| 1994 |
PITALRE (CDK9) is a nuclear CDC2-related serine/threonine protein kinase that phosphorylates the retinoblastoma protein (pRb) in vitro but cannot phosphorylate histone H1, indicating a substrate specificity distinct from CDC2. It associates with three cellular polypeptides of 80, 95, and 155 kDa and localizes primarily to the nucleus. |
Immunoprecipitation-associated in vitro kinase assay, immunofluorescence, cDNA cloning |
Proceedings of the National Academy of Sciences of the United States of America |
High |
8170997
|
| 1996 |
PITALRE (CDK9) is the catalytic subunit responsible for kinase activity in its multimeric complexes, demonstrated using a catalytically inactive mutant. Monomeric CDK9 is active in vitro but PITALRE in multimeric complexes exhibits several-fold higher activity, suggesting regulatory proteins modulate its activity and/or substrate recognition. |
Dominant-negative catalytic mutant overexpression, in vitro kinase assay, protein complex characterization |
The Biochemical journal |
High |
8870681
|
| 1996 |
PITALRE (CDK9) is a Ser/Thr proline-directed kinase. It phosphorylates myelin basic protein (MBP) on Ser-162 (a proline-directed residue) and Thr-97, with substrate site specificity distinguishable from CDC2 and CDK2. |
In vitro kinase assay with phosphopeptide mapping and phosphoamino acid analysis |
The Biochemical journal |
High |
9003389
|
| 1997 |
PITALRE (CDK9)-associated kinase activity phosphorylates pRb exclusively on serine residues at sites similar to those phosphorylated by CDC2 kinase in vitro. |
In vitro kinase assay with phosphoamino acid analysis |
Journal of cellular physiology |
Medium |
9258347
|
| 1998 |
PITALRE (CDK9) is the catalytic subunit of the Tat-associated kinase (TAK) and is required for HIV-1 Tat transactivation in vivo. A catalytic mutant (D167N) more efficiently squelches Tat transactivation than wild-type CDK9. Artificial tethering of PITALRE to a nascent RNA element, in the absence of Tat, activates HIV-1 LTR expression. |
Transient overexpression, catalytic mutant analysis, artificial RNA-tethering assay, HIV-1 LTR reporter assays |
Journal of virology |
High |
9557739
|
| 2001 |
CDK9 and cyclin T1 localize throughout the non-nucleolar nucleoplasm and concentrate at nuclear speckles that are enriched in splicing factors. The pattern is altered by transcription inhibitors. A central region of cyclin T1 mediates speckle accumulation and can recruit CDK9 and HIV Tat to this compartment. |
High-resolution immunofluorescence microscopy, cyclin T1 deletion mutants, co-expression experiments |
Journal of cell science |
High |
11282025
|
| 2003 |
A novel protein MAQ1 (HEXIM1) associates with the inactive P-TEFb complex in a manner dependent on 7SK snRNA. MAQ1 binds directly to the N-terminal cyclin homology region of cyclin T1 and T2, and this 7SK RNA/MAQ1 association competes with Tat binding to cyclin T1. Transcription inhibition releases both MAQ1 and 7SK RNA from P-TEFb, indicating a dynamic regulatory mechanism for CDK9 activity. |
Co-immunoprecipitation, yeast two-hybrid, transcription inhibitor treatment, protein complex characterization |
Molecular and cellular biology |
High |
12832472
|
| 2003 |
CDK9 protein levels are constitutively expressed throughout the cell cycle and are not regulated by the SCF(SKP2) ubiquitin ligase. Endogenous CDK9 is a stable protein (half-life 4–7 h), while overexpressed CDK9 is rapidly degraded (half-life <1 h). CDK9 kinase activity does not oscillate during the cell cycle. |
Cell cycle synchronization experiments, cycloheximide chase, SKP2 siRNA knockdown, proteasome inhibitor treatment, Western blot |
Molecular and cellular biology |
High |
12861003
|
| 2004 |
CDK9 (as part of P-TEFb) is recruited by STAT3 to the p21waf1 promoter to phosphorylate the CTD of RNA polymerase II at serine 2, enabling transcription elongation. BRG1 is recruited first to remodel chromatin, followed by CDK9 recruitment to drive elongation at the STAT3 target gene. |
Co-immunoprecipitation, pull-down, chromatin immunoprecipitation (ChIP), Southern blot accessibility assay |
Oncogene |
Medium |
15286705
|
| 2005 |
CDK9 has two isoforms, 42k and 55k. Both isoforms phosphorylate the CTD of RNA polymerase II with identical phosphorylation patterns on 144 peptide substrates. CDK9-42k localizes diffusely in the nucleoplasm while CDK9-55k accumulates in the nucleolus. Expression of the 55k isoform is induced upon macrophage differentiation while the 42k isoform predominates in activated lymphocytes. |
Immunofluorescence, kinase assay with peptide array, immunoblot of primary cells, promoter reporter assay |
Journal of cellular physiology |
High |
15452830
|
| 2005 |
The Cdk9(55) isoform is localized to the nucleus and is expressed as the predominant form in primary rat hepatocytes; as cells enter the cell cycle, CDK9(42) expression is induced and becomes the major form while CDK9(55) remains relatively constant. The relative abundance of the two isoforms varies across mouse tissues. |
Immunofluorescence, Western blot of murine tissues and primary hepatocytes, tetracycline-inducible expression |
Gene |
Medium |
15780980
|
| 2010 |
CDK9 phosphorylates the androgen receptor (AR) on serine 81 (S81) in vitro in a site-specific manner. CDK9 co-immunoprecipitates with AR. Overexpression of CDK9 with cyclin T increases S81 phosphorylation; CDK9 siRNA knockdown and CDK9 inhibitors reduce hormone-induced S81 phosphorylation. S81 phosphorylation regulates AR promoter selectivity and cell growth. |
In vitro kinase assay, co-immunoprecipitation, mass spectrometry, siRNA knockdown, pharmacological inhibition, reporter assay |
Molecular endocrinology (Baltimore, Md.) |
High |
20980437
|
| 2011 |
CDK9 in complex with cyclin K (not cyclin T) directly functions in maintaining genome integrity in response to replication stress. CDK9-cyclin K (but not CDK9-cyclin T) depletion impairs cell cycle recovery after replication stress, induces spontaneous DNA damage, and CDK9 accumulates on chromatin to limit single-stranded DNA accumulation. CDK9-cyclin K interacts with ATR and DNA damage response proteins. |
Cyclin-specific siRNA depletion, DNA damage assays, chromatin fractionation, co-immunoprecipitation, cell cycle analysis |
Cell cycle (Georgetown, Tex.) |
High |
21200140
|
| 2013 |
CDK9 physically interacts with Pirh2 and phosphorylates it on Ser-211 and Thr-217, rendering Pirh2 inactive and contributing to p53 stabilization. CDK9 also promotes phosphorylation of Mdm2 on Ser-395, preventing Mdm2-mediated p53 degradation. |
Co-immunoprecipitation, in vitro kinase assay, Western blot, site-directed mutagenesis |
Cell cycle (Georgetown, Tex.) |
Medium |
23603988
|
| 2017 |
CDK9 activity decreases the pause duration of promoter-proximally paused RNA Pol II and increases productive initiation frequency, demonstrating that CDK9 stimulates release of paused polymerase and activates transcription by increasing the number of transcribing polymerases and the amount of mRNA synthesized. CDK9 activity is also associated with long-range chromatin interactions. |
Chemical-genetic CDK9 inhibition in engineered human cells combined with multi-omics (transient transcriptome sequencing, 4sU-seq, Hi-C) |
eLife |
High |
28994650
|
| 2017 |
SIRT7 deacetylates CDK9 at lysine 48, counteracting GCN5-mediated acetylation, which activates CDK9 kinase activity to phosphorylate Pol II CTD serine 2 and promote transcription elongation. SIRT7 also promotes release of P-TEFb from the inactive 7SK snRNP complex. |
Proteomic identification of SIRT7 substrates, co-immunoprecipitation, in vitro deacetylation assay, CTD phosphorylation assay, SIRT7 depletion |
Nucleic acids research |
High |
28426094
|
| 2017 |
THAL-SNS-032, a CDK9 degrader (PROTAC with thalidomide moiety recruiting Cereblon E3 ligase), selectively degrades CDK9 without affecting other SNS-032 targets, demonstrating that CDK9 degradation induces distinct and prolonged pharmacological effects (including irreversible apoptosis after washout) compared with CDK9 kinase inhibition alone. |
PROTAC-mediated targeted protein degradation, washout experiments, transcriptome profiling, cell viability assays |
Nature chemical biology |
High |
29251720
|
| 2018 |
SUMO suppresses global transcription by promoting sumoylation of CDK9, which blocks CDK9 interaction with Cyclin T1 and thus prevents formation of the active P-TEFb complex. MYC antagonizes CDK9 sumoylation to amplify global transcription. A sumoylation-resistant CDK9 mutant confirms that CDK9 sumoylation inhibits global transcription. |
SUMO-MS, SUMOylation assays, co-immunoprecipitation, sumoylation-resistant mutant, transcription profiling |
Cell research |
High |
29588524
|
| 2018 |
CDK9 inhibition dephosphorylates the SWI/SNF protein BRG1 and contributes to reactivation of epigenetically silenced genes including tumor suppressor genes in cancer cells. CDK9 is essential for maintaining gene silencing at heterochromatic loci in addition to its role in transcription elongation. |
Live cell drug screen with genetic confirmation, siRNA knockdown, pharmacological inhibition, gene expression analysis, ChIP |
Cell |
High |
30454645
|
| 2019 |
TRIM28 SUMOylates CDK9 at lysines 44, 56, and 68 (using SUMO4), which inhibits CDK9 kinase activity and/or prevents P-TEFb assembly by blocking CDK9-Cyclin T1 interaction, thereby suppressing HIV-1 transcription and contributing to viral latency. |
Global site-specific SUMO-MS, serial SUMOylation assays, kinase activity assays, co-immunoprecipitation, site-directed mutagenesis of SUMOylation sites |
eLife |
High |
30652970
|
| 2019 |
CDK9 forms novel complexes (CTORC1 and CTORC2) with mTOR scaffold protein mLST8. In the nucleus, CDK9-RAPTOR-mLST8 (CTORC1) promotes transcription of leukemogenic genes. In the cytoplasm, CDK9-RICTOR-SIN1-mLST8 (CTORC2) controls mRNA translation through phosphorylation of LARP1 and rpS6. |
Proteomics/mass spectrometry of mTOR complex interactors, co-immunoprecipitation, subcellular fractionation, phosphorylation assays |
Blood |
Medium |
30587525
|
| 2019 |
CDK9 modulates the circadian clock by physically associating with REV-ERBα and attenuating its binding to the RORE element in the Bmal1 promoter. CDK9 knockdown in the anterior hypothalamus (SCN region) in mice alters respiratory exchange ratio, daily activity, and circadian period. |
siRNA screen, CDK9 siRNA knockdown, co-immunoprecipitation, in vivo hypothalamic knockdown, circadian phenotype measurement |
Biochemical and biophysical research communications |
Medium |
31005255
|
| 2020 |
CDK9 (P-TEFb) phosphorylates PP1 and PP4 phosphatase complexes (inhibitory phosphorylation), creating two distinct kinase-phosphatase switches: PP4 governs pause release at the 5' end of genes by dephosphorylating Spt5-Ser666 and the Spt5 CTR, while PP1 governs the elongation-termination transition at gene 3' ends by dephosphorylating the Spt5 CTR. Depletion of PP4 complex subunits redistributes paused Pol II into gene bodies. |
Kinase-phosphatase depletion experiments, phosphoproteomics, ChIP-seq, in vivo Spt5 phosphorylation analysis |
Nature communications |
High |
32859893
|
| 2020 |
CDK9 inhibition globally impairs splicing of thousands of mRNAs in prostate cancer cells, with no coordinated response between alternative splicing and the transcriptome. CDK9 inhibition causes loss of androgen receptor (AR) and AR-v7 splice variant expression, sensitizing CRPC cells to androgen deprivation. |
RNA-seq, splicing analysis, CDK9 inhibitor treatment, AR splice variant analysis, androgen deprivation assays |
RNA biology |
Medium |
34592899
|
| 2020 |
Cdk9 inhibition or H2B mono-ubiquitination (H2Bub1) loss independently induces intragenic antisense transcription in fission yeast, affecting largely distinct gene subsets. Combined ablation de-represses antisense transcription of over half the genome. CDK9-dependence correlates with high H2Bub1 occupancy. Combined perturbation impairs Clr6-CII (HDAC) recruitment and increases histone acetylation in coding regions. |
Chemical-genetic Cdk9 inhibition, H2Bub1 loss epistasis, genome-wide nascent RNA sequencing, ChIP-seq, genetic interaction analysis |
Nucleic acids research |
High |
32496538
|
| 2020 |
ASF1B forms stable complexes with CDK9 and positively regulates CDK9 protein stability, functioning as an oncogenic stabilizer of CDK9 in cervical cancer cells. |
Co-immunoprecipitation, siRNA knockdown, overexpression, xenograft models |
Cell death & disease |
Low |
32848135
|
| 2021 |
A PP2A complex recruited to transcription sites by Integrator complex subunit INTS6 dynamically antagonizes CDK9-mediated phosphorylation of key substrates including DSIF and RNAPII-CTD. Loss of INTS6 results in resistance to CDK9 inhibition and amplification of acute oncogenic transcriptional responses. Pharmacological PP2A activation synergizes with CDK9 inhibition. |
INTS6 loss-of-function, phosphoproteomic analysis of CDK9 substrates, pharmacological PP2A activation, cell viability assays, in vivo tumor models |
Cell |
High |
34004147
|
| 2021 |
CDK9 inhibits CDK9 substrates including SF3B1 (splicing factor), and inhibition causes loss of SF3B1 and polyadenylation factors from chromatin. CDK9 inhibition also causes premature transcription termination across the last exon and loss of polyadenylation of nascent transcripts. PP2A inhibition rescues premature termination caused by CDK9 inhibition, placing CDK9 and PP2A as opposing regulators of coupled transcription elongation, termination, and RNA processing. |
CDK9 inhibition and PP2A inhibition, ChIP-seq, metabolic RNA labeling, polyadenylation factor chromatin occupancy assays |
EMBO reports |
High |
35980303
|
| 2021 |
CSN6 stabilizes CDK9 protein by reducing CDK9 ubiquitination levels. The E3 ligase UBR5 is negatively regulated by CSN6 and promotes ubiquitination and degradation of CDK9. The CSN6-UBR5-CDK9 axis promotes melanoma proliferation and metastasis. |
Co-immunoprecipitation, ubiquitination assay, siRNA knockdown, overexpression, xenograft models |
Cell death & disease |
Medium |
33483464
|
| 2017 |
BRCA1 recruitment to DNA damage sites (ionizing radiation-induced foci) is dependent on CDK9. CDK9 interacts with endogenous BRCA1 and BARD1 through RING finger and BRCT domains, forms IRIF at DNA damage sites, and co-localizes with BRCA1. CDK9-deficient cells show altered γ-H2AX dynamics, reduced HR efficiency, and failure to form BRCA1 and RAD51 IRIF. |
Co-immunoprecipitation, immunofluorescence microscopy of IRIF, CDK9 siRNA knockdown, HR/NHEJ repair assays, genotoxic sensitivity assays |
Cell cycle (Georgetown, Tex.) |
Medium |
28278048
|
| 2019 |
Using analog-sensitive CDK9 combined with quantitative phosphoproteomics, 1,102 phosphosites and 120 potential cellular CDK9 substrates were identified. A substantial number of CDK9 substrates are splicing factors, establishing CDK9's role in transcription-coupled splicing. Cellular context fundamentally impacts CDK9 substrate selection compared to in vitro data. |
Analog-sensitive kinase technology, quantitative phosphoproteomics, chemical-genetic inhibition |
Oncotarget |
High |
31857848
|
| 2023 |
NELF-mediated promoter-proximal pausing establishes a strict checkpoint requiring Cdk9 kinase activity for pause release into productive elongation. In NELF-depleted cells, Cdk9 inhibition does not efficiently shut down gene transcription but instead allows defective, non-productive transcription to continue. Only NELF-dependent pausing creates this strict Cdk9 requirement. |
NELF depletion in Drosophila cells, chemical-genetic Cdk9 inhibition, nascent RNA sequencing, epistasis analysis |
Nature communications |
High |
37179384
|
| 2023 |
The CDK9 kinase domain mutation L156F confers resistance to CDK9 inhibitors including both ATP-competitive inhibitors and PROTAC degraders by causing steric hindrance to inhibitor binding and altering CDK9 thermal stability and catalytic activity. |
Acquired resistance cell line, genomic sequencing, CRISPR/Cas9 knock-in, kinase activity assays, thermal shift assay |
Acta pharmaceutica Sinica. B |
Medium |
37719386
|
| 2023 |
OTUD1 deubiquitinase binds CDK9 and catalyzes K63-linked deubiquitination on CDK9 (with Cys320 of OTUD1 being critical), promoting CDK9 phosphorylation and activation to induce inflammatory responses and fibrosis in kidney epithelial cells. |
Co-immunoprecipitation, deubiquitination assay with OTUD1 catalytic mutant, Otud1 knockout mice, CDK9 inhibitor treatment, phosphorylation assays |
Acta pharmacologica Sinica |
Medium |
38110583
|