Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts, USA.
Nature Structural & Molecular Biology (Impact Factor: 13.31). 09/2009; 16(8):847-52. DOI: 10.1038/nsmb.1636
Source: PubMed


We assess the role of intrinsic histone-DNA interactions by mapping nucleosomes assembled in vitro on genomic DNA. Nucleosomes strongly prefer yeast DNA over Escherichia coli DNA, indicating that the yeast genome evolved to favor nucleosome formation. Many yeast promoter and terminator regions intrinsically disfavor nucleosome formation, and nucleosomes assembled in vitro show strong rotational positioning. Nucleosome arrays generated by the ACF assembly factor have fewer nucleosome-free regions, reduced rotational positioning and less translational positioning than obtained by intrinsic histone-DNA interactions. Notably, nucleosomes assembled in vitro have only a limited preference for specific translational positions and do not show the pattern observed in vivo. Our results argue against a genomic code for nucleosome positioning, and they suggest that the nucleosomal pattern in coding regions arises primarily from statistical positioning from a barrier near the promoter that involves some aspect of transcriptional initiation by RNA polymerase II.

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Available from: James T Kadonaga, Jan 11, 2016
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    • "It has been established that nucleosome positioning is sensitive to the DNA sequence, with the binding affinity for a given 147 bp sequence varying over more than three orders of magnitude (Thå strö m et al., 1999). High-affinity binding to DNA sequences that contain 10 bp repeats of bendable AT/TA dinucleotides (Jiang and Pugh, 2009; Kaplan et al., 2009; Struhl and Segal, 2013; Zhang et al., 2009) has facilitated both high-throughput visualization of nucleosomes (Lee and Greene, 2011; Visnapuu and Greene, 2009) and the mapping out of the energy landscape for single nucleosomes or nucleosome arrays through mechanical disruption (Brower-Toland et al., 2002; Hall et al., 2009; Bancaud et al., 2007; Kruithof et al., 2009), providing quantitative insight into the underlying histone-DNA interactions. It is becoming increasingly clear that nucleosomes exhibit structural dynamics that are key to understanding the mechanisms regulating genome accessibility in transcription, replication , and repair (Bell et al., 2011; Choy and Lee, 2012; Gansen et al., 2009; Simon et al., 2011; Zentner and Henikoff, 2013). "

    Full-text · Dataset · Dec 2015
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    • "In yeast, the transcriptional start site (TSS) at most genes is located at approximately 12 to 13 nucleotides inside the 5 0 border of the +1 nucleosome, thus immediately downstream of the nucleosome-free region (NFR). The extent to which this canonical promoter nucleosome architecture is determined by the nucleosome DNA-binding specificity, transcription factors (TFs), and/ or nucleosome remodeling enzymes is controversial (Kaplan et al., 2009; Zhang et al., 2009), and its functional significance is still largely unknown. "
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    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.
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    • "Multiple distinct mechanisms responsible for establishing the chromatin landscape have been identified over decades of study. Nucleosome assembly is thermodynamically disfavored over relatively stiff Poly(dA:dT) sequences (Drew and Travers 1985; Anderson and Widom 2001); therefore, in a number of species (such as the budding yeast S. cerevisiae) promoters are thought to " program " intrinsic nucleosome depletion using such sequences (Iyer and Struhl 1995; Sekinger et al. 2005; Yuan et al. 2005; Yuan and Liu 2008; Kaplan et al. 2009; Zhang et al. 2009). Although cis-acting genomic sequence plays a key role in establishing nucleosome depletion at yeast promoters, the vast majority of nucleosome positions are established by trans-acting factors , a fact emphasized by the vast improvement in recapitulating relatively accurate in vivo nucleosome positions by supplementing in vitro reconstitutions with whole cell extract (Zhang et al. 2011). "
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    ABSTRACT: Packaging of genomic DNA into nucleosomes is nearly universally-conserved in eukaryotes, and many features of the nucleosome landscape are quite conserved. Nonetheless, quantitative aspects of nucleosome packaging differ between species, as for example the average length of linker DNA between nucleosomes can differ significantly even between closely-related species. We recently showed that the difference in nucleosome spacing between two Hemiascomycete species - Saccharomyces cerevisiae and Kluyveromyces lactis - is established by trans-acting factors rather than being encoded in cis in the DNA sequence. Here, we generated several S. cerevisiae strains in which endogenous copies of candidate nucleosome spacing factors are deleted and replaced with the orthologous factors from K. lactis. We find no change in nucleosome spacing in such strains in which histone H1 or Isw1 complexes are swapped. In contrast, the K. lactis gene encoding the ATP-dependent remodeler Chd1 was found to direct longer internucleosomal spacing in S. cerevisiae, establishing that this remodeler is partially responsible for the relatively long internucleosomal spacing observed in K. lactis. By analyzing several chimaeric proteins, we find that sequence differences that contribute to the spacing activity of this remodeler are dispersed throughout the coding sequence, but that the strongest spacing effect is linked to the understudied N-terminal end of Chd1. Taken together, our data find a role for sequence evolution of a chromatin remodeler in establishing quantitative aspects of the chromatin landscape in a species-specific manner. Copyright © 2015 Author et al.
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