Coordination of Transcription, RNA Processing, and Surveillance by P-TEFb Kinase on Heat Shock Genes

Molecular Cell

Volumn 13, Issue 1, 2004, Pages 55-65

  Ni, Zhuoyu ^a   Schwartz, Brian E ^a,c   Werner, Janis ^a   Suarez, Jose Ramon ^b   Lis, John T ^a  

^a Cornell University ^*  (United States)

^b SANOFI   (France)

^c HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FLAVOPIRIDOL; HEAT SHOCK PROTEIN; HEAT SHOCK PROTEIN 26; HEAT SHOCK PROTEIN 70; POSITIVE TRANSCRIPTION ELONGATION FACTOR; PROTEIN DERIVATIVE; PROTEIN KINASE; PROTEIN KINASE INHIBITOR; RNA; RNA POLYMERASE II; SERINE; UNCLASSIFIED DRUG;

ANIMAL CELL; ANIMAL TISSUE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; DROSOPHILA; GENE EXPRESSION; GENE INDUCTION; GENETIC TRANSCRIPTION; HEAT SHOCK; IN VIVO STUDY; INSECT CELL; NONHUMAN; POLYTENE CHROMOSOME; PROTEIN PHOSPHORYLATION; RNA DEGRADATION; RNA PROCESSING; TRANSCRIPTION REGULATION;

ANIMALIA; INSECTA;

EID: 1642441939     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1097-2765(03)00526-4     Document Type: Article

References (54)

1. Ahn S., Kim M., Buratowski S. Phsophorylation of Serine 2 within the RNA polymerase II C-terminal domain couples transcription and 3′ end processing. Mol. Cell. 13:2004;67-76. , this issue.
2. Akoulitchev S., Makela T.P., Weinberg R.A., Reinberg D. Requirement for TFIIH kinase activity in transcription by RNA polymerase II. Nature. 377:1995;557-560.
3. Andrulis E.D., Guzman E., Doring P., Werner J., Lis J.T. High-resolution localization of Drosophila Spt5 and Spt6 at heat shock genes in vivo. roles in promoter proximal pausing and transcription elongation Genes Dev. 14:2000;2635-2649.
4. Andrulis E.D., Werner J., Nazarian A., Erdjument-Bromage H., Tempst P., Lis J.T. The RNA processing exosome is linked to elongating RNA polymerase II in Drosophila. Nature. 420:2002;837-841.
5. Barilla D., Lee B.A., Proudfoot N.J. Cleavage/polyadenylation factor IA associates with the carboxyl-terminal domain of RNA polymerase II in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA. 98:2001;445-450.
6. Benyajati C., Mueller L., Xu N., Pappano M., Gao J., Mosammaparast M., Conklin D., Granok H., Craig C., Elgin S. Multiple isoforms of GAGA factor, a critical component of chromatin structure. Nucleic Acids Res. 25:1997;3345-3353.
7. Boehm A.K., Saunders A., Werner J., Lis J.T. Transcription factor and polymerase recruitment, modification, and movement on dhsp70 in vivo in the minutes following heat shock. Mol. Cell. Biol. 23:2003;7628-7637.
8. Bond G.L., Prives C., Manley J.L. Poly(A) polymerase phosphorylation is dependent on novel interactions with cyclins. Mol. Cell. Biol. 20:2000;5310-5320.
9. Bourgeois C.F., Kim Y.K., Churcher M.J., West M.J., Karn J. Spt5 cooperates with human immunodeficiency virus type 1 Tat by preventing premature RNA release at terminator sequences. Mol. Cell. Biol. 22:2002;1079-1093.
10. Burkard K.T., Butler J.S. A nuclear 3′-5′ exonuclease involved in mRNA degradation interacts with Poly(A) polymerase and the hnRNA protein Npl3p. Mol. Cell. Biol. 20:2000;604-616.
11. Chao S.H., Price D.H. Flavopiridol inactivates P-TEFb and blocks most RNA polymerase II transcription in vivo. J. Biol. Chem. 276:2001;31793-31799.
12. Chao S.H., Fujinaga K., Marion J.E., Taube R., Sausville E.A., Senderowicz A.M., Peterlin B.M., Price D.H. Flavopiridol inhibits P-TEFb and blocks HIV-1 replication. J. Biol. Chem. 275:2000;28345-28348.
13. Cho E.J., Kobor M.S., Kim M., Greenblatt J., Buratowski S. Opposing effects of Ctk1 kinase and Fcp1 phosphatase at Ser 2 of the RNA polymerase II C-terminal domain. Genes Dev. 15:2001;3319-3329.
14. Clemens J.C., Worby C.A., Simonson-Leff N., Muda M., Maehama T., Hemmings B.A., Dixon J.E. Use of double-stranded RNA interference in Drosophila cell lines to dissect signal transduction pathways. Proc. Natl. Acad. Sci. USA. 97:2000;6499-6503.
15. Dahmus M.E. Reversible phosphorylation of the C-terminal domain of RNA polymerase II. J. Biol. Chem. 271:1996;19009-19012.
16. Epshtein V., Nudler E. Cooperation between RNA polymerase molecules in transcription elongation. Science. 300:2003;801-805.
17. Hartzog G.A., Wada T., Handa H., Winston F. Evidence that Spt4, Spt5, and Spt6 control transcription elongation by RNA polymerase II in Saccharomyces cerevisiae. Genes Dev. 12:1998;357-369.
18. Hilleren P., McCarthy T., Rosbash M., Parker R., Jensen T.H. Quality control of mRNA 3′-end processing is linked to the nuclear exosome. Nature. 413:2001;538-542.
19. Hirose Y., Manley J.L. RNA polymerase II is an essential mRNA polyadenylation factor. Nature. 395:1998;93-96.
20. Ho C.K., Shuman S. Distinct roles for CTD Ser-2 and Ser-5 phosphorylation in the recruitment and allosteric activation of mammalian mRNA capping enzyme. Mol. Cell. 3:1999;405-411.
21. Ivanov D., Kwak Y.T., Guo J., Gaynor R.B. Domains in the SPT5 protein that modulate its transcriptional regulatory properties. Mol. Cell. Biol. 20:2000;2970-2983.
22. Kobor M.S., Greenblatt J. Regulation of transcription elongation by phosphorylation. Biochim. Biophys. Acta. 1577:2002;261-275.
23. Komarnitsky P., Cho E.J., Buratowski S. Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription. Genes Dev. 14:2000;2452-2460.
24. Larochelle S., Chen J., Knights R., Pandur J., Morcillo P., Erdjument-Bromage H., Tempst P., Suter B., Fisher R.P. T-loop phosphorylation stabilizes the CDK7-cyclin H-MAT1 complex in vivo and regulates its CTD kinase activity. EMBO J. 20:2001;3749-3759.
25. Lavoie S.B., Albert A.L., Handa H., Vicent M., Bensaude O. The peptidyl-prolyl isomerase Pin1 interacts with hSpt5 phosphorylated by Cdk9. J. Mol. Biol. 312:2001;675-685.
26. Licatalosi D.D., Geiger G., Minet M., Schroeder S., Cilli K., McNeil J.B., Bentley D.L. Functional interaction of yeast pre-mRNA 3′ end processing factors with RNA polymerase II. Mol. Cell. 9:2002;1101-1111.
27. Lindstrom D.L., Hartzog G.A. Genetic interactions of Spt4-Spt5 and TFIIS with the RNA polymerase II CTD and CTD modifying enzymes in Saccharomyces cerevisiae. Genetics. 159:2001;487-497.
28. Lindstrom D.L., Squazzo S.L., Muster N., Burckin T.A., Wachter K.C., Emigh C.A., McCleery J.A., Yates J.R. 3rd, Hartzog G.A. Dual roles for Spt5 in pre-mRNA processing and transcription elongation revealed by identification of Spt5-associated proteins. Mol. Cell. Biol. 23:2003;1368-1378.
29. Lis J. Promoter-associated pausing in promoter architecture and postinitiation transcriptional regulation. Cold Spring Harb. Symp. Quant. Biol. 63:1998;347-356.
30. Lis J.T., Mason P., Peng J., Price D.H., Werner J. P-TEFb kinase recruitment and function at heat shock loci. Genes Dev. 14:2000;792-803.
31. Marshall N.F., Price D.H. Purification of P-TEFb, a transcription factor required for the transition into productive elongation. J. Biol. Chem. 270:1995;12335-12338.
32. Marshall N.F., Peng J., Xie Z., Price D.H. Control of RNA polymerase II elongation potential by a novel carboxyl-terminal domain kinase. J. Biol. Chem. 271:1996;27176-27183.
33. Moore M.J. Nuclear RNA turnover. Cell. 108:2002;431-434.
34. O'Brien T., Lis J.T. Rapid changes in Drosophila transcription after an instantaneous heat shock. Mol. Cell. Biol. 13:1993;3456-3463.
35. O'Brien T., Hardin S., Greenleaf A., Lis J.T. Phosphorylation of RNA polymerase II C-terminal domain and transcriptional elongation. Nature. 370:1994;75-77.
36. O'Brien T., Wilkins R.C., Giardina C., Lis J.T. Distribution of GAGA protein on Drosophila genes in vivo. Genes Dev. 9:1995;1098-1110.
37. O'Connell P.O., Rosbash M. Sequence, structure, and codon preference of the Drosophila ribosomal protein 49 gene. Nucleic Acids Res. 12:1984;5495-5513.
38. Peng J., Marshall N.F., Price D.H. Identification of a cyclin subunit required for the function of Drosophila P-TEFb. J. Biol. Chem. 273:1998;13855-13860.
39. Ping Y.H., Rana T.M. DSIF and NELF interact with RNA polymerase II elongation complex and HIV-1 Tat stimulates P-TEFb-mediated phosphorylation of RNA polymerase II and DSIF during transcription elongation. J. Biol. Chem. 276:2001;12951-12958.
40. Price D.H. P-TEFb, a cyclin-dependent kinase controlling elongation by RNA polymerase II. Mol. Cell. Biol. 20:2000;2629-2634.
41. Proudfoot N., O'Sullivan J. Polyadenylation. a tail of two complexes Curr. Biol. 12:2002;R855-R857.
42. Proudfoot N.J., Furger A., Dye M.J. Integrating mRNA processing with transcription. Cell. 108:2002;501-512.
43. Ramanathan M., Rajpara S.M., Reza S.M., Lees E., Shuman S., Mathews M.B., Pe'ery T. Three RNA polymerase II carboxyl-terminal domain kinases display distinct substrate preferences. J. Biol. Chem. 276:2001;10913-10920.
44. Rougvie A.E., Lis J.T. The RNA polymerase II molecule at the 5′ end of the uninduced hsp70 gene of D. melanogaster is transcriptionally engaged. Cell. 54:1988;795-804.
45. Schwartz B.E., Larochelle S., Suter B., Lis J.T. Cdk7 is required for full activation of Drosophila heat shock genes and RNA polymerase II phosphorylation in vivo. Mol. Cell. Biol. 23:2003;6876-6886. a.
46. Schwartz, B.E., Werner, J., and Lis, J.T. (2003b). Indirect immunofluorescent labeling of Drosophila polytene chromosomes: visualizing protein interactions with chromatin in vivo. In Methods in Enzymology, C. Wu and C.D. Allis, eds. (Elsevier Press, in press).
47. Shim E.Y., Walker A.K., Shi Y., Blackwell T.K. CDK-9/cyclin T (P-TEFb) is required in two postinitiation pathways for transcription in the C. elegans embryo. Genes Dev. 16:2002;2135-2146.
48. Simon J.A., Lis J.T. A germline transformation analysis reveals flexibility in the organization of heat shock consensus elements. Nucleic Acids Res. 15:1987;2971-2988.
49. Skaar D.A., Greenleaf A.L. The RNA polymerase II CTD kinase CTDK-I affects pre-mRNA 3′ cleavage/polyadenylation through the processing component Pti1p. Mol. Cell. 10:2002;1429-1439.
50. Thummel C.S., Burtis K.C., Hogness D.S. Spatial and temporal patterns of E74 transcription during Drosophila development. Cell. 61:1990;101-111.
51. Wen Y., Shatkin A.J. Transcription elongation factor hSPT5 stimulates mRNA capping. Genes Dev. 13:1999;1774-1779.
52. Yamaguchi Y., Takagi T., Wada T., Yano K., Furuya A., Sugimoto S., Hasegawa J., Handa H. NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation. Cell. 97:1999;41-51.
53. Zhou M., Halanski M.A., Radonovich M.F., Kashanchi F., Peng J., Price D.H., Brady J.N. Tat modifies the activity of CDK9 to phosphorylate serine 5 of the RNA polymerase II carboxyl-terminal domain during human immunodeficiency virus type 1 transcription. Mol. Cell. Biol. 20:2000;5077-5086.
54. Zhu Y., Pe'ery T., Peng J., Ramanathan Y., Marshall N., Marshall T., Amendt B., Mathews M.B., Price D.H. Transcription elongation factor P-TEFb is required for HIV-1 tat transactivation in vitro. Genes Dev. 11:1997;2622-2632.