Promoter-associated pausing in promoter architecture and postinitiation transcriptional regulation

Cold Spring Harbor Symposia on Quantitative Biology

Volumn 63, Issue , 1998, Pages 347-356

  Lis, J ^a  

^a Department of Obstetrics Gynecology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONFERENCE PAPER; DNA SEQUENCE; DROSOPHILA; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; PROTEIN CROSS LINKING; PROTEIN PROTEIN INTERACTION; RNA TRANSLATION; TRANSCRIPTION REGULATION; CHROMATIN STRUCTURE; ELECTRON MICROSCOPY; EUKARYOTIC CELL; GENE EXPRESSION; IMMUNOFLUORESCENCE; POLYMERASE CHAIN REACTION; PROTEIN MODIFICATION; TRANSCRIPTION INITIATION; TRANSCRIPTION TERMINATION;

DNA BINDING PROTEIN; HEAT SHOCK PROTEIN 70; MESSENGER RNA; MYC PROTEIN; PROTEIN C FOS; RNA POLYMERASE II; TATA BINDING PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR IID;

EID: 0032459466     PISSN: 00917451     EISSN: None     Source Type: Book Series    
DOI: 10.1101/sqb.1998.63.347     Document Type: Conference Paper

References (59)

1. Albert T., Mautner J., Funk J.O., Hoertnagel K., Pullner A., and Eick D. 1997. Nucleosomal structures of c-myc promoters with transcriptionally engaged RNA polymerase II. Mol. Cell. Biol. 17: 4363.
2. Benjamin L.R. and Gilmour D.S. 1998. Nucleosomes are not necessary for promoter-proximal pausing in vitro on the Drosophila hsp70 promoter. Nucleic Acids Res. 26: 1051.
3. Blau J., Xiao H., McCracken S., O'Hare P., Greenblatt J., and Bentley D. 1996. Three functional classes of transcriptional activation domains. Mol. Cell. Biol. 16: 2044.
4. Brown S.A. and Kingston R.E. 1997. Disruption of downstream chromatin directed by a transcriptional activator. Genes Dev. 11:3116.
5. Buratowski S., Hahn S., Guarente L., and Sharp P.A. 1989. Five intermediate complexes in transcription initiation by RNA polymerase II. Cell 56: 549.
6. II60 of Drosophila. Genes Dev. 11: 3020.
7. Cismowski M.J., Laff G.M., Solomon M.J., and Reed S.I. 1995. KIN28 encodes a C-terminal domain kinase that controls mRNA transcription in Saccharomyces cerevisiae but lacks cyclin-dependent kinase-activating kinase (CAK) activity. Mol. Cell. Biol. 15: 2983.
8. Cullen B.R. 1993. Does HIV-1 Tat induce a change in viral initiation rights? Cell 73: 417.
9. Dahmus M.E. 1994. The role of multisite phosphorylation in the regulation of RNA polymerase II activity. Prog. Nucleic Acid Res. Mol. Biol. 48: 143.
10. Dubois M.F., Vincent M., Vigneron M., Adamczewski J., Egly J.M., and Bensaude O. 1997. Heat-shock inactivation of the TFIIH-associated kinase and change in the phosphorylation sites on the C-terminal domain of RNA polymerase II. Nucleic Acids Res. 25: 694.
11. Giardina C. and Lis J.T. 1993. DNA melting on yeast RNA polymerase II promoters. Science 261: 759.
12. _. 1995. Dynamic protein-DNA architecture of a yeast heat shock promoter. Mol. Cell. Biol. 15: 2737.
13. Giardina C., Perez Riba M., and Lis J.T. 1992. Promoter melting and TFIID complexes on Drosophila genes in vivo. Genes Dev. 6: 2190.
14. Gilmour D.S. and Lis J.T. 1985. In vivo interactions of RNA polymerase II with genes of Drosophila melanogaster. Mol. Cell. Biol. 5: 2009.
15. _. 1986. RNA polymerase II interacts with the promoter region of the noninduced hsp-70 gene in Drosophila melanogaster cells. Mol. Cell. Biol. 6: 3984.
16. n repeats. J. Mol. Biol. 211: 751.
17. Goodrich J.A. and Tjian R. 1994. Transcription factors IIE and IIH and ATP hydrolysis direct promoter clearance by RNA polymerase II. Cell 77: 145.
18. Grant P.A., Duggan L., Cote J., Roberts S.M., Brownell I.E., Candau R., Ohba R., Owen-Hughes T., Allis C.D., Winston F., Berger S.L., and Workman J.L. 1997. Yeast Gcn5 functions in two multisubunit complexes to acetylate nucleosomal histones: Characterization of an Ada complex and the SAGA (Spt/Ada) complex. Genes Dev. 11: 1640.
19. Hagler J. and Shuman S. 1992. A freeze-frame view of eukaryotic transcription during elongation and capping of nascent mRNA. Science 255: 983.
20. Hansen S.K., Takada S., Jacobson R.H., Lis J.T., and Tjian R. 1997. Transcription properties of a cell type-specific TATA-binding protein, TRF. Cell 91: 71.
21. Holstege F.C.P., Fiedler U., and Timmers H.T.M. 1997. Three transitions in the RNA polymerase II transcription complex during initiation. EMBO J. 16: 7468.
22. Kim Y.-J., Bjorklund S., Li Y., Sayre M.H., and Kornberg R.D. 1994. A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II. Cell 77: 599.
23. Krumm A., Hickey L.B., and Groudine M. 1995. Promoter-proximal pausing of RNA polymerase II defines a general rate-limiting step after transcription initiation. Genes Dev. 9: 559.
24. Krumm A., Meulia T., and Groudine M. 1993. Common mechanisms for the control of eukaryotic transcriptional elongation. BioEssays 15: 659.
25. Krumm A., Meulia T., Brunvand M., and Groudine M. 1992. The block to transcriptional elongation within the human c-myc gene is determined in the promoter-proximal region. Genes Dev. 6: 2201.
26. Lee H.S., Kraus K.W., Wolfner M.F., and Lis J.T. 1992. DNA sequence requirements for generating paused polymerase at the start of Hsp70. Genes Dev. 6: 284.
27. Leuther K.K., Bushnell D.A., and Kornberg R.D. 1996. Two-dimensional crystallography of TFIIB- and IIE-RNA polymerase II complexes: Implications for start site selection and initiation complex formation. Cell 85: 773.
28. Li B., Weber J.A., Chen Y., Greenleaf A.L., and Gilmour D.S. 1996. Analyses of promoter-proximal pausing by RNA polymerse II on the hsp70 heat shock gene promoter in a Drosophila nuclear extract. Mol. Cell. Biol. 16: 5433.
29. Lis J. and Wu C. 1995. Promoter potentiation and activation: Chromatin structure and transcriptional induction of heat shock genes. In Chromatin structure and gene expression (ed. S.C.R. Elgin), p. 71. IRL Press, Oxford, United Kingdom.
30. Lis J.T., Simon J., and Sutton C. 1983. New heat shock puffs and β-galactosidase activity resulting from transformation of Drosophila with and hsp70-lacZ hybrid gene. Cell 35: 403.
31. Lis J.T., Neckameyer W., Dubensky R., and Costlow N. 1981. Cloning and characterization of nine heat-shock-induced mRNAs of Drosophila melanogaster. Gene 15: 67.
32. Lu H., Flores O., Weinmann R., and Reinberg D. 1991. The non-phosphorylated form of RNA polymerase II preferentially associates with the preinitiation complex. Proc. Natl. Acad. Sci. 88: 10004.
33. n repeats is critical for the formation of the DNase I hypersensitive sites in the Drosophila hsp26 gene. J. Mol. Biol. 225: 985.
34. Mason P.B., Jr. and Lis J.T. 1997. Cooperative and competitive protein interactions at the hsp70 promoter. J. Biol. Chem. 272: 33227.
35. O'Brien T. and Lis J.T. 1991. RNA polymerase II pauses at the 5′ end of the transcriptionally induced Drosophila hsp70 gene. Mol. Cell. Biol. 11: 5285.
36. _. 1993. Rapid changes in Drosophila transcription after an instantaneous heat shock. Mol. Cell. Biol. 13: 3456.
37. O'Brien T., Hardin S., Greenleaf A., and Lis J.T. 1994. Phosphorylation of RNA polymerase II C-terminal domain and transcriptional elongation. Nature 370: 75.
38. O'Brien T., Wilkins R.C., Giardina C., and Lis J.T. 1995. Distribution of GAGA protein on Drosophila genes in vivo. Genes Dev. 9: 1098.
39. Orphanides G., Lagrange T., and Reinberg D. 1996. The general transcription factors of RNA polymerase II. Genes Dev. 10: 2657.
40. Plet A., Eick D., and Blanchard J.M. 1995. Elongation and premature termination of transcripts initiated from c-fos and c-myc promoters show dissimilar patterns. Oncogene 10: 319.
41. Ptashne M. and Gann A. 1997. Transcriptional activation by recruitment. Nature 386: 569.
42. Purnell B.A., Emanuel P.A., and Gilmour D.S. 1994. TFIID sequence recognition of the initiator and sequences farther downstream in Drosophila class II genes. Genes Dev. 8: 830.
43. Rasmussen E.B. and Lis J.T. 1993. In vivo transcriptional pausing and cap formation on three Drosophila heat shock genes. Proc. Natl. Acad. Sci. 90: 7923.
44. _. 1995. Short transcripts of the ternary complex provide insight into RNA polymerase II elongational pausing. J. Mol. Biol. 252: 522.
45. Rougvie A.E. and Lis J.T. 1988. The RNA polymerase II molecule at the 5′ end of the uninduced hsp70 gene of Drosophila melanogaster is transcriptionally engaged. Cell 54: 795.
46. _. 1990. Postinitiation transcriptional control in Drosophila melanogaster. Mol. Cell. Biol. 10: 6041.
47. Shopland L.S., Hirayoshi K., Fernandes M., and Lis J.T. 1995. 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. 9: 2756.
48. Stewart A.F., Herrera R.E., and Nordheim A. 1990. Rapid induction of c-fos transcription reveals quantitative linkage of RNA polymerase II and DNA topoisomerase I enzyme activities. Cell 60: 141.
49. Strobl L.J. and Eick D. 1992. Hold back of RNA polymerase II at the transcription start site mediates down-regulation of c-mycin vivo. EMBO J. 11: 3307.
50. Taylor I.C.A., Workman J.L., Schuetz T.J., and Kingston R.E. 1991. Facilitated binding of GAL4 and heat shock factor to nucleosomal templates: Differential function of DNA-binding domains. Genes Dev. 5: 1285.
51. Thompson C.M., Koleske A.J., Chao D.M., and Young R.A. 1993. A multisubunit complex associated with the RNA polymerase II CTD and TATA-binding protein in yeast. Cell 73: 1361.
52. Valay J.G., Simon M., Dubois M.F., Bensaude O., Facca C., and Faye G. 1995. The KIN28 gene is required both for RNA polymerase II mediated transcription and phosphorylation of the Rpblp CTD. J. Mol. Biol. 249: 535.
53. Weeks J.R., Hardin S.E., Shen J., Lee J.M., and Greenleaf A.L. 1993. Locus-specific variation in phosphorylation state of RNA polymerase II in vivo: Correlations with gene activity and transcript processing. Genes Dev. 7: 2329.
54. Westwood J.T., Clos J., and Wu C. 1991. Stress-induced oligomerization and chromosomal relocalization of heat-shock factor. Nature 353: 822.
55. Wilkins R.C. and Lis J.T. 1997. Dynamics of potentiation and activation: GAGA factor and its role in heat shock gene regulation. Nucleic Acids Res. 25: 3963.
56. Wu C. 1980. The 5′ end of Drosophila heat shock genes in chromatin are hypersensitive to DNase I. Nature 286: 854.
57. _. 1997. Chromatin remodeling and the control of gene expression. J. Biol. Chem. 272: 28171.
58. Xiao H. and Lis J.T. 1988. Germline transformation used to define key features of heat-shock response elements. Science 239: 1139.
59. Xiao H., Friesen J.D., and Lis J.T. 1994. A highly conserved domain of RNA polymerase II shares a functional element with acidic activation domains of upstream transcription factors. Mol. Cell. Biol. 14: 7507.