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Mol Cell. 2015 Nov 5;60(3):422-34. doi: 10.1016/j.molcel.2015.10.002.

Nucleosome Stability Distinguishes Two Different Promoter Types at All Protein-Coding Genes in Yeast.

Author information

1
Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), 30 quai Ernest-Ansermet, 1211 Geneva, Switzerland.
2
Swiss Institute of Bioinformatics (SIB) and Bioinformatics and Biostatistics Core Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
3
Center for Advanced Modeling Sciences, Computer Science Department, University of Geneva, 7 route de Drize, 1227 Carouge, Switzerland.
4
Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), 30 quai Ernest-Ansermet, 1211 Geneva, Switzerland. Electronic address: David.Shore@unige.ch.

Abstract

Previous studies indicate that eukaryotic promoters display a stereotypical chromatin landscape characterized by a well-positioned +1 nucleosome near the transcription start site and an upstream -1 nucleosome that together demarcate a nucleosome-free (or -depleted) region. Here we present evidence that there are two distinct types of promoters distinguished by the resistance of the -1 nucleosome to micrococcal nuclease digestion. These different architectures are characterized by two sequence motifs that are broadly deployed at one set of promoters where a nuclease-sensitive ("fragile") nucleosome forms, but concentrated in a narrower, nucleosome-free region at all other promoters. The RSC nucleosome remodeler acts through the motifs to establish stable +1 and -1 nucleosome positions, while binding of a small set of general regulatory (pioneer) factors at fragile nucleosome promoters plays a key role in their destabilization. We propose that the fragile nucleosome promoter architecture is adapted for regulation of highly expressed, growth-related genes.

PMID:
26545077
DOI:
10.1016/j.molcel.2015.10.002
[Indexed for MEDLINE]
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