Regulation of Polymerase II Transcription by 7SK snRNA: Two Distinct RNA Elements Direct P-TEFb and HEXIM1 Binding

REFERENCES

• Berkhout, B., R. H. Silverman, and K. T. Jeang. 1989. Tat trans-activates the human immunodeficiency virus through a nascent RNA target. Cell 59:273–282.
   PubMed Web of Science ®Google Scholar
• Brasier, A. R., and J. J. Fortin. 1994. Nonisotopic assays for reporter gene activity, p. 9.7.12-9.7.21. In F. M. Ausubel, R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl (ed.), Current protocols in molecular biology, vol. 1. John Wiley & Sons, Inc., New York, N.Y.
   Google Scholar
• Byers, S. A., J. P. Price, J. J. Cooper, Q. Li, and D. H. Price. 2005. HEXIM2, a HEXIM1 related protein, regulates P-TEFb through association with 7SK. J. Biol. Chem. 280:16360–16367.
   PubMed Web of Science ®Google Scholar
• Callige, M., I. Kieffer, and H. Richard-Foy. 2005. CSN5/Jab1 is involved in ligand-dependent degradation of ERa by the proteasome. Mol. Cell. Biol. 11:4349–4358.
   Google Scholar
• Chao, S.-H., and D. H. Price. 2001. Flavopiridol inactivates P-TEFb and blocks most RNA polymerase II transcription in vivo. J. Biol. Chem. 276:31793–31799.
   PubMed Web of Science ®Google Scholar
• Chen, R., Z. Yang, and Q. Zhou. 2004. Phosphorylated positive transcription elongation factor b (P-TEFb) is tagged for inhibition through association with 7SK snRNA. J. Biol. Chem. 279:4153–4160.
   PubMed Web of Science ®Google Scholar
• Cho, E. J., M. S. Kobor, M. Kim, J. Greenblatt, and S. Buratowski. 2001. Opposing effects of Ctk1 kinase and Fcp1 phosphatase at Ser 2 of the RNA polymerase II C-terminal domain. Genes Dev. 15:3319–3329.
   PubMed Web of Science ®Google Scholar
• Ganot, P., B. E. Jady, M. L. Bortolin, X. Darzacq, and T. Kiss. 1999. Nucleolar factors direct the 2′-O-ribose methylation and pseudouridylation of U6 spliceosomal RNA. Mol. Cell. Biol. 19:6906–6917.
   PubMed Web of Science ®Google Scholar
• Garriga, J., and X. Grana. 2004. Cellular control of gene expression by T-type cyclin/CDK9 complexes. Gene 337:15–23.
   PubMed Web of Science ®Google Scholar
• Goodall, G. J., K. Wiebauer, and W. Filipowicz. 1990. Analysis of pre-mRNA processing in transfected plant protoplasts. Methods Enzymol. 181:148–161.
   PubMedGoogle Scholar
• Gursoy, H. C., D. Koper, and B. J. Benecke. 2000. The vertebrate 7S K RNA separates hagfish (Myxine glutinosa) and lamprey (Lampetra fluviatilis). J. Mol. Evol 50:456–464.
   PubMedGoogle Scholar
• Haaland, R. E., C. H. Herrmann, and A. P. Rice. 2003. Increased association of 7SK snRNA with Tat cofactor P-TEFb following activation of peripheral blood lymphocytes. AIDS 17:2429–2436.
   PubMed Web of Science ®Google Scholar
• Karn, J. 1999. Tackling Tat. J. Mol. Biol. 293:235–254.
   PubMed Web of Science ®Google Scholar
• Kobor, M. S., and J. Greenblatt. 2002. Regulation of transcription elongation by phosphorylation. Biochim. Biophys. Acta 1577:261–275.
   PubMed Web of Science ®Google Scholar
• Kruger, W., and B. J. Benecke. 1987. Structural and functional analysis of a human 7 S K RNA gene. J. Mol. Biol. 195:31–41.
   PubMedGoogle Scholar
• Michels, A. A., A. Fraldi, Q. Li, T. E. Adamson, F. Bonnet, V. T. Nguyen, S. C. Sedore, J. P. Price, D. H. Price, L. Lania, and O. Bensaude. 2004. Binding of the 7SK snRNA turns the HEXIM1 protein into a P-TEFb (CDK9/cyclin T) inhibitor. EMBO J. 23:2608–2619.
   PubMed Web of Science ®Google Scholar
• Michels, A. A., V. T. Nguyen, A. Fraldi, V. Labas, M. Edwards, F. Bonnet, L. Lania, and O. Bensaude. 2003. MAQ1 and 7SK RNA interact with CDK9/cyclin T complexes in a transcription-dependent manner. Mol. Cell. Biol. 23:4859–4869.
   PubMed Web of Science ®Google Scholar
• Murphy, S., F. Altruda, E. Ullu, M. Tripodi, L. Silengo, and M. Melli. 1984. DNA sequences complementary to human 7 SK RNA show structural similarities to the short mobile elements of the mammalian genome. J. Mol. Biol. 177:575–590.
   PubMedGoogle Scholar
• Murphy, S., C. Di Liegro, and M. Melli. 1987. The in vitro transcription of the 7SK RNA gene by RNA polymerase III is dependent only on the presence of an upstream promoter. Cell 51:81–87.
   PubMedGoogle Scholar
• Nguyen, V. T., T. Kiss, A. A. Michels, and O. Bensaude. 2001. 7SK small nuclear RNA binds to and inhibits the activity of CDK9/cyclin T complexes. Nature 414:322–325.
   PubMed Web of Science ®Google Scholar
• O'Keeffe, B., Y. Fong, D. Chen, S. Zhou, and Q. Zhou. 2000. Requirement for a kinase-specific chaperone pathway in the production of a Cdk9/cyclin T1 heterodimer responsible for P-TEFb-mediated tat stimulation of HIV-1 transcription. J. Biol. Chem. 275:279–287.
   PubMed Web of Science ®Google Scholar
• Peng, J., N. F. Marshall, and D. H. Price. 1998. Identification of a cyclin subunit required for the function of Drosophila P-TEFb. J. Biol. Chem. 273:13855–13860.
   PubMed Web of Science ®Google Scholar
• Price, D. H. 2000. P-TEFb, a cyclin-dependent kinase controlling elongation by RNA polymerase II. Mol. Cell. Biol. 20:2629–2634.
   PubMed Web of Science ®Google Scholar
• Reddy, R., D. Henning, C. S. Subrahmanyam, and H. Busch. 1984. Primary and secondary structure of 7-3 (K) RNA of Novikoff hepatoma. J. Biol. Chem. 259:12265–12270.
   PubMedGoogle Scholar
• Richter, S., H. Cao, and T. M. Rana. 2002. Specific HIV-1 TAR RNA loop sequence and functional groups are required for human cyclin T1-Tat-TAR ternary complex formation. Biochemistry 41:6391–6397.
   PubMedGoogle Scholar
• Richter, S., Y. H. Ping, and T. M. Rana. 2002. TAR RNA loop: a scaffold for the assembly of a regulatory switch in HIV replication. Proc. Natl. Acad. Sci. USA 99:7928–7933.
   PubMed Web of Science ®Google Scholar
• Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
   Google Scholar
• Sano, M., M. Abdellatif, H. Oh, M. Xie, L. Bagella, A. Giordano, L. H. Michael, F. J. DeMayo, and M. D. Schneider. 2002. Activation and function of cyclin T-Cdk9 (positive transcription elongation factor-b) in cardiac muscle-cell hypertrophy. Nat. Med. 8:1310–1317.
   PubMed Web of Science ®Google Scholar
• Shim, E. Y., A. K. Walker, Y. Shi, and T. K. Blackwell. 2002. CDK-9/cyclin T (P-TEFb) is required in two postinitiation pathways for transcription in the C. elegans embryo. Genes Dev. 16:2135–2146.
   PubMed Web of Science ®Google Scholar
• Wada, T., T. Takagi, Y. Yamaguchi, D. Watanabe, and H. Handa. 1998. Evidence that P-TEFb alleviates the negative effect of DSIF on RNA polymerase II-dependent transcription in vitro. EMBO J. 17:7395–7403.
   PubMed Web of Science ®Google Scholar
• Wassarman, D. A., and J. A. Steitz. 1991. Structural analyses of the 7SK ribonucleoprotein (RNP), the most abundant human small RNP of unknown function. Mol. Cell. Biol. 11:3432–3445.
   PubMed Web of Science ®Google Scholar
• Wei, P., M. E. Garber, S. M. Fang, W. H. Fischer, and K. A. Jones. 1998. A novel CDK9-associated C-type cyclin interacts directly with HIV-1 Tat and mediates its high-affinity, loop-specific binding to TAR RNA. Cell 92:451–562.
   PubMed Web of Science ®Google Scholar
• Wei, W. Z., R. F. Gill, R. F. Jones, D. Lichlyter, and J. P. Abastado. 1996. Induction of cytotoxic T lymphocytes to murine mammary tumor cells with a Kd-restricted immunogenic peptide. Int. J. Cancer 66:659–663.
   PubMedGoogle Scholar
• Wittmann, B. M., N. Wang, and M. M. Montano. 2003. Identification of a novel inhibitor of breast cell growth that is down-regulated by estrogens and decreased in breast tumors. Cancer Res. 63:5151–5158.
   PubMedGoogle Scholar
• Yamaguchi, Y., T. Takagi, T. Wada, K. Yano, A. Furuya, S. Sugimoto, J. Hasegawa, and H. Handa. 1999. NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation. Cell 97:41–51.
   PubMed Web of Science ®Google Scholar
• Yang, Z., Q. Zhu, K. Luo, and Q. Zhou. 2001. The 7SK small nuclear RNA inhibits the CDK9/cyclin T1 kinase to control transcription. Nature 414:317–322.
   PubMed Web of Science ®Google Scholar
• Yik, J. H., R. Chen, R. Nishimura, J. L. Jennings, A. J. Link, and Q. Zhou. 2003. Inhibition of P-TEFb (CDK9/Cyclin T) kinase and RNA polymerase II transcription by the coordinated actions of HEXIM1 and 7SK snRNA. Mol. Cell 12:971–982.
   PubMed Web of Science ®Google Scholar
• Yik, J. H., R. Chen, A. C. Pezda, C. S. Samford, and Q. Zhou. 2004. A human immunodeficiency virus type 1 Tat-like arginine-rich RNA-binding domain is essential for HEXIM1 to inhibit RNA polymerase II transcription through 7SK snRNA-mediated inactivation of P-TEFb. Mol. Cell. Biol. 24:5094–5105.
   PubMed Web of Science ®Google Scholar
• Yik, J. H., R. Chen, A. C. Pezda, and Q. Zhou. 2005. Compensatory contributions of HEXIM1 and HEXIM2 in maintaining the balance of active and inactive P-TEFb complexes for control of transcription. J. Biol. Chem. 280:16368–16376.
   PubMedGoogle Scholar
• Zhang, J., N. Tamilarasu, S. Hwang, M. E. Garber, I. Huq, K. A. Jones, and T. M. Rana. 2000. HIV-1 TAR RNA enhances the interaction between Tat and cyclin T1. J. Biol. Chem. 275:34314–34319.
   PubMedGoogle Scholar
• Zhu, Y., T. Peery, J. Peng, Y. Ramanathan, N. F. Marshall, T. Marshall, B. Amendt, B. Mathews, and D. H. Price. 1997. Transcription elongation factor P-TEFb is required for HIV-1 tat transactivation in vitro. Genes Dev. 11:2622–2632.
   PubMed Web of Science ®Google Scholar