Uncoupling Gene Activity from Chromatin Structure: Promoter Mutations Can Inactivate Transcription of the Yeast HSP82 Gene Without Eliminating Nucleosome-free Regions

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 1992 Oct 1

PMID 1409619

Citations 19

Authors

M S Lee

W T Garrard

Affiliations

Soon will be listed here.

Abstract

DNase I-hypersensitive sites represent "nucleosome-free" regions in chromatin where the underlying DNA sequence is highly accessible to trans-acting proteins. Here we demonstrate that it is possible to uncouple gene activity from hypersensitive site formation. Point or substitution mutations were introduced into the promoter of the yeast chromosomal HSP82 gene, encoding the 83-kDa heat shock protein (HSP), via site-directed integration. Mutating either the TATA box or heat shock element 1 (HSE1) significantly reduced basal and heat-induced transcription while mutating both essentially inactivated expression. Dormant transcription units exhibited arrays of sequence-positioned nucleosomes; nevertheless, the inactivated genes still retained a hypersensitive site within their mutated promoters. In addition, all yeast strains maintained a heat-inducible hypersensitive site at -600 base pairs (bp), while several mutant strains converted a constitutive hypersensitive site at -300 bp into a heat-inducible one. Thus, mutations in cis-acting elements within a promoter can inactivate transcription without eliminating nucleosome-free regions.

Citing Articles

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Preferential accessibility of the yeast his3 promoter is determined by a general property of the DNA sequence, not by specific elements.

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References

Roeder R . The complexities of eukaryotic transcription initiation: regulation of preinitiation complex assembly. Trends Biochem Sci. 1991; 16(11):402-8. DOI: 10.1016/0968-0004(91)90164-q. View

Finkelstein D, Strausberg S . Heat shock-regulated production of Escherichia coli beta-galactosidase in Saccharomyces cerevisiae. Mol Cell Biol. 1983; 3(9):1625-33. PMC: 370016. DOI: 10.1128/mcb.3.9.1625-1633.1983. View

Chasman D, Lue N, Buchman A, LaPointe J, Lorch Y, Kornberg R . A yeast protein that influences the chromatin structure of UASG and functions as a powerful auxiliary gene activator. Genes Dev. 1990; 4(4):503-14. DOI: 10.1101/gad.4.4.503. View

Zimarino V, Tsai C, Wu C . Complex modes of heat shock factor activation. Mol Cell Biol. 1990; 10(2):752-9. PMC: 360875. DOI: 10.1128/mcb.10.2.752-759.1990. View

Lue N, Buchman A, Kornberg R . Activation of yeast RNA polymerase II transcription by a thymidine-rich upstream element in vitro. Proc Natl Acad Sci U S A. 1989; 86(2):486-90. PMC: 286495. DOI: 10.1073/pnas.86.2.486. View

Winter E, Varshavsky A . A DNA binding protein that recognizes oligo(dA).oligo(dT) tracts. EMBO J. 1989; 8(6):1867-77. PMC: 401036. DOI: 10.1002/j.1460-2075.1989.tb03583.x. View

McDaniel D, Caplan A, Lee M, Adams C, Fishel B, Gross D . Basal-level expression of the yeast HSP82 gene requires a heat shock regulatory element. Mol Cell Biol. 1989; 9(11):4789-98. PMC: 363627. DOI: 10.1128/mcb.9.11.4789-4798.1989. View

Pavlovic B, Horz W . The chromatin structure at the promoter of a glyceraldehyde phosphate dehydrogenase gene from Saccharomyces cerevisiae reflects its functional state. Mol Cell Biol. 1988; 8(12):5513-20. PMC: 365655. DOI: 10.1128/mcb.8.12.5513-5520.1988. View

Wiederrecht G, Seto D, Parker C . Isolation of the gene encoding the S. cerevisiae heat shock transcription factor. Cell. 1988; 54(6):841-53. DOI: 10.1016/s0092-8674(88)91197-x. View

10.

Gross D, Garrard W . Nuclease hypersensitive sites in chromatin. Annu Rev Biochem. 1988; 57:159-97. DOI: 10.1146/annurev.bi.57.070188.001111. View

11.

Jakobsen B, Pelham H . Constitutive binding of yeast heat shock factor to DNA in vivo. Mol Cell Biol. 1988; 8(11):5040-2. PMC: 365598. DOI: 10.1128/mcb.8.11.5040-5042.1988. View

12.

Xiao H, Lis J . Germline transformation used to define key features of heat-shock response elements. Science. 1988; 239(4844):1139-42. DOI: 10.1126/science.3125608. View

13.

Buchman A, Kimmerly W, Rine J, Kornberg R . Two DNA-binding factors recognize specific sequences at silencers, upstream activating sequences, autonomously replicating sequences, and telomeres in Saccharomyces cerevisiae. Mol Cell Biol. 1988; 8(1):210-25. PMC: 363104. DOI: 10.1128/mcb.8.1.210-225.1988. View

14.

Finkelstein D, Garrard W . Sharp boundaries demarcate the chromatin structure of a yeast heat-shock gene. J Mol Biol. 1987; 193(1):71-80. DOI: 10.1016/0022-2836(87)90628-0. View

15.

Sorger P, Lewis M, Pelham H . Heat shock factor is regulated differently in yeast and HeLa cells. Nature. 1987; 329(6134):81-4. DOI: 10.1038/329081a0. View

16.

Shore D, Nasmyth K . Purification and cloning of a DNA binding protein from yeast that binds to both silencer and activator elements. Cell. 1987; 51(5):721-32. DOI: 10.1016/0092-8674(87)90095-x. View

17.

Thoma F . Protein-DNA interactions and nuclease-sensitive regions determine nucleosome positions on yeast plasmid chromatin. J Mol Biol. 1986; 190(2):177-90. DOI: 10.1016/0022-2836(86)90291-3. View

18.

Lohr D, Hopper J . The relationship of regulatory proteins and DNase I hypersensitive sites in the yeast GAL1-10 genes. Nucleic Acids Res. 1985; 13(23):8409-23. PMC: 322142. DOI: 10.1093/nar/13.23.8409. View

19.

DOUGLAS H, Hawthorne D . Regulation of genes controlling synthesis of the galactose pathway enzymes in yeast. Genetics. 1966; 54(3):911-6. PMC: 1211212. DOI: 10.1093/genetics/54.3.911. View

20.

Wu C . The 5' ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I. Nature. 1980; 286(5776):854-60. DOI: 10.1038/286854a0. View