Structural changes in the RNA polymerase II transcription complex during transition from initiation to elongation

Molecular and Cellular Biology

Volumn 18, Issue 9, 1998, Pages 5343-5354

  Samkurashvili, Irakli ^a,b   Luse, Donal S ^b  

^a UNIVERSITY OF CINCINNATI COLLEGE OF MEDICINE   (United States)

^b LERNER RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA POLYMERASE;

ARTICLE; DNA FLANKING REGION; DNA FOOTPRINTING; ENZYME ACTIVITY; GENETIC TRANSCRIPTION; HEREDITY; PRIORITY JOURNAL; RNA SYNTHESIS; RNA TRANSCRIPTION;

EID: 0031840489     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: 10.1128/MCB.18.9.5343     Document Type: Article

References (32)

1. Borukhov, S., V. Sagitov, and A. Goldfarb. 1993. Transcript cleavage factors from E. coli. Cell 72:459-466.
2. Chamberlin, M. J. 1995. New models for the mechanism of transcription elongation and its regulation, p. 1-21. In The Harvey lectures, series 88. Wiley-Liss, Inc., New York, N.Y.
3. Gu, W., W. Powell, J. Mote, Jr., and D. Reines. 1993. Nascent RNA cleavage by arrested RNA polymerase II does not require upstream translocation of the elongation complex on DNA. J. Biol. Chem. 268:25604-25616.
4. Gu, W., and D. Reines. 1995. Identification of a decay in transcription potential that results in elongation factor dependence of RNA polymerase II. J. Biol. Chem. 270:11238-11244.
5. Gu, W. G., M. Wind, and D. Reines. 1996. Increased accommodation of nascent RNA in a product site on RNA polymerase II during arrest. Proc. Natl. Acad. Sci. USA 93:6935-6940.
6. Guajardo, R., and R. Sousa. 1997. A model for the mechanism of polymerase translocation. J. Mol. Biol. 265:8-19.
7. Izban, M. G., and D. S. Luse. 1991. Transcription on nucleosomal templates by RNA polymerase II in vitro: inhibition of elongation with enhancement of sequence-specific pausing. Genes Dev. 5:683-696.
8. Izban, M. G., and D. S. Luse. 1992. Factor-stimulated RNA polymerase II transcribes at physiological elongation rates on naked DNA but very poorly on chromatin templates. J. Biol. Chem. 267:13647-13655.
9. Izban, M. G., and D. S. Luse. 1992. The RNA polymerase II ternary complex cleaves the nascent transcript in a 3′ →5′ direction in the presence of elongation factor SII. Genes Dev. 6:1342-1356.
10. Izban, M. G., and D. S. Luse. 1993. SII-facilitated transcript cleavage in RNA polymerase II complexes stalled early after initiation occurs in primarily dinucleotide increments. J. Biol. Chem. 268:12864-12873.
11. Izban, M. G., and D. S. Luse. 1993. The increment of SII-facilitated transcript cleavage varies dramatically between elongation competent and incompetent RNA polymerase II ternary complexes. J. Biol. Chem. 268:12874-12885.
12. Komissarova, N., and M. Kashlev. 1997. RNA polymerase switches between inactivated and activated states by translocating back and forth along the DNA and the RNA. J. Biol. Chem. 272:15329-15338.
13. Komissarova, N., and M. Kashlev. 1997. Transcriptional arrest: Escherichia coli RNA polymerase translocates backward, leaving the 3' end of the RNA intact and extruded. Proc. Natl. Acad. Sci. USA 94:1755-1760.
14. Krumm, A., T. Meulia, M. Brunvand, and M. Groudine. 1992. The block to transcriptional elongation within the human c-myc gene is determined in the promoter-proximal region. Genes Dev. 6:2201-2213.
15. Krummel, B., and M. J. Chamberlin. 1992. Structural analysis of ternary complexes of Escherichia coli RNA polymerase-deoxyribonuclease I foot-printing of defined complexes. J. Mol. Biol. 225:239-250.
16. Landick, R. 1997. RNA polymerase slides home: pause and termination site recognition. Cell 88:741-744.
17. Lis, J., and C. Wu. 1993. Protein traffic on the heat shock promoter: parking, stalling, and trucking along. Cell 74:1-4.
18. McKean, D., and D. Luse. Unpublished observations.
19. Nudler, E., A. Goldfarb, and M. Kashlev. 1994. Discontinuous mechanism of transcription elongation. Science 265:793-796.
20. Nudler, E., A. Mustaev, E. Lukhtanov, and A. Goldfarb. 1997. The RNA-DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase. Cell 89:33-41.
21. Orlova, M., J. Newlands, A. Das, A. Goldfarb, and S. Borukhov. 1995. Intrinsic transcript cleavage activity of RNA polymerase. Proc. Natl. Acad. Sci. USA 92:4596-4600.
22. Rasmussen, E. B., and J. T. Lis. 1995. Short transcripts of the ternary complex provide insight into RNA polymerase II elongational pausing. J. Mol. Biol. 252:522-535.
23. Reeder, T. C., and D. K. Hawley. 1996. Promoter proximal sequences modulate RNA polymerase II elongation by a novel mechanism. Cell 87:767-777.
24. Reines, D., P. Ghanouni, Q. Q. Li, and J. Mote. 1992. The RNA polymerase II elongation complex. Factor-dependent transcription elongation involves nascent RNA cleavage. J. Biol. Chem. 267:15516-15522.
25. Rice, G. A., M. J. Chamberlin, and C. M. Kane. 1993. Contacts between mammalian RNA polymerase II and the template DNA in a ternary elongation complex. Nucleic Acids Res. 21:113-118.
26. Rougvie, A. E., and J. T. Lis. 1990. Postinitiation transcriptional control in Drosophila melanogaster. Mol. Cell. Biol. 10:6041-6045.
27. Rudd, M. D., M. G. Izban, and D. S. Luse. 1994. The active site of RNA polymerase II participates in transcript cleavage within arrested ternary complexes. Proc. Natl. Acad. Sci. USA 91:8057-8061.
28. Samkurashvili, I., and D. S. Luse. 1996. Translocation and transcriptional arrest during transcript elongation by RNA polymerase II. J. Biol. Chem. 271:23495-23505.
29. Sawadogo, M., and R. G. Roeder. 1985. Factors involved in specific transcription by human RNA polymerase II: analysis by a rapid and quantitative in vitro assay. Proc. Natl. Acad. Sci. USA 82:4394-4398.
30. Uptain, S. M., C. M. Kane, and M. J. Chamberlin. 1997. Basic mechanisms of transcript elongation and its regulation. Annu. Rev. Biochem. 66:117-172.
31. Wang, D., T. I. Meier, C. L. Chan, G. Feng, D. N. Lee, and R. Landick. 1995. Discontinuous movements of DNA and RNA in RNA polymerase accompany formation of a paused transcription complex. Cell 81:341-350.
32. Zawel, L., K. P. Kumar, and D. Reinberg. 1995. Recycling of the general transcription factors during RNA polymerase II transcription. Genes Dev. 9:1479-1490.