The regulation of elongation by eukaryotic RNA polymerase II: A recent view

Molecules and Cells

Volumn 11, Issue 3, 2001, Pages 267-274

  Kim, Dong Ki ^b   Yamaguchi, Yuki ^a   Wada, Tadashi ^b   Handa, Hiroshi ^a,b  

^a Frontier Collaborative Research Center   (Japan)

^b TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

Author keywords

DRB; DSIF (hSpt4 hSpt5); Elongation; NELF

Indexed keywords

DNA DIRECTED RNA POLYMERASE III; MESSENGER RNA;

GENETIC TRANSCRIPTION; METABOLISM; PHYSIOLOGY; REVIEW;

RNA POLYMERASE III; RNA, MESSENGER; TRANSCRIPTION, GENETIC;

EID: 0035973595     PISSN: 10168478     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Short Survey

References (69)

1. Andrulis, E. D., Guzman, E., Doring, P., Werner, J., and Lis, J. T. (2000) 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, 2635-2649.
2. Aso, T., Conaway, J. W., and Conaway, R. C. (1995) The RNA polymerase II elongation complex. FASEB J. 9, 1419-1428.
3. Basrai, M. A., Kingsbury, J., Koshland, D., Spencer, F., and Hieter, P. (1996) Faithful chromosome transmission requires Spt4p, a putative regulator of chromatin structure in Saccharomyces cerevisiae. Mol. Cell. Biol. 16, 2838-2847.
4. Bentley, D. L. (1999) Coupling RNA polymerase II transcription with pre-mRNA processing. Curr. Opin. Cell. Biol. 11, 347-351.
5. Chang, C. H. and Luse, D. S. (1997) The H3/H4 tetramer blocks transcript elongation by RNA polymerase II in vitro. J. Biol. Chem. 272, 23427-23434.
6. Chodosh, L. A., Fire, A., Samuals, M., and Sharp, P. A. (1989) 5,6-Dichloro-1-β-D-ribofuranosylbenzimidazole inhibits transcription elongation by RNA polymerase II in vitro. J. Biol. Chem. 264, 2250-2257.
7. Conaway, J. W., Shilatifard, A., Dvir, A., and Conaway, R. C. (2000) Control of elongation by RNA polymerase II. Trends Biochem. Sci. 25, 375-380.
8. Cramer, P., Bushnell, D. A., Fu, J., Gnatt, A. L., Maier-Davis, B., Thompson, N. E., Burgess, R. R., Edwards, A. M., David, P. R., and Kornberg, R. D. (2000) Architecture of RNA polymerase II and implications for the transcription mechanism. Science 288, 640-649.
9. Dvir, A., Conaway, R. C., and Conaway, J. W. (1996) Promoter escape by RNA polymerase II. A role for an ATP cofactor in suppression of arrest by polymerase at promoter-proximal sites. J. Biol. Chem. 20, 23352-23356.
10. Dynlacht, B. D. (1997) Regulation of transcription by proteins that control the cell cycle. Nature 389, 149-152.
11. Gu, W., Wind, M., and Reines, D. (1996) Increased accommodation of nascent RNA in a product site on RNA polymerase II during arrest. Proc. Natl. Acad. Sci. USA 93, 6935-6940.
12. Guo, S., Yamaguchi, Y., Schilbach, S., Wada, T., Lee, J., Goddard, A., French, D., Handa, H., and Rosenthal, A. (2000) A regulator of transcriptional elongation controls vertebrate neuronal development. Nature 408, 366-369.
13. Gusarov, I. and Nudler, E. (1999) The mechanism of intrinsic transcription termination. Mol. Cell 3, 495-504.
14. Hartzog, G. A., Basrai, M. A., Ricupero-Hovasse, S. L., Hieter, P., and Winston, F. (1996) Identification and analysis of a functional human homolog of the SPT4 gene of Saccharomyces cerevisiae. Mol. Cell. Biol. 16, 2848-2856.
15. Hartzog, G. A., Wada, T., Handa, H., and Winston, F. (1998) Evidence that Spt4, Spt5, and Spt6 control transcription elongation by RNA polymerase II in Saccharomyces cerevisiae. Genes Dev. 12, 357-369.
16. Hirose, Y., Tacke, R., and Manley, J. L. (1999) Phosphorylated RNA polymerase II stimulates pre-mRNA splicing. Genes Dev. 13, 1234-1239.
17. Ivanov, D., Kwak , Y. T., Guo, J., and Gaynor, R. B. (2000) Domains in the SPT5 protein that modulate its transcriptional regulatory properties. Mol. Cell. Biol. 20, 2970-2983.
18. Jansen, L. E., den Dulk, H., Brouns, R. M., de Ruijter, M., Brandsma, J. A., and Brouwer, J. (2000) Spt4 modulates Rad26 requirement in transcription-coupled nucleotide excision repair. EMBO J. 19, 6498-6507.
19. Kaplan, C. D., Morris, J. R., Wu, C., and Winston, F. (2000) Spt5 and spt6 are associated with active transcription and have characteristics of general elongation factors in D melanogaster. Genes Dev. 14, 2623-2634.
20. Karn, J. (1999) Tackling Tat. J. Mol. Biol. 293, 235-254.
21. Kim, J. B. and Sharp, P. A. (2001) P-TEFb phosphorylates hSPT5 and RNA polymerase II CTD independently of CAK. J. Biol. Chem. 276, 12317-12323.
22. Kim, J. B., Yamaguchi, Y., Wada, T., Handa, H., and Sharp, P. A. (1999) Tat-SF1 protein associates with RAP30 and human SPT5 proteins. Mol. Cell. Biol. 19, 5960-5968.
23. Kingston, R. E. and Narlikar, G. J. (1999) ATP-dependent remodeling and acetylation as regulators of chromatin fluidity. Genes Dev. 13, 2339-2352.
24. Komarnitsky, P., Cho, E. J., and Buratowski, S. (2000) Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription. Genes Dev. 14, 2452-2460.
25. Komissarova, N. and Kashlev, M. (1998) Functional topography of nascent RNA in elongation intermediates of RNA polymerase. Proc. Natl. Acacl. Sci. USA 95, 14699-14704.
26. Kornberg, R. D. and Lorch, Y. (1999) Twenty-five years of the nucleosome, fundamental particle of the eukaryotic chromosome. Cell 98, 285-294.
27. Korzheva, N., Mustaev, A., Kozlov, M., Malhotra, A., Nikiforov, V., Goldfarb, A., and Darst, S. A. (2000) A structural model of transcription elongation. Science 289, 619-625.
28. Liu, M., Xie, Z., and Price, D. H. (1998) A human RNA polymerase II transcription termination factor is a SWI2/SNF2 family member. J. Biol. Chem. 273, 25541-25544.
29. Luse, D. S. and Samkurashvili, I. (1998) The transition from initiation to elongation by RNA polymerase II. Cold Spring Harb Symp. Quant Biol. 63, 289-300.
30. Marshall, N. F. and Price, D. H. (1992) Control of formation of two distinct class of RNA polymerase II elongation complexes. Mol. Cell. Biol. 12, 2078-2090.
31. Marshall, N. F. and Price, D. H. (1995) Purification of P-TEFb, a transcription factor required for the transition into productive elongation. J. Biol. Chem. 270, 12335-12338.
32. Marshall, N. F, Peng, J., Xie, Z., and Price, D. H. (1996) Control of RNA polymerase II elongation potential by a novel carboxyl-terminal domain kinase. J. Biol. Chem. 271, 27176-27183.
33. Miller, T., Williams, K., Johnstone, R. W., and Shilatifard, A. (2000) Identification, cloning, expression, and biochemical characterization of the testis specific RNA polymerase II elongation factor ELL3. J. Biol. Chem. 275, 32052-32056.
34. Misteli, T. and Spector, D. L. (1998) The cellular organization of gene expression. Curr. Opin. Cell. Biol. 10, 323-331.
35. Misteli, T. and Spector, D. L. (1999) RNA polymerase II targets pre-mRNA splicing factors to transcription sites in vivo. Mol. Cell 3, 697-705.
36. Monsalve, M., Wu, Z., Adelmant, G., Puigserver, P, Fan, M., and Spiegelman, B. M. (2000) Direct coupling of transcription and mRNA processing through the thermogenic coactivator PGC-1. Mol. Cell 6, 307-316.
37. Nudler, E. (1999) Transcription elongation: structural basis and mechanisms. J. Mol. Biol. 288, 1-12.
38. Nudler, E., Avetissova, E., Markovtsov, V., and Goldfarb, A. (1996) Transcription processivity: protein-DNA interactions holding together the elongation complex. Science 273, 211-217.
39. Orphanides, G., LeRoy, G., Chang, C. H., Luse, D. S., and Reinberg, D. (1998) FACT, a factor that facilitates transcript elongation through nucleosomes. Cell 92, 105-116.
40. Orphanides, G., Wu, W. H., Lane, W. S., Hampsey, M., and Reinberg, D. (1999) The chromatin-specific transcription elongation factor FACT comprises human SPT16 and SSRP1 proteins. Nature 400, 284-288.
41. Otero, G., Fellows, J., Li, Y., de Bizemont, T., Dirac, A. M., Gustafsson, C. M., Erdjument-Bromage, H., Tempst, P., and Svejstrup, J. Q. (1999) Elongator, a multisubunit component of a novel RNA polymerase II holoenzyme for transcriptional elongation. Mol. Cell 3, 109-118.
42. Parada, C. A. and Roeder, R. G. (1996) Enhanced processivity of RNApolymaerase II triggered by Tat-induced phosphorylation of its carboxy-terminal domain. Nature 384, 375-378.
43. Parada, C. A. and Roeder, R. G. (1999) A novel RNA polymerase II-containing complex potentiates Tat-enhanced HIV-1 transcription. EMBO J. 18, 3688-3701.
44. Pazin, M. J. and Kadonaga, J. T. (1997) What's up and down with histone deacetylation and transcription? Cell 89, 325-328.
45. Poglitsch, C. L., Meredith, G. D., Gnatt, A. L., Jensen, G. J., Chang, W. H., Fu, J., and Kornberg, R. D. (1999) Electron crystal structure of an RNA polymerase II transcription elongation complex. Cell 98, 791-798.
46. Price, D. H. (2000) P-TEFb, a cyclin-dependent kinase controlling elongation by RNA polymerase II. Mol. Cell. Biol. 20, 2629-2634.
47. Roeder, R. G. (1996) The role of general initiation factors in transcription by RNA polymerase II. Trends Biochem. Sci. 21, 327-335.
48. Samkurashvili, I. and Luse, D. S. (1998) Structural changes in the RNA polymerase II transcription complex during transition from initiation to elongation. Mol. Cell. Biol. 18, 5343-5354.
49. Schmidt, A. E., Miller, T., Schmidt, S. L., Shiekhattar, R., and Shilatifard, A. (1999) Cloning and characterization of the EAP30 subunit of the ELL complex that confers derepression of transcription by RNA polymerase II. J. Biol. Chem. 274, 21981-21985.
50. Schroeder, S. C., Schwer, B., Shuman, S., and Bentley, D. L. (2000) Dynamic association of capping enzymes with transcribing RNA polymerase II. Genes Dev. 14, 2435-2440.
51. Sehgal, P. B., Darnell, J. E. Jr., and Tamm, I. (1976) The inhibition by DRB (5,6-dichloro-1-β-D-ribofuranosylbenzimidazole) of hnRNA and mRNA production in HeLa cells. Cell 9, 473-480.
52. Shilatifard, A. (1998) Factors regulating the transcriptional elongation activity of RNA polymerase II. FASEB J. 12, 1437-1446.
53. Sune, C. and Garcia-Blanco, M. A. (1999) Transcriptional cofactor CA150 regulates RNA polymerase II elongation in a TATA-box-dependent manner. Mol. Cell. Biol. 19, 4719-4728.
54. Swanson, M. S. and Winston, F. (1992) SPT4, SPT5, and SPT6 interactions: effects on transcription and viability in Saccharomyces cerevisiae. Genetics 132, 325-336.
55. Takagi, Y., Conaway, R. C., and Conaway, J. W. (1996) Characterization of elongin C functional domains required for interaction with elongin B and activation of elongin A. J. Biol. Chem. 271, 25562-25568.
56. Tamm, I., Nemes, M. M., and Osterhout, S. (1954) Influenza virus multiplication in the chorioallantoic membrane in vitro: kinetic aspects of inhibition by 5,6-dichloro-1-β-D-ribofuranosylbenzimidazole. J. Exp. Med. 100, 541-562.
57. Toulme, F., Guerin, M., Robichon, N., Leng, M., and Rahmouni, A. R. (1999) In vivo evidence for back and forth oscillations of the transcription elongation complex. EMBO J. 18, 5052-5060.
58. Wada, T., Takagi, T., Yamaguchi, Y., Ferdous, A., Imai, T., Hirose, S., Sugimoto, S., Yano, K., Hartzog, G. A., Winston, F., Buratowski, S., and Handa, H. (1998a) DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs. Genes Dev. 12, 343-356.
59. Wada, T., Takagi, T., Yamaguchi, Y., Watanabe, D., and Handa, H. (1998b) Evidence that P-TEFb alleviates the negative effect of DSIF on RNA polymerase II -dependent transcription in vitro. EMBO J. 17, 7395-7403.
60. Wada, T., Orphanides, G., Hasegawa, J., Kim, D. K., Yamaguchi, Y., Fukuda, A., Hisatake, K., Oh, S., Reinberg, D., and Handa, H. (2000) FACT relieves DSIF/NELF-mediated inhibition of transcriptional elongation and reveals functional differences between P-TEFb and TFIIH. Mol. Cell 5, 1067-1072.
61. Wei, P., Garber, M. E., Fang, S. M., Fischer, W. H., and Jones, K. A. (1998) A Novel CDK-associated C-type cyclin interacts directly with HIV-1 Tat and mediates its high-affinity, loop-specific binding to TAR RNA. Cell 92, 451-462.
62. Wen, Y. and Shatkin, A. J. (1999) Transcription elongation factor hSPT5 stimulates mRNA capping. Genes Dev. 13, 1774-1779.
63. Yamaguchi, Y., Takagi, T., Wada, T., Yano, K., Furuya, A., Sugimoto, S., Hasegawa, J., and Handa, H. (1999a) NELF, a mullisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation. Cell 97, 41-51.
64. Yamaguchi, Y., Wada, T., Watanabe, D., Takagi, T., Hasegawa, J., and Handa, H. (1999b) Structure and function of the human transcription elongation factor DSIF. J. Biol. Chem. 274, 8085-8092.
65. Van, Q., Moreland, R. J., Weliky Conaway, J., and Conaway, R. C. (1999) Dual roles for transcription factor IIF in promoter escape by RNA polymerase II. J. Biol. Chem. 274, 35668-35675.
66. Yue, Z., Maldonado, E., Pillutla, R., Cho, H., Reinberg, D., and Shatkin, A. J. (1997) Mammalian capping enzyme complements mutant Saccharomyces cerevisiae lacking mRNA guanylyltransferase and selectively binds the elongating form of RNA polymerase II. Proc. Natl. Acad. Sci. USA 94, 12898-12903.
67. Zandomeni, R., Mittleman, B., Bunick, D., Ackerman, S., and Weinmann, R. (1982) Mechanism of action of dichloro-1-β-D-ribofuranosylbenzimidazole: effect on in vitro transcription. Proc. Natl. Acad. Sci. USA 79, 3167-3170.
68. Zhu, Y., Pe'ery, T., Peng, J., Ramanathan, Y. Marshall, N., Marshall, T., Amendt, B., Mathews, M. B., and Price, D. H. (1997) Transcription elongation factor P-TEFb is required for HIV-1 tat transactivation in vitro. Genes Dev. 11, 2622-2632.
69. Zorio, D. A. and Bentley, D. L. (2001) Transcription elongation: the 'Foggy' is liftingellipsis. Curr. Biol. 11, 144-145.