Analog-sensitive cell line identifies cellular substrates of CDK9

Decker, Tim-Michael; Forné, Ignasi; Straub, Tobias; Elsaman, Hesham; Ma, Guoli; Shah, Nilay; Imhof, Axel; Eick, Dirk

doi:10.18632/oncotarget.27334

Cited by 22 publications

(24 citation statements)

References 45 publications

(50 reference statements)

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“…Among them is transcription termination factor Xrm2, suggesting that P-TEFb is also involved in the regulation of transcription termination, which is consistent with the observation by Kouzarides and colleagues that aberrant stimulation of P-TEFb activity results in global transcriptional readthrough in ES cells [114]. Interestingly, another HTS search using an analogue-sensitive CDK9 mutant followed by mass spectrometry (MS) conducted by Eick and colleagues identified putative CDK9 substrates that showed a minimum overlap with the putative substrates identified by the Fisher group [113,115]. Further studies are required to complete the list of CDK9 substrates in cells.…”

Section: Substrates Of Cdk9supporting

confidence: 82%

P-TEFb as A Promising Therapeutic Target

Fujinaga

2020

Molecules

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The positive transcription elongation factor b (P-TEFb) was first identified as a general factor that stimulates transcription elongation by RNA polymerase II (RNAPII), but soon afterwards it turned out to be an essential cellular co-factor of human immunodeficiency virus (HIV) transcription mediated by viral Tat proteins. Studies on the mechanisms of Tat-dependent HIV transcription have led to radical advances in our knowledge regarding the mechanism of eukaryotic transcription, including the discoveries that P-TEFb-mediated elongation control of cellular transcription is a main regulatory step of gene expression in eukaryotes, and deregulation of P-TEFb activity plays critical roles in many human diseases and conditions in addition to HIV/AIDS. P-TEFb is now recognized as an attractive and promising therapeutic target for inflammation/autoimmune diseases, cardiac hypertrophy, cancer, infectious diseases, etc. In this review article, I will summarize our knowledge about basic P-TEFb functions, the regulatory mechanism of P-TEFb-dependent transcription, P-TEFb’s involvement in biological processes and diseases, and current approaches to manipulating P-TEFb functions for the treatment of these diseases.

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Section: Substrates Of Cdk9supporting

confidence: 82%

P-TEFb as A Promising Therapeutic Target

Fujinaga

2020

Molecules

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“…Crystal structures of the complex have been determined (Baumli et al 2008;Tahirov et al 2010), which reveal an organization and interfaces common among CDK:Cyclin pairs but also distinct features. Substrates for the CDK9 kinase have been identified from proteomics experiments in human cell extracts (Sansó et al 2016) or from analog-sensitive cell lines (Decker et al 2019). These studies revealed dozens of high-confidence targets, with many representing transcription cofactors or RNA processing factors.…”

Section: P-tefbmentioning

confidence: 99%

Structure and mechanism of the RNA polymerase II transcription machinery

2020

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RNA polymerase II (Pol II) transcribes all protein-coding genes and many noncoding RNAs in eukaryotic genomes. Although Pol II is a complex, 12-subunit enzyme, it lacks the ability to initiate transcription and cannot consistently transcribe through long DNA sequences. To execute these essential functions, an array of proteins and protein complexes interact with Pol II to regulate its activity. In this review, we detail the structure and mechanism of over a dozen factors that govern Pol II initiation (e.g., TFIID, TFIIH, and Mediator), pausing, and elongation (e.g., DSIF, NELF, PAF, and P-TEFb). The structural basis for Pol II transcription regulation has advanced rapidly in the past decade, largely due to technological innovations in cryoelectron microscopy. Here, we summarize a wealth of structural and functional data that have enabled a deeper understanding of Pol II transcription mechanisms; we also highlight mechanistic questions that remain unanswered or controversial.

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“…Comparison of CDK7 phosphosites with those from other transcription-associated kinases CDK8/CDK19 (Poss et al 2016), CDK9 (Sansó et al 2016;Decker et al 2019), and CDK12/CDK13 (Krajewska et al 2019) revealed few B A C Figure 2. SILAC phosphoproteomic overview and identification of phosphorylation sites significantly changed by SY-351 treatment.…”

Section: Sy-351: a Potent Highly Selective Covalent Cdk7 Inhibitormentioning

confidence: 99%

Selective inhibition of CDK7 reveals high-confidence targets and new models for TFIIH function in transcription

et al. 2020

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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 and SF3B1) are phosphorylated by the three-subunit CDK-activating kinase (CAK; CCNH, MAT1, and 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.

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Analog-sensitive cell line identifies cellular substrates of CDK9

Cited by 22 publications

References 45 publications

P-TEFb as A Promising Therapeutic Target

P-TEFb as A Promising Therapeutic Target

Structure and mechanism of the RNA polymerase II transcription machinery

Selective inhibition of CDK7 reveals high-confidence targets and new models for TFIIH function in transcription

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