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PMID: 10958664 Published · ppublish English Journal Article Research Support, U.S. Gov't, P.H.S.

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

Molecular and cellular biology ·Vol. 20 ·No. 18 ·2000-09-00 ·Pages 6668-76

Mai X, Chou S, Struhl K

Abstract

Yeast promoter regions are often more accessible to nuclear proteins than are nonpromoter regions. As assayed by HinfI endonuclease cleavage in living yeast cells, HinfI sites located in the promoters of all seven genes tested were 5- to 20-fold more accessible than sites in adjacent nonpromoter regions. HinfI hypersensitivity within the his3 promoter region is locally determined, since it was observed when this region was translocated to the middle of the ade2 structural gene. Detailed analysis of the his3 promoter indicated that preferential accessibility is not determined by specific elements such as the Gcn4 binding site, poly(dA-dT) sequences, TATA elements, or initiator elements or by transcriptional activity. However, progressive deletion of the promoter region in either direction resulted in a progressive loss of HinfI accessibility. Preferential accessibility is independent of the Swi-Snf chromatin remodeling complex, Gcn5 histone acetylase complexes Ada and SAGA, and Rad6, which ubiquitinates histone H2B. These results suggest that preferential accessibility of the his3 (and presumably other) promoter regions is determined by a general property of the DNA sequence (e.g., base composition or a related feature) rather than by defined sequence elements. The organization of the compact yeast genome into inherently distinct promoter and nonpromoter regions may ensure that transcription factors bind preferentially to appropriate sites in promoters rather than to the excess of irrelevant but equally high-affinity sites in nonpromoter regions.

MeSH Terms
Adaptor Proteins, Signal Transducing Adenosine Triphosphatases Binding Sites Carboxy-Lyases/genetics Chromatin Chromosomal Proteins, Non-Histone DNA, Fungal/metabolism DNA-Binding Proteins/genetics,metabolism Deoxyribonucleases, Type II Site-Specific/metabolism Fungal Proteins/genetics,metabolism Genes, Fungal Histone Acetyltransferases Hydro-Lyases/genetics Ligases/genetics,metabolism Nuclear Proteins Promoter Regions, Genetic Protein Kinases/metabolism Saccharomyces cerevisiae/genetics,metabolism Saccharomyces cerevisiae Proteins Trans-Activators/genetics,metabolism Transcription Factors/genetics,metabolism Ubiquitin-Conjugating Enzymes
Chemicals
Adaptor Proteins, Signal Transducing Chromatin Chromosomal Proteins, Non-Histone DNA, Fungal DNA-Binding Proteins Fungal Proteins HFI1 protein, S cerevisiae Nuclear Proteins SAGA protein, Emericella nidulans SWI1 protein, S cerevisiae Saccharomyces cerevisiae Proteins Trans-Activators Transcription Factors GCN5 protein, S cerevisiae Histone Acetyltransferases RAD6 protein, S cerevisiae Ubiquitin-Conjugating Enzymes Protein Kinases Deoxyribonucleases, Type II Site-Specific GANTC-specific type II deoxyribonucleases Adenosine Triphosphatases SNF2 protein, S cerevisiae Carboxy-Lyases phosphoribosylaminoimidazole carboxylase Hydro-Lyases imidazoleglycerolphosphate dehydratase Ligases
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Mai X
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.
Chou S
Struhl K
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Article Info
Journal
Molecular and cellular biology
Abbr.
Mol Cell Biol
ISSN
0270-7306
DOI
10.1128/MCB.20.18.6668-6676.2000
Published
2000-09-00
Pages
6668-76
Language
English
Region
United States
NLM ID
8109087
PMCID
PMC86173
Subset
IM
Grants
NIGMS NIH HHS · R01 GM030186 · United States
NIGMS NIH HHS · R37 GM030186 · United States
NIGMS NIH HHS · GM30186 · United States
External Links
PubMed source DOI: 10.1128/MCB.20.18.6668-6676.2000 PMC Full Text View journal details
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