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Nucleosome stability distinguishes two different promoter types at all protein-coding genes in yeast

Authors: Slawomir Kubik, Maria Jessica Bruzzone, Philippe Jacquet, Jean-Luc Falcone, Jacques Rougemont, & David Shore

Summary:

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.

Source: Molecular Cell; Vol. 60, Issue 3, 422-434 (11/05/15)