Promoter-proximal Pol II: When stalling speeds things up

Cell Cycle

Volumn 7, Issue 11, 2008, Pages 1539-1544

  Nechaev, Sergei ^a   Adelman, Karen ^a  

^a NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

Author keywords

Development; Gene regulation; RNA polymerase II; Transcription elongation

Indexed keywords

HEAT SHOCK PROTEIN 70; MYC PROTEIN; NEGATIVE ELONGATION FACTOR; POL PROTEIN; RNA POLYMERASE II; TRANSCRIPTION ELONGATION FACTOR;

ANIMAL CELL; DNA SEQUENCE; DROSOPHILA; ENZYME MECHANISM; GENE EXPRESSION REGULATION; MAMMAL; NONHUMAN; PROMOTER PROXIMAL REGION; PROMOTER REGION; PROTEIN LOCALIZATION; REGULATORY MECHANISM; REVIEW; RNA SYNTHESIS; STIMULUS RESPONSE; TRANSCRIPTION REGULATION;

MAMMALIA;

EID: 45849129033     PISSN: 15384101     EISSN: 15514005     Source Type: Journal    
DOI: 10.4161/cc.7.11.6006     Document Type: Review

References (47)

1. Lis J. Promoter-associated pausing in promoter architecture and postinitiation transcriptional regulation. Cold Spring Harb Symp Quant Biol 1998; 63:347-56.
2. Gilmour DS, Lis JT. RNA polymerase II interacts with the promoter region of the noninduced hsp70 gene in Drosophila melanogaster cells. Mol Cell Biol 1986; 6:3984-9.
3. Rougvie AE, Lis JT. The RNA polymerase II molecule at the 5′ end of the uninduced hsp70 gene of D. melanogaster is transcriptionally engaged. Cell 1988; 54:795-804.
4. Rasmussen EB, Lis JT. In vivo transcriptional pausing and cap formation on three Drosophila heat shock genes. Proc Natl Acad Sci USA 1993; 90:7923-7.
5. Rasmussen EB, Lis JT. Short transcripts of the ternary complex provide insight into RNA polymerase II elongational pausing. J Mol Biol 1995; 252:522-35.
6. Aida M, Chen Y, Nakajima K, Yamaguchi Y, Wada T, Handa H. Transcriptional pausing caused by NELF plays a dual role in regulating immediate-early expression of the junB gene. Mol Cell Biol 2006; 26:6094-104.
7. Krumm A, Meulia T, Brunvand M, Groudine M. The block to transcriptional elongation within the human c-myc gene is determined in the promoter-proximal region. Genes Dev 1992; 6:2201-13.
8. Marshall NF, Price DH. Control of formation of two distinct classes of RNA polymerase II elongation complexes. Mol Cell Biol 1992; 12:2078-90.
9. Law A, Hirayoshi K, O'Brien T, Lis JT. Direct cloning of DNA that interacts in vivo with a specific protein: application to RNA polymerase II and sites of pausing in Drosophila. Nucleic Acids Res 1998; 26:919-24.
10. Rougvie AE, Lis JT. Postinitiation transcriptional control in Drosophila melanogaster. Mol Cell Biol 1990; 10:6041-5.
11. Kim TH, Barrera LO, Zheng M, Qu C, Singer MA, Richmond TA, Wu Y, Green RD, Ren B. A high-resolution map of active promoters in the human genome. Nature 2005; 436:876-80.
12. Guenther MG, Levine SS, Boyer LA, Jaenisch R, Young RA. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 2007; 130:77-88.
13. Muse GW, Gilchrist DA, Nechaev S, Shah R, Parker JS, Grissom SF, Zeitlinger J, Adelman K. RNA polymerase is poised for activation across the genome. Nat Genet 2007; 39:1507-11.
14. Zeitlinger J, Stark A, Kellis M, Hong JW, Nechaev S, Adelman K, Levine M, Young RA. RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nat Genet 2007; 39:1512-6.
15. Cartwright IL, Cryderman DE, Gilmour DS, Pile LA, Wallrath LL, Weber JA, Elgin SC. Analysis of Drosophila chromatin structure in vivo. Methods Enzymol 1999; 304:462-96.
16. Wang X, Lee C, Gilmour DS, Gergen JP. Transcription elongation controls cell fate specification in the Drosophila embryo. Genes Dev 2007; 21:1031-6.
17. Zeitlinger J, Zinzen RP, Stark A, Kellis M, Zhang H, Young RA, Levine M. Whole-genome ChIP-chip analysis of Dorsal, Twist and Snail suggests integration of diverse patterning processes in the Drosophila embryo. Genes Dev 2007; 21:385-90.
18. Giardina C, Perez Riba M, Lis JT. Promoter melting and TFIID complexes on Drosophila genes in vivo. Genes Dev 1992; 6:2190-200.
19. O'Brien T, Lis JT. RNA polymerase II pauses at the 5′ end of the transcriptionally induced Drosophila hsp70 gene. Mol Cell Biol 1991; 11:5285-90.
20. Shopland LS, Hirayoshi K, Fernandes M, Lis JT. HSF access to heat shock elements in vivo depends critically on promoter architecture defined by GAGA factor, TFIID and RNA polymerase II binding sites. Genes Dev 1995; 9:2756-69.
21. Aiyar SE, Sun JL, Blair AL, Moskaluk CA, Lu YZ, Ye QN, Yamaguchi Y, Mukherjee A, Ren DM, Handa H, Li R. Attenuation of estrogen receptor alpha-mediated transcription through estrogen-stimulated recruitment of a negative elongation factor. Genes Dev 2004; 18:2134-46.
22. McChesney PA, Aiyar SE, Lee OJ, Zaika A, Moskaluk C, Li R, El-Rifai W. Cofactor of BRCA1: a novel transcription factor regulator in upper gastrointestinal adenocarcinomas. Cancer Res 2006; 66:1346-53.
23. Wang YV, Tang H, Gilmour DS. Identification in vivo of different rate-limiting steps associated with transcriptional activators in the presence and absence of a GAGA element. Mol Cell Biol 2005; 25:3543-52.
24. Adelman K, Marr MT, Werner J, Saunders A, Ni Z, Andrulis ED, Lis JT. Efficient release from promoter-proximal stall sites requires transcript cleavage factor TFIIS. Mol Cell 2005; 17:103-12.
25. Krumm A, Hickey LB, Groudine M. Promoter-proximal pausing of RNA polymerase II defines a general rate-limiting step after transcription initiation. Genes Dev 1995; 9:559-72.
26. Wu CH, Madabusi L, Nishioka H, Emanuel P, Sypes M, Arkhipova I, Gilmour DS. Analysis of core promoter sequences located downstream from the TATA element in the hsp70 promoter from Drosophila melanogaster. Mol Cell Biol 2001; 21:1593-602.
27. Tang H, Liu Y, Madabusi L, Gilmour DS. Promoter-proximal pausing on the hsp70 promoter in Drosophila melanogaster depends on the upstream regulator. Mol Cell Biol 2000; 20:2569-80.
28. Andrulis ED, Guzman E, Doring P, Werner J, Lis JT. High-resolution localization of Drosophila Spt5 and Spt6 at heat shock genes in vivo: roles in promoter proximal pausing and transcription elongation. Genes Dev 2000; 14:2635-49.
29. Kaplan CD, Morris JR, Wu C, Winston F. Spt5 and spt6 are associated with active transcription and have characteristics of general elongation factors in D. melanogaster. Genes Dev 2000; 14:2623-34.
30. Wu CH, Yamaguchi Y, Benjamin LR, Horvat-Gordon M, Washinsky J, Enerly E, Larsson J, Lambertsson A, Handa H, Gilmour D. NELF and DSIF cause promoter proximal pausing on the hsp70 promoter in Drosophila. Genes Dev 2003; 17:1402-14.
31. Cheng B, Price DH. Properties of RNA polymerase II elongation complexes before and after the P-TEFb-mediated transition into productive elongation. J Biol Chem 2007; 282:21901-12.
32. Yamaguchi Y, Inukai N, Narita T, Wada T, Handa H. Evidence that negative elongation factor represses transcription elongation through binding to a DRB sensitivity-inducing factor/RNA polymerase II complex and RNA. Mol Cell Biol 2002; 22:2918-27.
33. Yamaguchi Y, Wada T, Watanabe D, Takagi T, Hasegawa J, Handa H. Structure and function of the human transcription elongation factor DSIF. J Biol Chem 1999; 274:8085-92.
34. Pei Y, Schwer B, Shuman S. Interactions between Fission Yeast Cdk9, Its Cyclin Partner Pch1, and mRNA Capping Enzyme Pct1 Suggest an Elongation Checkpoint for mRNA Quality Control. J Biol Chem 2003; 278:7180-8.
35. Lee C, Li X, Hechmer A, Eisen M, Biggin MD, Venters BJ, Jiang C, Li J, Pugh BF, Gilmour DS. NELF and GAGA factor are linked to promoter proximal pausing at many genes in Drosophila. Mol Cell Biol 2008.
36. Lee H, Kraus KW, Wolfner MF, Lis JT. DNA sequence requirements for generating paused polymerase at the start of hsp70. Genes Dev 1992; 6:284-95.
37. Leibovitch BA, Lu Q, Benjamin LR, Liu Y, Gilmour DS, Elgin SC. GAGA factor and the TFIID complex collaborate in generating an open chromatin structure at the Drosophila melanogaster hsp26 promoter. Mol Cell Biol 2002; 22:6148-57.
38. Weber JA, Taxman DJ, Lu Q, Gilmour DS. Molecular architecture of the hsp70 promoter after deletion of the TATA box or the upstream regulation region. Mol Cell Biol 1997; 17:3799-808.
39. Tsukiyama T, Becker PB, Wu C. ATP-dependent nucleosome disruption at a heat-shock promoter mediated by binding of GAGA transcription factor. Nature 1994; 367:525-32.
40. Lis JT, Mason P, Peng J, Price DH, Werner J. P-TEFb kinase recruitment and function at heat shock loci. Genes Dev 2000; 14:792-803.
41. Peterlin BM, Price DH. Controlling the elongation phase of transcription with P-TEFb. Mol Cell 2006; 23:297-305.
42. Renner DB, Yamaguchi Y, Wada T, Handa H, Price DH. A highly purified RNA polymerase II elongation control system. J Biol Chem 2001; 276:42601-9.
43. Wada T, Takagi T, Yamaguchi Y, Watanabe D, Handa H. Evidence that P-TEFb alleviates the negative effect of DSIF on RNA polymerase II-dependent transcription in vitro. Embo J 1998; 17:7395-403.
44. Chao SH, Price DH. Flavopiridol inactivates P-TEFb and blocks most RNA polymerase II transcription in vivo. J Biol Chem 2001; 276:31793-9.
45. Saunders A, Core LJ, Lis JT. Breaking barriers to transcription elongation. Nat Rev Mol Cell Biol 2006; 7:557-67.
46. Hanyu Nakamura K, Sonobe Nojima H, Tanigawa A, Lasko P, Nakamura A. Drosophila Pgc protein inhibits P-TEFb recruitment to chromatin in primordial germ cells. Nature 2008.
47. Yang Z, Yik JH, Chen R, He N, Jang MK, Ozato K, Zhou Q. Recruitment of P-TEFb for stimulation of transcriptional elongation by the bromodomain protein Brd4. Mol Cell 2005; 19:535-45.