Skip to main content
NCBI home page
Molecular and Cellular Biology logoLink to Molecular and Cellular Biology
. 1995 May;15(5):2737–2744. doi: 10.1128/mcb.15.5.2737

Dynamic protein-DNA architecture of a yeast heat shock promoter.

C Giardina 1, J T Lis 1
PMCID: PMC230504  PMID: 7739554

Abstract

Here we present an in vivo footprinting analysis of the Saccharomyces cerevisiae HSP82 promoter. Consistent with current models, we find that yeast heat shock factor (HSF) binds to strong heat shock elements (HSEs) in non-heat-shocked cells. Upon heat shock, however, additional binding of HSF becomes apparent at weak HSEs of the promoter as well. Recovery from heat shock results in a dramatic reduction in HSF binding at both strong and weak HSEs, consistent with a model in which HSF binding is subject to a negative feedback regulation by heat shock proteins. In vivo KMnO4 footprinting reveals that the interaction of the TATA-binding protein (TBP) with this promoter is also modulated: heat shock slightly increases TBP binding to the promoter and this binding is reduced upon recovery from heat shock. KMnO4 footprinting does not reveal a high density of polymerase at the promoter prior to heat shock, but a large open complex between the transcriptional start site and the TATA box is formed rapidly upon activation, similar to that observed in other yeast genes.

Full Text

The Full Text of this article is available as a PDF (414.4 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Abravaya K., Myers M. P., Murphy S. P., Morimoto R. I. The human heat shock protein hsp70 interacts with HSF, the transcription factor that regulates heat shock gene expression. Genes Dev. 1992 Jul;6(7):1153–1164. doi: 10.1101/gad.6.7.1153. [DOI] [PubMed] [Google Scholar]
  2. Abravaya K., Phillips B., Morimoto R. I. Heat shock-induced interactions of heat shock transcription factor and the human hsp70 promoter examined by in vivo footprinting. Mol Cell Biol. 1991 Jan;11(1):586–592. doi: 10.1128/mcb.11.1.586. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Boorstein W. R., Craig E. A. Transcriptional regulation of SSA3, an HSP70 gene from Saccharomyces cerevisiae. Mol Cell Biol. 1990 Jun;10(6):3262–3267. doi: 10.1128/mcb.10.6.3262. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Duncan R., Bazar L., Michelotti G., Tomonaga T., Krutzsch H., Avigan M., Levens D. A sequence-specific, single-strand binding protein activates the far upstream element of c-myc and defines a new DNA-binding motif. Genes Dev. 1994 Feb 15;8(4):465–480. doi: 10.1101/gad.8.4.465. [DOI] [PubMed] [Google Scholar]
  5. Farrelly F. W., Finkelstein D. B. Complete sequence of the heat shock-inducible HSP90 gene of Saccharomyces cerevisiae. J Biol Chem. 1984 May 10;259(9):5745–5751. [PubMed] [Google Scholar]
  6. Fernandes M., Xiao H., Lis J. T. Fine structure analyses of the Drosophila and Saccharomyces heat shock factor--heat shock element interactions. Nucleic Acids Res. 1994 Jan 25;22(2):167–173. doi: 10.1093/nar/22.2.167. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Giardina C., Lis J. T. DNA melting on yeast RNA polymerase II promoters. Science. 1993 Aug 6;261(5122):759–762. doi: 10.1126/science.8342041. [DOI] [PubMed] [Google Scholar]
  8. Giardina C., Pérez-Riba M., Lis J. T. Promoter melting and TFIID complexes on Drosophila genes in vivo. Genes Dev. 1992 Nov;6(11):2190–2200. doi: 10.1101/gad.6.11.2190. [DOI] [PubMed] [Google Scholar]
  9. Gilmour D. S., Lis J. T. RNA polymerase II interacts with the promoter region of the noninduced hsp70 gene in Drosophila melanogaster cells. Mol Cell Biol. 1986 Nov;6(11):3984–3989. doi: 10.1128/mcb.6.11.3984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Gilmour D. S., Thomas G. H., Elgin S. C. Drosophila nuclear proteins bind to regions of alternating C and T residues in gene promoters. Science. 1989 Sep 29;245(4925):1487–1490. doi: 10.1126/science.2781290. [DOI] [PubMed] [Google Scholar]
  11. Gilson E., Roberge M., Giraldo R., Rhodes D., Gasser S. M. Distortion of the DNA double helix by RAP1 at silencers and multiple telomeric binding sites. J Mol Biol. 1993 May 20;231(2):293–310. doi: 10.1006/jmbi.1993.1283. [DOI] [PubMed] [Google Scholar]
  12. Gross D. S., Adams C. C., Lee S., Stentz B. A critical role for heat shock transcription factor in establishing a nucleosome-free region over the TATA-initiation site of the yeast HSP82 heat shock gene. EMBO J. 1993 Oct;12(10):3931–3945. doi: 10.1002/j.1460-2075.1993.tb06071.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Gross D. S., English K. E., Collins K. W., Lee S. W. Genomic footprinting of the yeast HSP82 promoter reveals marked distortion of the DNA helix and constitutive occupancy of heat shock and TATA elements. J Mol Biol. 1990 Dec 5;216(3):611–631. doi: 10.1016/0022-2836(90)90387-2. [DOI] [PubMed] [Google Scholar]
  14. Høj A., Jakobsen B. K. A short element required for turning off heat shock transcription factor: evidence that phosphorylation enhances deactivation. EMBO J. 1994 Jun 1;13(11):2617–2624. doi: 10.1002/j.1460-2075.1994.tb06552.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Ingles C. J., Shales M., Cress W. D., Triezenberg S. J., Greenblatt J. Reduced binding of TFIID to transcriptionally compromised mutants of VP16. Nature. 1991 Jun 13;351(6327):588–590. doi: 10.1038/351588a0. [DOI] [PubMed] [Google Scholar]
  16. Jakobsen B. K., Pelham H. R. Constitutive binding of yeast heat shock factor to DNA in vivo. Mol Cell Biol. 1988 Nov;8(11):5040–5042. doi: 10.1128/mcb.8.11.5040. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Jurivich D. A., Sistonen L., Kroes R. A., Morimoto R. I. Effect of sodium salicylate on the human heat shock response. Science. 1992 Mar 6;255(5049):1243–1245. doi: 10.1126/science.1546322. [DOI] [PubMed] [Google Scholar]
  18. Kainz M., Roberts J. Structure of transcription elongation complexes in vivo. Science. 1992 Feb 14;255(5046):838–841. doi: 10.1126/science.1536008. [DOI] [PubMed] [Google Scholar]
  19. Kim J. L., Nikolov D. B., Burley S. K. Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature. 1993 Oct 7;365(6446):520–527. doi: 10.1038/365520a0. [DOI] [PubMed] [Google Scholar]
  20. Kim Y., Geiger J. H., Hahn S., Sigler P. B. Crystal structure of a yeast TBP/TATA-box complex. Nature. 1993 Oct 7;365(6446):512–520. doi: 10.1038/365512a0. [DOI] [PubMed] [Google Scholar]
  21. Lee D. K., Horikoshi M., Roeder R. G. Interaction of TFIID in the minor groove of the TATA element. Cell. 1991 Dec 20;67(6):1241–1250. doi: 10.1016/0092-8674(91)90300-n. [DOI] [PubMed] [Google Scholar]
  22. Lee M. S., Garrard W. T. Transcription-induced nucleosome 'splitting': an underlying structure for DNase I sensitive chromatin. EMBO J. 1991 Mar;10(3):607–615. doi: 10.1002/j.1460-2075.1991.tb07988.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Lee M. S., Garrard W. T. Uncoupling gene activity from chromatin structure: promoter mutations can inactivate transcription of the yeast HSP82 gene without eliminating nucleosome-free regions. Proc Natl Acad Sci U S A. 1992 Oct 1;89(19):9166–9170. doi: 10.1073/pnas.89.19.9166. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Lin Y. S., Green M. R. Mechanism of action of an acidic transcriptional activator in vitro. Cell. 1991 Mar 8;64(5):971–981. doi: 10.1016/0092-8674(91)90321-o. [DOI] [PubMed] [Google Scholar]
  25. Lu Q., Wallrath L. L., Allan B. D., Glaser R. L., Lis J. T., Elgin S. C. Promoter sequence containing (CT)n.(GA)n repeats is critical for the formation of the DNase I hypersensitive sites in the Drosophila hsp26 gene. J Mol Biol. 1992 Jun 20;225(4):985–998. doi: 10.1016/0022-2836(92)90099-6. [DOI] [PubMed] [Google Scholar]
  26. O'Brien T., Lis J. T. RNA polymerase II pauses at the 5' end of the transcriptionally induced Drosophila hsp70 gene. Mol Cell Biol. 1991 Oct;11(10):5285–5290. doi: 10.1128/mcb.11.10.5285. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. O'Brien T., Lis J. T. Rapid changes in Drosophila transcription after an instantaneous heat shock. Mol Cell Biol. 1993 Jun;13(6):3456–3463. doi: 10.1128/mcb.13.6.3456. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Pelham H. R. A regulatory upstream promoter element in the Drosophila hsp 70 heat-shock gene. Cell. 1982 Sep;30(2):517–528. doi: 10.1016/0092-8674(82)90249-5. [DOI] [PubMed] [Google Scholar]
  29. Perisic O., Xiao H., Lis J. T. Stable binding of Drosophila heat shock factor to head-to-head and tail-to-tail repeats of a conserved 5 bp recognition unit. Cell. 1989 Dec 1;59(5):797–806. doi: 10.1016/0092-8674(89)90603-x. [DOI] [PubMed] [Google Scholar]
  30. Rabindran S. K., Wisniewski J., Li L., Li G. C., Wu C. Interaction between heat shock factor and hsp70 is insufficient to suppress induction of DNA-binding activity in vivo. Mol Cell Biol. 1994 Oct;14(10):6552–6560. doi: 10.1128/mcb.14.10.6552. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Rasmussen E. B., Lis J. T. In vivo transcriptional pausing and cap formation on three Drosophila heat shock genes. Proc Natl Acad Sci U S A. 1993 Sep 1;90(17):7923–7927. doi: 10.1073/pnas.90.17.7923. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Rougvie A. E., Lis J. T. Postinitiation transcriptional control in Drosophila melanogaster. Mol Cell Biol. 1990 Nov;10(11):6041–6045. doi: 10.1128/mcb.10.11.6041. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. 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. 1988 Sep 9;54(6):795–804. doi: 10.1016/s0092-8674(88)91087-2. [DOI] [PubMed] [Google Scholar]
  34. Rubin C. M., Schmid C. W. Pyrimidine-specific chemical reactions useful for DNA sequencing. Nucleic Acids Res. 1980 Oct 24;8(20):4613–4619. doi: 10.1093/nar/8.20.4613. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Sorger P. K., Lewis M. J., Pelham H. R. Heat shock factor is regulated differently in yeast and HeLa cells. Nature. 1987 Sep 3;329(6134):81–84. doi: 10.1038/329081a0. [DOI] [PubMed] [Google Scholar]
  36. Sorger P. K., Pelham H. R. Purification and characterization of a heat-shock element binding protein from yeast. EMBO J. 1987 Oct;6(10):3035–3041. doi: 10.1002/j.1460-2075.1987.tb02609.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Starr D. B., Hawley D. K. TFIID binds in the minor groove of the TATA box. Cell. 1991 Dec 20;67(6):1231–1240. doi: 10.1016/0092-8674(91)90299-e. [DOI] [PubMed] [Google Scholar]
  38. Thomas G. H., Elgin S. C. Protein/DNA architecture of the DNase I hypersensitive region of the Drosophila hsp26 promoter. EMBO J. 1988 Jul;7(7):2191–2201. doi: 10.1002/j.1460-2075.1988.tb03058.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Tsukiyama T., Becker P. B., Wu C. ATP-dependent nucleosome disruption at a heat-shock promoter mediated by binding of GAGA transcription factor. Nature. 1994 Feb 10;367(6463):525–532. doi: 10.1038/367525a0. [DOI] [PubMed] [Google Scholar]
  40. Westwood J. T., Clos J., Wu C. Stress-induced oligomerization and chromosomal relocalization of heat-shock factor. Nature. 1991 Oct 31;353(6347):822–827. doi: 10.1038/353822a0. [DOI] [PubMed] [Google Scholar]
  41. Wu C. An exonuclease protection assay reveals heat-shock element and TATA box DNA-binding proteins in crude nuclear extracts. Nature. 1985 Sep 5;317(6032):84–87. doi: 10.1038/317084a0. [DOI] [PubMed] [Google Scholar]
  42. Wu C. Two protein-binding sites in chromatin implicated in the activation of heat-shock genes. Nature. 1984 May 17;309(5965):229–234. doi: 10.1038/309229a0. [DOI] [PubMed] [Google Scholar]
  43. Wu C., Wilson S., Walker B., Dawid I., Paisley T., Zimarino V., Ueda H. Purification and properties of Drosophila heat shock activator protein. Science. 1987 Nov 27;238(4831):1247–1253. doi: 10.1126/science.3685975. [DOI] [PubMed] [Google Scholar]
  44. Xiao H., Friesen J. D., Lis J. T. A highly conserved domain of RNA polymerase II shares a functional element with acidic activation domains of upstream transcription factors. Mol Cell Biol. 1994 Nov;14(11):7507–7516. doi: 10.1128/mcb.14.11.7507. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Xiao H., Lis J. T. Germline transformation used to define key features of heat-shock response elements. Science. 1988 Mar 4;239(4844):1139–1142. doi: 10.1126/science.3125608. [DOI] [PubMed] [Google Scholar]
  46. Xiao H., Lis J. T., Xiao H., Greenblatt J., Friesen J. D. The upstream activator CTF/NF1 and RNA polymerase II share a common element involved in transcriptional activation. Nucleic Acids Res. 1994 Jun 11;22(11):1966–1973. doi: 10.1093/nar/22.11.1966. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Xiao H., Perisic O., Lis J. T. Cooperative binding of Drosophila heat shock factor to arrays of a conserved 5 bp unit. Cell. 1991 Feb 8;64(3):585–593. doi: 10.1016/0092-8674(91)90242-q. [DOI] [PubMed] [Google Scholar]
  48. de Banzie J. S., Sinclair L., Lis J. T. Expression of the major heat shock gene of Drosophila melanogaster in Saccharomyces cerevisiae. Nucleic Acids Res. 1986 Apr 25;14(8):3587–3601. doi: 10.1093/nar/14.8.3587. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Molecular and Cellular Biology are provided here courtesy of Taylor & Francis

RESOURCES