assays, we establish that CDK7 directly activates other transcription-associated kinases CDK9, CDK12, and CDK13, invoking a “master regulator” role in transcription. We further demonstrate that TFIIH restricts CDK7 kinase function to the RNAPII CTD, whereas other substrates (e.g. SPT5, SF3B1) are phosphorylated by the 3-subunit CDK-activating kinase (CAK; CCNH, MAT1, CDK7). These results suggest new models for CDK7 function in transcription and implicate CAK dissociation from TFIIH as essential for kinase activation. This straightforward regulatory strategy ensures CDK7 activation is spatially and temporally linked to transcription, and may apply toward other transcription-associated kinases.
2020-10-31 | GSE151699 | GEO
Project description:CDK7 phosphorylates the RNA polymerase II (pol II) CTD and activates the P-TEFb- associated kinase, CDK9, but its regulatory roles remain obscure. Using human CDK7 analog-sensitive (CDK7as) cells, we observed reduced capping enzyme recruitment, increased pol II promoter-proximal pausing, and defective termination at gene 3'-ends upon CDK7 inhibition. We also found that CDK7 regulates chromatin modifications downstream of transcription start sites. H3K4me3 spreading was restricted at gene 5'-ends and H3K36me3 was displaced toward gene 3'-ends in CDK7as cells. Together, these results implicate a CDK7-dependent "CTD code" that regulates epigenetic marks in addition to RNA processing and pol II pausing.
2017-08-01 | GSE100040 | GEO
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
Project description:The TFIIH kinase CDK7 governs RNA polymerase II initiation, elongation, termination, and RNA processing
| PRJNA949515 | ENA
Project description:Cyclin-dependent kinase 7 (CDK7), part of general transcription factor TFIIH, promotes gene transcription by phosphorylating the C-terminal domain of RNA polymerase II (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 Pol II retention at promoters, leading to decreased Pol II initiation and immediate global downregulation of transcript synthesis. Elongation, termination, and recruitment of co-transcriptional factors are not directly affected. Although Pol II, initiation factors, and Mediator accumulate at promoters, Pol II complexes can also proceed into gene bodies without promoter-proximal pausing while retaining initiation factors and Mediator. Further downstream, Pol II phosphorylation increases, initiation factors and Mediator are released, allowing recruitment of elongation factors and increase in Pol II elongation velocity. Collectively, CDK7 kinase activity promotes the release of initiation factors and Mediator from Pol II, facilitating Pol II escape from the promoter.
2024-06-01 | GSE218269 | GEO
Project description:Cyclin dependent kinases activation and RNA polymerase II transcription are linked by the Cdk7 kinase that phosphorylates Cdks as a trimeric CAK complex, and serine 5 within the PolII C-terminal domain (CTD) as TFIIH bound CAK. However, the physiological importance of integrating these processes is not understood. Beside the Cdk7 ortholog Mcs6, fission yeast possesses a second CAK, Csk1. Both enzymes were proposed to act redundantly to activate Cdc2. Using an improved analogue sensitive Mcs6-as kinase, we show that Csk1 is not a relevant CAK for Cdc2. Further analyses revealed that Csk1 lacks a 20 amino acid sequence required for its budding yeast counterpart, Cak1, to bind Cdc2. Transcriptome profiling of the Mcs6-as mutant in the presence or absence of the budding yeast Cak1 kinase, in order to uncouple the CTD kinase and CAK activities of Mcs6, revealed an unanticipated role of the CAK branch in the transcriptional control of the cluster of genes implicated in ribosome biogenesis and cell growth. The analysis of a Cdc2 CAK site mutant confirmed these data. Our data show that the Cdk7 kinase modulates transcription through both its well-described RNA Polymerase II CTD kinase activity, but also through the Cdc2 activating kinase activity.
2012-02-19 | GSE27425 | GEO
Project description:In this study we perform precision nuclear run-on sequencing (PRO-seq) to measure the altered transcriptional response upon CDK7 inhibition or RNA-seq to elucidate the response of CDK7 inhibition on steady-state RNA. We performed a heat shock time course in PRO-seq with and without the Syros CDK7 inhibitor SY5609. Matching this data we performed three deeply sequenced RNA-seq experiments with SY5609 that include no heat shock, heat shock with recovery and long heat shock with no recovery. We additionally generated two more RNA-seq datasets in heat shock conditions with another Syros inhibitor, SY5102 and in a CDK7-analog sensitive OV90 cell line treated with 3MBPP1.
2024-12-19 | GSE228346 | GEO