The Chromatin Structure at the Promoter of a Glyceraldehyde Phosphate Dehydrogenase Gene from Saccharomyces Cerevisiae Reflects Its Functional State

Overview

Journal Mol Cell Biol

Specialty Cell Biology

Date 1988 Dec 1

PMID 2854200

Citations 22

Authors

B Pavlovic

W Horz

Affiliations

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Abstract

The chromatin structure of TDH3, one of three genes encoding glyceraldehyde phosphate dehydrogenases in Saccharomyces cerevisiae, was analyzed by nuclease digestion. A large hypersensitive region was found at the TDH3 promoter extending from the RNA initiation site at position -40 to position -560. This hypersensitive domain is nucleosome free and includes all putative cis-acting regulatory DNA elements. It is equally present in cells grown on fermentable as well as nonfermentable carbon sources. In a mutant which lacks the trans-activating protein GCR1 and which as a consequence expresses TDH3 at less than 5% of the wild-type level, the chromatin structure is different. Hypersensitivity between -40 and -370 is lost, due to the deposition of nucleosomes on a stretch that is nucleosome free in wild-type cells. Hypersensitivity is retained, however, further upstream (from -370 to -560). A similarly altered chromatin structure, as in a ger1 mutant, is found in wild-type cells when they approach stationary phase. This is the first evidence for a growth-dependent regulation of the TDH3 promoter.

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References

Wintersberger U, Smith P, Letnansky K . Yeast chromatin. Preparation from isolated nuclei, histone composition and transcription capacity. Eur J Biochem. 1973; 33(1):123-30. DOI: 10.1111/j.1432-1033.1973.tb02663.x. View

Matsumoto K, Uno I, Ishikawa T . Genetic analysis of the role of cAMP in yeast. Yeast. 1985; 1(1):15-24. DOI: 10.1002/yea.320010103. View

Holland M, Holland J . Isolation and characterization of a gene coding for glyceraldehyde-3-phosphate dehydrogenase from Saccharomyces cerevisiae. J Biol Chem. 1979; 254(12):5466-74. View

Holland J, Holland M . The primary structure of a glyceraldehyde-3-phosphate dehydrogenase gene from Saccharomyces cerevisiae. J Biol Chem. 1979; 254(19):9839-45. View

Nedospasov S, Georgiev G . Non-random cleavage of SV40 DNA in the compact minichromosome and free in solution by micrococcal nuclease. Biochem Biophys Res Commun. 1980; 92(2):532-9. DOI: 10.1016/0006-291x(80)90366-6. View

Holland J, Holland M . Structural comparison of two nontandemly repeated yeast glyceraldehyde-3-phosphate dehydrogenase genes. J Biol Chem. 1980; 255(6):2596-605. View

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

Clifton D, FRAENKEL D . The gcr (glycolysis regulation) mutation of Saccharomyces cerevisiae. J Biol Chem. 1981; 256(24):13074-8. View

Kunkel G, Martinson H . Nucleosomes will not form on double-stranded RNa or over poly(dA).poly(dT) tracts in recombinant DNA. Nucleic Acids Res. 1981; 9(24):6869-88. PMC: 327648. DOI: 10.1093/nar/9.24.6869. View

10.

Holland J, Labieniec L, Swimmer C, Holland M . Homologous nucleotide sequences at the 5' termini of messenger RNAs synthesized from the yeast enolase and glyceraldehyde-3-phosphate dehydrogenase gene families. The primary structure of a third yeast glyceraldehyde-3-phosphate dehydrogenase gene. J Biol Chem. 1983; 258(8):5291-9. View

11.

Musti A, Zehner Z, Bostian K, Paterson B, Kramer R . Transcriptional mapping of two yeast genes coding for glyceraldehyde 3-phosphate dehydrogenase isolated by sequence homology with the chicken gene. Gene. 1983; 25(1):133-43. DOI: 10.1016/0378-1119(83)90175-0. View

12.

Guarente L . Yeast promoters: positive and negative elements. Cell. 1984; 36(4):799-800. DOI: 10.1016/0092-8674(84)90028-x. View

13.

PRUNELL A . Nucleosome reconstitution on plasmid-inserted poly(dA) . poly(dT). EMBO J. 1982; 1(2):173-9. PMC: 553016. DOI: 10.1002/j.1460-2075.1982.tb01143.x. View

14.

Boucherie H . Protein synthesis during transition and stationary phases under glucose limitation in Saccharomyces cerevisiae. J Bacteriol. 1985; 161(1):385-92. PMC: 214883. DOI: 10.1128/jb.161.1.385-392.1985. View

15.

Bitter G, Egan K . Expression of heterologous genes in Saccharomyces cerevisiae from vectors utilizing the glyceraldehyde-3-phosphate dehydrogenase gene promoter. Gene. 1984; 32(3):263-74. DOI: 10.1016/0378-1119(84)90002-7. View

16.

Kaback D, Feldberg L . Saccharomyces cerevisiae exhibits a sporulation-specific temporal pattern of transcript accumulation. Mol Cell Biol. 1985; 5(4):751-61. PMC: 366779. DOI: 10.1128/mcb.5.4.751-761.1985. View

17.

Weintraub H . Assembly and propagation of repressed and depressed chromosomal states. Cell. 1985; 42(3):705-11. DOI: 10.1016/0092-8674(85)90267-3. View

18.

Rudolph H, Hinnen A . One-step gene replacement in yeast by cotransformation. Gene. 1985; 36(1-2):87-95. DOI: 10.1016/0378-1119(85)90072-1. View

19.

McAlister L, Holland M . Differential expression of the three yeast glyceraldehyde-3-phosphate dehydrogenase genes. J Biol Chem. 1985; 260(28):15019-27. View

20.

Struhl K . Naturally occurring poly(dA-dT) sequences are upstream promoter elements for constitutive transcription in yeast. Proc Natl Acad Sci U S A. 1985; 82(24):8419-23. PMC: 390927. DOI: 10.1073/pnas.82.24.8419. View