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

• DOI: 10.1016/j.molcel.2015.10.002
• Publication Date: 2015-11-05T17:00:35Z
• Authors: Slawomir Kubik; Maria Jessica Bru...; Philippe Jacquet; Jean-Luc Falcone; Jacques Rougemont; David Shore
• Keywords: 0303 health sciences; 03 medical and health sciences; Saccharomyces cerevisiae Proteins; Gene Expression Regulation, Fungal; Cell Biology; Saccharomyces cerevisiae; Promoter Regions, Genetic; Molecular Biology; Nucleosomes

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.