* 603251

CYCLIN-DEPENDENT KINASE 9; CDK9


Alternative titles; symbols

PITALRE
CTK1, YEAST, HOMOLOG OF; CTK1


HGNC Approved Gene Symbol: CDK9

Cytogenetic location: 9q34.11     Genomic coordinates (GRCh38): 9:127,786,034-127,790,792 (from NCBI)


TEXT

Description

Positive transcription factor b (P-TEFb) controls the elongation phase of transcription by RNA polymerase II (see POLR2A; 180660). P-TEFb is a heterodimer of CDK9 and 1 of 4 cyclin partners, cyclin T1 (CCNT1; 143055), cyclin K (CCNK; 603544), or cyclin T2a or T2b, which are isoforms of CCNT2 (603862) (Shore et al., 2003).


Cloning and Expression

To identify CDC2 (116940) family members, Grana et al. (1994) performed PCR on a mouse embryonic cDNA library using degenerate oligonucleotides based on regions conserved among CDC2-related proteins. They used a resulting PCR product to screen a human cDNA library and isolated a CDK9 cDNA. The predicted 372-amino acid protein contains the 11 conserved regions characteristic of the protein kinase catalytic domain, a putative nuclear localization signal, and a putative ATP-binding site. The authors called the protein PITALRE because it contains a pro-ile-thr-ala-leu-arg-glu motif similar to the PSTAIRE motif found in prototypic CDC2 kinases. CDK9 shares 41 to 43% amino acid sequence identity with CDC2, CDK2 (116953), CDK3 (123828), and CDK5 (123831). Subcellular fractionation and Western blot analyses demonstrated that CDK9 has a molecular mass of 43 kD and is located primarily in the nucleus. Northern blot analysis indicated that CDK9 was expressed as 2.8- and 3.2-kb mRNAs in all tissues tested, with the highest levels in liver and placenta.

Independently, Best et al. (1995) cloned human CDK9 cDNAs and designated the gene C-2k.

By RT-PCR of HeLa cell total RNA, Shore et al. (2003) cloned a splice variant of CDK9 that originates from an upstream promoter region. The deduced protein, CDK9-55, has a calculated molecular mass of 53.4 kD and contains a 117-amino acid N-terminal extension with a proline-rich region and a glycine-rich region. Using antibodies specific to the N-terminal extension, Shore et al. (2003) showed that CDK9-55 had an apparent molecular mass of 55 kD. The ratio of CDK9-55 to the shorter CDK9 isoform, CDK9-42, differed between HeLa cell nuclear extracts and mouse fibroblasts, but CDK9-42 was the predominant isoform in both.


Gene Function

Grana et al. (1994) found that 3 cellular proteins coimmunoprecipitated with CDK9, and CDK9 immunocomplexes had an RB1 (614041) kinase activity.

Garriga et al. (1996) found that monomeric CDK9, in contrast to other CDKs, is active. The association of CDK9 with other proteins modulates its activity and/or its ability to recognize substrates in vivo.

Yang et al. (2001) identified 7SK snRNA (606515) as a specific P-TEFb-associated factor. 7SK inhibits general and human immunodeficiency virus (HIV)-1 Tat-specific transcriptional activities of P-TEFb in vivo and in vitro by inhibiting the kinase activity of CDK9 and preventing recruitment of P-TEFb to the HIV-1 promoter. 7SK is efficiently dissociated from P-TEFb (the CDK9/cyclin T1 heterodimer) by treatment of cells with ultraviolet irradiation and actinomycin D. As these 2 agents have been shown to enhance significantly HIV-1 transcription and phosphorylation of RNA polymerase II, Yang et al. (2001) concluded that their data provide a mechanistic explanation for this stimulatory effect. Yang et al. (2001) further suggested that the 7SK/P-TEFb interaction may serve as a principal control point for the induction of cellular and HIV-1 viral gene expression during stress-related responses. The study demonstrated the involvement of an snRNA in controlling the activity of CDK/cyclin kinase.

Nguyen et al. (2001) independently showed that in human HeLa cells more than half of the P-TEFb is sequestered in larger complexes that also contain 7SK RNA. P-TEFb and 7SK associate in a specific and reversible manner. In contrast to the smaller P-TEFb complexes, which have a high kinase activity, the large 7SK/P-TEFb complexes show very weak kinase activity. Inhibition of cellular transcription by chemical agents or ultraviolet irradiation triggers complete disruption of the P-TEFb/7SK complex, and enhances CDK9 activity. Nguyen et al. (2001) concluded that transcription-dependent interaction of P-TEFb with 7SK may therefore contribute to an important feedback loop modulating the activity of RNA Pol II.

Fong and Zhou (2001) demonstrated that splicing factors function directly to promote transcriptional elongation. The spliceosomal U small nuclear ribonucleoproteins (snRNPs) interact with human transcription elongation factor TAT-SF1 (300346) and strongly stimulate polymerase elongation when directed to an intron-free HIV-1 template. Fong and Zhou (2001) suggested that this effect is likely to be mediated through the binding of TAT-SF1 to elongation factor P-TEFb. Inclusion of splicing signals in the nascent transcript further stimulates transcription, supporting the notion that the recruitment of U snRNPs near the elongating polymerase is important for transcription. Because the TAT-SF1--U snRNP complex also stimulates splicing in vitro, Fong and Zhou (2001) proposed that it may serve as a dual-function factor to couple transcription and splicing and to facilitate their reciprocal activation.

By immunoprecipitation analysis, Shore et al. (2003) showed that CDK9-55 immunoprecipitated with cyclin T1, cyclin T2a, and cyclin T2b from HeLa cell nuclear extracts. CDK9-55 could phosphorylate the C-terminal domain of Drosophila Polr2a. Differential extraction of size-fractionated HeLa cell P-TEFb complexes showed that, like CDK9-42, CDK9-55 associated with high molecular mass complexes containing 7SK RNA and with low molecular mass complexes lacking 7SK RNA. Western blot analysis showed that untreated human macrophages expressed more CDK9-55 than CDK9-42, but macrophages activated by lipopolysaccharide or infected with HIV expressed more CDK9-42 than CDK9-55.

Sano et al. (2004) found that 8 ventricle samples from patients with heart failure due to dilated cardiomyopathy showed increased CDK9 activity against the C-terminal domain of POLR2A compared with controls. Increased CDK7 activity was also present in a minority of patient samples. Substantial hyperphosphorylation of endogenous POLR2A was more frequent at the CDK9 site than the CDK7 site in failing hearts. Sano et al. (2004) noted that cardiomyocyte-restricted expression of cyclin T1 in mice maintains Cdk9 activity at its elevated embryonic level. They found that maintenance of Cdk9 in mouse hearts through cyclin T1 expression resulted in myocyte enlargement and selective suppression of Pgc1 (PPARGC1A; 604517), a master regulator of mitochondrial biogenesis and function, leading to mitochondrial defects, enhanced myocyte apoptosis, predisposition to heart failure, and early death.

Jang et al. (2005) found that epitope-tagged mouse Brd4 (608749) interacted with cyclin T1 and CDK9 in P-TEFb complexes contained in HeLa cell nuclear extracts. The bromodomain of Brd4 was required for the interaction. Brd4 overexpression increased P-TEFb-dependent phosphorylation of the C-terminal domain of RNA polymerase II and stimulated transcription from a reporter plasmid driven by an HIV-1 promoter. Conversely, reduced Brd4 expression in mouse fibroblasts by small interfering RNA reduced RNA polymerase II C-terminal domain phosphorylation and transcription. Chromatin immunoprecipitation assays indicated that recruitment of P-TEFb to a promoter was dependent on Brd4 and was enhanced by increased chromatin acetylation.

About half of cellular P-TEFb exists in an inactive complex with 7SK and the HEXIM1 protein (607328). Yang et al. (2005) demonstrated that the remaining half associated with BRD4. In stress-induced HeLa cells, 7SK/HEXIM1-bound P-TEFb was converted into the BRD4-associated form. The association of P-TEFb with BRD4 was necessary to form the transcriptionally active P-TEFb, to recruit P-TEFb to a promoter, and to enable P-TEFb to contact the Mediator complex (see 602984). The P-TEFb recruitment function of BRD4 could be substituted by that of HIV-1 Tat, which recruited P-TEFb directly for activated HIV-1 transcription.

Yik et al. (2005) found that human HEXIM1 or HEXIM2 (615695) inhibited CDK9 kinase activity and P-TEFb-dependent transcription in conjunction with 7SK RNA.

Rother and Strasser (2007) found that the yeast CDK9 homolog, Ctk1, functioned in translation by enhancing decoding fidelity. Ctk1 associated with translating ribosomes in vivo and was needed for efficient translation. Ctk1 phosphorylated the small ribosomal subunit Rps2 (603624), and absence of Rps2 phosphorylation led to defects in translation elongation due to increased frequency of miscoding.

Wagner et al. (2008) found that injection of microRNA miR1 (see MIRN1-1; 609326) into fertilized mouse oocytes resulted in the early appearance of cardiac hypertrophy. Abnormal growth of the ventricular wall in experimental mice was associated with a significant increase in the level of Cdk9 mRNA, an miR1 target. Cdk9 protein content was even more elevated, and there was increased phosphorylation of RNA polymerase II. miR1 expression was not significantly changed in experimental mice, and there was no significant change in expression of other miR1 targets. Similar cardiac hypertrophy and biochemical changes were found in embryos developed from fertilized mouse oocytes that had been microinjected with 20-nucleotide sequences randomly chosen from the Cdk9 coding sequence.

The RNA polymerase II largest subunit, POLR2A (180660), contains a C-terminal domain (CTD) with up to 52 Tyr(1)-Ser(2)-Pro(3)-Thr(4)-Ser(5)-Pro(6)-Ser(7) consensus repeats. Serines 2, 5, and 7 are known to be phosphorylated, and these modifications help to orchestrate the interplay between transcription and processing of mRNA precursors. Hsin et al. (2011) provided evidence that phosphorylation of CTD Thr(4) residues is required specifically for histone mRNA 3-prime end processing, functioning to facilitate recruitment of 3-prime processing factors to histone genes. Like Ser(2), Thr(4) phosphorylation requires the CTD kinase CDK9 and is evolutionarily conserved from yeast to human. Hsin et al. (2011) concluded that their data illustrated how a CTD modification can play a highly specific role in facilitating efficient gene expression.


Gene Structure

Liu and Rice (2000) determined that the CDK9 gene contains 7 exons. RNase protection and primer extension analyses indicated that the major transcription site for the CDK9 gene is at nucleotide -79. Further promoter analysis suggested that the region between nucleotides -219 and -89 contains other important regulatory elements.


Biochemical Features

Crystal Structure

Tahirov et al. (2010) described the crystal structure of the HIV Tat-P-TEFb complex, which is composed of HIV-1 Tat, human CDK9, and human cyclin T1 (CCTN1; 143055). Tat adopts a structure complementary to the surface of P-TEFb and makes extensive contacts, mainly with the cyclin T1 subunit of P-TEFb, but also with the T-loop of the CDK9 subunit. The structure provides a plausible explanation for the tolerance of Tat to sequence variations at certain sites. Importantly, Tat induces significant conformational changes in P-TEFb.


Mapping

By analysis of somatic cell hybrids, Bullrich et al. (1995) mapped the CDK9 gene to 9q34.1, a region associated with abnormalities and allelic losses in several malignancies.


REFERENCES

  1. Best, J. L., Presky, D. H., Swerlick, R. A., Burns, D. K., Chu, W. Cloning of a full-length cDNA sequence encoding a cdc2-related protein kinase from human endothelial cells. Biochem. Biophys. Res. Commun. 208: 562-568, 1995. [PubMed: 7695608, related citations] [Full Text]

  2. Bullrich, F., MacLachlan, T. K., Sang, N., Druck, T., Veronese, M. L., Allen, S. L., Chiorazzi, N., Koff, A., Heubner, K., Croce, C. M., Giordano, A. Chromosomal mapping of members of the cdc2 family of protein kinases, cdk3, cdk6, PISSLRE, and PITALRE, and a cdk inhibitor, p27-Kip1, to regions involved in human cancer. Cancer Res. 55: 1199-1205, 1995. [PubMed: 7882308, related citations]

  3. Fong, Y. W., Zhou, Q. Stimulatory effect of splicing factors on transcriptional elongation. Nature 414: 929-933, 2001. [PubMed: 11780068, related citations] [Full Text]

  4. Garriga, J., Mayol, X., Grana, X. The CDC2-related kinase PITALRE is the catalytic subunit of active multimeric protein complexes. Biochem. J. 319: 293-298, 1996. [PubMed: 8870681, related citations] [Full Text]

  5. Grana, X., De Luca, A., Sang, N., Fu, Y., Claudio, P. P., Rosenblatt, J., Morgan, D. O., Giordano, A. PITALRE, a nuclear CDC2-related protein kinase that phosphorylates the retinoblastoma protein in vitro. Proc. Nat. Acad. Sci. 91: 3834-3838, 1994. [PubMed: 8170997, related citations] [Full Text]

  6. Hsin, J.-P., Sheth, A., Manley, J. L. RNAP II CTD phosphorylated on threonine-4 is required for histone mRNA 3-prime end processing. Science 334: 683-686, 2011. [PubMed: 22053051, images, related citations] [Full Text]

  7. Jang, M. K., Mochizuki, K., Zhou, M., Jeong, H.-S., Brady, J. N., Ozato, K. The bromodomain protein Brd4 is a positive regulatory component of P-TEFb and stimulates RNA polymerase II-dependent transcription. Molec. Cell 19: 523-534, 2005. [PubMed: 16109376, related citations] [Full Text]

  8. Liu, H., Rice, A. P. Genomic organization and characterization of promoter function of the human CDK9 gene. Gene 252: 51-59, 2000. [PubMed: 10903437, related citations] [Full Text]

  9. Nguyen, V. T., Kiss, T., Michels, A. A., Bensaude, O. 7SK small nuclear RNA binds to and inhibits the activity of CDK9/cyclin T complexes. Nature 414: 322-325, 2001. [PubMed: 11713533, related citations] [Full Text]

  10. Rother, S., Strasser, K. The RNA polymerase II CTD kinase Ctk1 functions in translation elongation. Genes Dev. 21: 1409-1421, 2007. [PubMed: 17545469, images, related citations] [Full Text]

  11. Sano, M., Wang, S. C., Shirai, M., Scaglia, F., Xie, M., Sakai, S., Tanaka, T., Kulkarni, P. A., Barger, P. M., Youker, K. A., Taffet, G. E., Hamamori, Y., Michael, L. H., Craigen, W. J., Schneider, M. D. Activation of cardiac Cdk9 represses PGC-1 and confers a predisposition to heart failure. EMBO J. 23: 3559-3569, 2004. [PubMed: 15297879, images, related citations] [Full Text]

  12. Shore, S. M., Byers, S. A., Maury, W., Price, D. H. Identification of a novel isoform of Cdk9. Gene 307: 175-182, 2003. [PubMed: 12706900, related citations] [Full Text]

  13. Tahirov, T. H., Babayeva, N. D., Varzavand, K., Cooper, J. J., Sedore, S. C., Price, D. H. Crystal structure of HIV-1 Tat complexed with human P-TEFb. Nature 465: 747-751, 2010. [PubMed: 20535204, images, related citations] [Full Text]

  14. Wagner, K. D., Wagner, N., Ghanbarian, H., Grandjean, V., Gounon, P., Cuzin, F., Rassoulzadegan, M. RNA induction and inheritance of epigenetic cardiac hypertrophy in the mouse. Dev. Cell 14: 962-969, 2008. [PubMed: 18539123, related citations] [Full Text]

  15. Yang, Z., Yik, J. H. N., Chen, R., He, N., Jang, M. K., Ozato, K., Zhou, Q. Recruitment of P-TEFb for stimulation of transcriptional elongation by the bromodomain protein Brd4. Molec. Cell 19: 535-545, 2005. [PubMed: 16109377, related citations] [Full Text]

  16. Yang, Z., Zhu, Q., Luo, K., Zhou, Q. The 7SK small nuclear RNA inhibits the CDK9/cyclin T1 kinase to control transcription. Nature 414: 317-322, 2001. [PubMed: 11713532, related citations] [Full Text]

  17. Yik, J. H. N., Chen, R., Pezda, A. C., Zhou, Q. Compensatory contributions of HEXIM1 and HEXIM2 in maintaining the balance of active and inactive positive transcription elongation factor b complexes for control of transcription. J. Biol. Chem. 280: 16368-16376, 2005. [PubMed: 15713661, related citations] [Full Text]


Patricia A. Hartz - updated : 3/18/2014
Ada Hamosh - updated : 11/29/2011
Ada Hamosh - updated : 8/20/2010
Patricia A. Hartz - updated : 8/14/2008
Patricia A. Hartz - updated : 6/26/2007
Patricia A. Hartz - updated : 4/11/2007
Patricia A. Hartz - updated : 9/22/2005
Ada Hamosh - updated : 1/3/2002
Ada Hamosh - updated : 11/28/2001
Paul J. Converse - updated : 10/12/2000
Creation Date:
Rebekah S. Rasooly : 11/3/1998
carol : 09/26/2016
mgross : 03/19/2014
mcolton : 3/18/2014
alopez : 11/30/2011
terry : 11/29/2011
alopez : 6/17/2011
alopez : 8/30/2010
terry : 8/20/2010
mgross : 2/20/2009
mgross : 8/14/2008
terry : 8/14/2008
mgross : 7/11/2007
terry : 6/26/2007
mgross : 5/4/2007
mgross : 5/4/2007
terry : 4/11/2007
wwang : 9/26/2005
wwang : 9/22/2005
carol : 7/8/2003
alopez : 1/9/2002
terry : 1/3/2002
carol : 11/28/2001
mcapotos : 10/19/2000
mcapotos : 10/16/2000
terry : 10/12/2000
psherman : 11/3/1998

* 603251

CYCLIN-DEPENDENT KINASE 9; CDK9


Alternative titles; symbols

PITALRE
CTK1, YEAST, HOMOLOG OF; CTK1


HGNC Approved Gene Symbol: CDK9

Cytogenetic location: 9q34.11     Genomic coordinates (GRCh38): 9:127,786,034-127,790,792 (from NCBI)


TEXT

Description

Positive transcription factor b (P-TEFb) controls the elongation phase of transcription by RNA polymerase II (see POLR2A; 180660). P-TEFb is a heterodimer of CDK9 and 1 of 4 cyclin partners, cyclin T1 (CCNT1; 143055), cyclin K (CCNK; 603544), or cyclin T2a or T2b, which are isoforms of CCNT2 (603862) (Shore et al., 2003).


Cloning and Expression

To identify CDC2 (116940) family members, Grana et al. (1994) performed PCR on a mouse embryonic cDNA library using degenerate oligonucleotides based on regions conserved among CDC2-related proteins. They used a resulting PCR product to screen a human cDNA library and isolated a CDK9 cDNA. The predicted 372-amino acid protein contains the 11 conserved regions characteristic of the protein kinase catalytic domain, a putative nuclear localization signal, and a putative ATP-binding site. The authors called the protein PITALRE because it contains a pro-ile-thr-ala-leu-arg-glu motif similar to the PSTAIRE motif found in prototypic CDC2 kinases. CDK9 shares 41 to 43% amino acid sequence identity with CDC2, CDK2 (116953), CDK3 (123828), and CDK5 (123831). Subcellular fractionation and Western blot analyses demonstrated that CDK9 has a molecular mass of 43 kD and is located primarily in the nucleus. Northern blot analysis indicated that CDK9 was expressed as 2.8- and 3.2-kb mRNAs in all tissues tested, with the highest levels in liver and placenta.

Independently, Best et al. (1995) cloned human CDK9 cDNAs and designated the gene C-2k.

By RT-PCR of HeLa cell total RNA, Shore et al. (2003) cloned a splice variant of CDK9 that originates from an upstream promoter region. The deduced protein, CDK9-55, has a calculated molecular mass of 53.4 kD and contains a 117-amino acid N-terminal extension with a proline-rich region and a glycine-rich region. Using antibodies specific to the N-terminal extension, Shore et al. (2003) showed that CDK9-55 had an apparent molecular mass of 55 kD. The ratio of CDK9-55 to the shorter CDK9 isoform, CDK9-42, differed between HeLa cell nuclear extracts and mouse fibroblasts, but CDK9-42 was the predominant isoform in both.


Gene Function

Grana et al. (1994) found that 3 cellular proteins coimmunoprecipitated with CDK9, and CDK9 immunocomplexes had an RB1 (614041) kinase activity.

Garriga et al. (1996) found that monomeric CDK9, in contrast to other CDKs, is active. The association of CDK9 with other proteins modulates its activity and/or its ability to recognize substrates in vivo.

Yang et al. (2001) identified 7SK snRNA (606515) as a specific P-TEFb-associated factor. 7SK inhibits general and human immunodeficiency virus (HIV)-1 Tat-specific transcriptional activities of P-TEFb in vivo and in vitro by inhibiting the kinase activity of CDK9 and preventing recruitment of P-TEFb to the HIV-1 promoter. 7SK is efficiently dissociated from P-TEFb (the CDK9/cyclin T1 heterodimer) by treatment of cells with ultraviolet irradiation and actinomycin D. As these 2 agents have been shown to enhance significantly HIV-1 transcription and phosphorylation of RNA polymerase II, Yang et al. (2001) concluded that their data provide a mechanistic explanation for this stimulatory effect. Yang et al. (2001) further suggested that the 7SK/P-TEFb interaction may serve as a principal control point for the induction of cellular and HIV-1 viral gene expression during stress-related responses. The study demonstrated the involvement of an snRNA in controlling the activity of CDK/cyclin kinase.

Nguyen et al. (2001) independently showed that in human HeLa cells more than half of the P-TEFb is sequestered in larger complexes that also contain 7SK RNA. P-TEFb and 7SK associate in a specific and reversible manner. In contrast to the smaller P-TEFb complexes, which have a high kinase activity, the large 7SK/P-TEFb complexes show very weak kinase activity. Inhibition of cellular transcription by chemical agents or ultraviolet irradiation triggers complete disruption of the P-TEFb/7SK complex, and enhances CDK9 activity. Nguyen et al. (2001) concluded that transcription-dependent interaction of P-TEFb with 7SK may therefore contribute to an important feedback loop modulating the activity of RNA Pol II.

Fong and Zhou (2001) demonstrated that splicing factors function directly to promote transcriptional elongation. The spliceosomal U small nuclear ribonucleoproteins (snRNPs) interact with human transcription elongation factor TAT-SF1 (300346) and strongly stimulate polymerase elongation when directed to an intron-free HIV-1 template. Fong and Zhou (2001) suggested that this effect is likely to be mediated through the binding of TAT-SF1 to elongation factor P-TEFb. Inclusion of splicing signals in the nascent transcript further stimulates transcription, supporting the notion that the recruitment of U snRNPs near the elongating polymerase is important for transcription. Because the TAT-SF1--U snRNP complex also stimulates splicing in vitro, Fong and Zhou (2001) proposed that it may serve as a dual-function factor to couple transcription and splicing and to facilitate their reciprocal activation.

By immunoprecipitation analysis, Shore et al. (2003) showed that CDK9-55 immunoprecipitated with cyclin T1, cyclin T2a, and cyclin T2b from HeLa cell nuclear extracts. CDK9-55 could phosphorylate the C-terminal domain of Drosophila Polr2a. Differential extraction of size-fractionated HeLa cell P-TEFb complexes showed that, like CDK9-42, CDK9-55 associated with high molecular mass complexes containing 7SK RNA and with low molecular mass complexes lacking 7SK RNA. Western blot analysis showed that untreated human macrophages expressed more CDK9-55 than CDK9-42, but macrophages activated by lipopolysaccharide or infected with HIV expressed more CDK9-42 than CDK9-55.

Sano et al. (2004) found that 8 ventricle samples from patients with heart failure due to dilated cardiomyopathy showed increased CDK9 activity against the C-terminal domain of POLR2A compared with controls. Increased CDK7 activity was also present in a minority of patient samples. Substantial hyperphosphorylation of endogenous POLR2A was more frequent at the CDK9 site than the CDK7 site in failing hearts. Sano et al. (2004) noted that cardiomyocyte-restricted expression of cyclin T1 in mice maintains Cdk9 activity at its elevated embryonic level. They found that maintenance of Cdk9 in mouse hearts through cyclin T1 expression resulted in myocyte enlargement and selective suppression of Pgc1 (PPARGC1A; 604517), a master regulator of mitochondrial biogenesis and function, leading to mitochondrial defects, enhanced myocyte apoptosis, predisposition to heart failure, and early death.

Jang et al. (2005) found that epitope-tagged mouse Brd4 (608749) interacted with cyclin T1 and CDK9 in P-TEFb complexes contained in HeLa cell nuclear extracts. The bromodomain of Brd4 was required for the interaction. Brd4 overexpression increased P-TEFb-dependent phosphorylation of the C-terminal domain of RNA polymerase II and stimulated transcription from a reporter plasmid driven by an HIV-1 promoter. Conversely, reduced Brd4 expression in mouse fibroblasts by small interfering RNA reduced RNA polymerase II C-terminal domain phosphorylation and transcription. Chromatin immunoprecipitation assays indicated that recruitment of P-TEFb to a promoter was dependent on Brd4 and was enhanced by increased chromatin acetylation.

About half of cellular P-TEFb exists in an inactive complex with 7SK and the HEXIM1 protein (607328). Yang et al. (2005) demonstrated that the remaining half associated with BRD4. In stress-induced HeLa cells, 7SK/HEXIM1-bound P-TEFb was converted into the BRD4-associated form. The association of P-TEFb with BRD4 was necessary to form the transcriptionally active P-TEFb, to recruit P-TEFb to a promoter, and to enable P-TEFb to contact the Mediator complex (see 602984). The P-TEFb recruitment function of BRD4 could be substituted by that of HIV-1 Tat, which recruited P-TEFb directly for activated HIV-1 transcription.

Yik et al. (2005) found that human HEXIM1 or HEXIM2 (615695) inhibited CDK9 kinase activity and P-TEFb-dependent transcription in conjunction with 7SK RNA.

Rother and Strasser (2007) found that the yeast CDK9 homolog, Ctk1, functioned in translation by enhancing decoding fidelity. Ctk1 associated with translating ribosomes in vivo and was needed for efficient translation. Ctk1 phosphorylated the small ribosomal subunit Rps2 (603624), and absence of Rps2 phosphorylation led to defects in translation elongation due to increased frequency of miscoding.

Wagner et al. (2008) found that injection of microRNA miR1 (see MIRN1-1; 609326) into fertilized mouse oocytes resulted in the early appearance of cardiac hypertrophy. Abnormal growth of the ventricular wall in experimental mice was associated with a significant increase in the level of Cdk9 mRNA, an miR1 target. Cdk9 protein content was even more elevated, and there was increased phosphorylation of RNA polymerase II. miR1 expression was not significantly changed in experimental mice, and there was no significant change in expression of other miR1 targets. Similar cardiac hypertrophy and biochemical changes were found in embryos developed from fertilized mouse oocytes that had been microinjected with 20-nucleotide sequences randomly chosen from the Cdk9 coding sequence.

The RNA polymerase II largest subunit, POLR2A (180660), contains a C-terminal domain (CTD) with up to 52 Tyr(1)-Ser(2)-Pro(3)-Thr(4)-Ser(5)-Pro(6)-Ser(7) consensus repeats. Serines 2, 5, and 7 are known to be phosphorylated, and these modifications help to orchestrate the interplay between transcription and processing of mRNA precursors. Hsin et al. (2011) provided evidence that phosphorylation of CTD Thr(4) residues is required specifically for histone mRNA 3-prime end processing, functioning to facilitate recruitment of 3-prime processing factors to histone genes. Like Ser(2), Thr(4) phosphorylation requires the CTD kinase CDK9 and is evolutionarily conserved from yeast to human. Hsin et al. (2011) concluded that their data illustrated how a CTD modification can play a highly specific role in facilitating efficient gene expression.


Gene Structure

Liu and Rice (2000) determined that the CDK9 gene contains 7 exons. RNase protection and primer extension analyses indicated that the major transcription site for the CDK9 gene is at nucleotide -79. Further promoter analysis suggested that the region between nucleotides -219 and -89 contains other important regulatory elements.


Biochemical Features

Crystal Structure

Tahirov et al. (2010) described the crystal structure of the HIV Tat-P-TEFb complex, which is composed of HIV-1 Tat, human CDK9, and human cyclin T1 (CCTN1; 143055). Tat adopts a structure complementary to the surface of P-TEFb and makes extensive contacts, mainly with the cyclin T1 subunit of P-TEFb, but also with the T-loop of the CDK9 subunit. The structure provides a plausible explanation for the tolerance of Tat to sequence variations at certain sites. Importantly, Tat induces significant conformational changes in P-TEFb.


Mapping

By analysis of somatic cell hybrids, Bullrich et al. (1995) mapped the CDK9 gene to 9q34.1, a region associated with abnormalities and allelic losses in several malignancies.


REFERENCES

  1. Best, J. L., Presky, D. H., Swerlick, R. A., Burns, D. K., Chu, W. Cloning of a full-length cDNA sequence encoding a cdc2-related protein kinase from human endothelial cells. Biochem. Biophys. Res. Commun. 208: 562-568, 1995. [PubMed: 7695608] [Full Text: https://doi.org/10.1006/bbrc.1995.1375]

  2. Bullrich, F., MacLachlan, T. K., Sang, N., Druck, T., Veronese, M. L., Allen, S. L., Chiorazzi, N., Koff, A., Heubner, K., Croce, C. M., Giordano, A. Chromosomal mapping of members of the cdc2 family of protein kinases, cdk3, cdk6, PISSLRE, and PITALRE, and a cdk inhibitor, p27-Kip1, to regions involved in human cancer. Cancer Res. 55: 1199-1205, 1995. [PubMed: 7882308]

  3. Fong, Y. W., Zhou, Q. Stimulatory effect of splicing factors on transcriptional elongation. Nature 414: 929-933, 2001. [PubMed: 11780068] [Full Text: https://doi.org/10.1038/414929a]

  4. Garriga, J., Mayol, X., Grana, X. The CDC2-related kinase PITALRE is the catalytic subunit of active multimeric protein complexes. Biochem. J. 319: 293-298, 1996. [PubMed: 8870681] [Full Text: https://doi.org/10.1042/bj3190293]

  5. Grana, X., De Luca, A., Sang, N., Fu, Y., Claudio, P. P., Rosenblatt, J., Morgan, D. O., Giordano, A. PITALRE, a nuclear CDC2-related protein kinase that phosphorylates the retinoblastoma protein in vitro. Proc. Nat. Acad. Sci. 91: 3834-3838, 1994. [PubMed: 8170997] [Full Text: https://doi.org/10.1073/pnas.91.9.3834]

  6. Hsin, J.-P., Sheth, A., Manley, J. L. RNAP II CTD phosphorylated on threonine-4 is required for histone mRNA 3-prime end processing. Science 334: 683-686, 2011. [PubMed: 22053051] [Full Text: https://doi.org/10.1126/science.1206034]

  7. Jang, M. K., Mochizuki, K., Zhou, M., Jeong, H.-S., Brady, J. N., Ozato, K. The bromodomain protein Brd4 is a positive regulatory component of P-TEFb and stimulates RNA polymerase II-dependent transcription. Molec. Cell 19: 523-534, 2005. [PubMed: 16109376] [Full Text: https://doi.org/10.1016/j.molcel.2005.06.027]

  8. Liu, H., Rice, A. P. Genomic organization and characterization of promoter function of the human CDK9 gene. Gene 252: 51-59, 2000. [PubMed: 10903437] [Full Text: https://doi.org/10.1016/s0378-1119(00)00215-8]

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Contributors:
Patricia A. Hartz - updated : 3/18/2014
Ada Hamosh - updated : 11/29/2011
Ada Hamosh - updated : 8/20/2010
Patricia A. Hartz - updated : 8/14/2008
Patricia A. Hartz - updated : 6/26/2007
Patricia A. Hartz - updated : 4/11/2007
Patricia A. Hartz - updated : 9/22/2005
Ada Hamosh - updated : 1/3/2002
Ada Hamosh - updated : 11/28/2001
Paul J. Converse - updated : 10/12/2000

Creation Date:
Rebekah S. Rasooly : 11/3/1998

Edit History:
carol : 09/26/2016
mgross : 03/19/2014
mcolton : 3/18/2014
alopez : 11/30/2011
terry : 11/29/2011
alopez : 6/17/2011
alopez : 8/30/2010
terry : 8/20/2010
mgross : 2/20/2009
mgross : 8/14/2008
terry : 8/14/2008
mgross : 7/11/2007
terry : 6/26/2007
mgross : 5/4/2007
mgross : 5/4/2007
terry : 4/11/2007
wwang : 9/26/2005
wwang : 9/22/2005
carol : 7/8/2003
alopez : 1/9/2002
terry : 1/3/2002
carol : 11/28/2001
mcapotos : 10/19/2000
mcapotos : 10/16/2000
terry : 10/12/2000
psherman : 11/3/1998