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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    • "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.
    G3-Genes Genomes Genetics 07/2015; 5(9). DOI:10.1534/g3.115.020271 · 3.20 Impact Factor
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    • "Specifically, we recapitulated across thousands of sequences the intrinsically nucleosome disfavoring nature of poly(dA:dT) tracts (Struhl and Segal 2013) that was previously deduced only from a handful of direct in vitro tests comparing nucleosome formation on sequences with or without such a tract (Anderson and Widom 2001; Bao et al. 2006) and mostly from the generally low nucleosome occupancy of regions enriched with these tracts genome-wide (Field et al. 2008; Kaplan et al. 2009; Zhang et al. 2009). We found that sequences lacking a 15-bp poly(dA:dT) tract generally show a higher nucleosome binding score than sequences with such a tract present, which in turn show a higher binding score than sequences with two such tracts present (Fig. 6B). "
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    ABSTRACT: Binding of transcription factors (TFs) to regulatory sequences is a pivotal step in the control of gene expression. Despite many advances in the characterization of sequence motifs recognized by TFs, our ability to quantitatively predict TF binding to different regulatory sequences is still limited. Here, we present a novel experimental assay termed BunDLE-seq that provides quantitative measurements of TF binding to thousands of fully designed sequences of 200 bp in length within a single experiment. Applying this binding assay to two yeast TFs we demonstrate that sequences outside the core TF binding site profoundly affect TF binding. We show that TF-specific models based on the sequence or DNA shape of the regions flanking the core binding site are highly predictive of the measured differential TF binding. We further characterize the dependence of TF binding, accounting for measurements of single and co-occurring binding events, on the number and location of binding sites and on the TF concentration. Finally, by coupling our in vitro TF binding measurements, and another application of our method probing nucleosome formation, to in vivo expression measurements carried out with the same template sequences now serving and promoters, we offer insights into mechanisms that may determine the different expression outcomes observed. Our assay thus paves the way to a more comprehensive understanding of TF binding to regulatory sequences, and allows the characterization of TF binding determinants within and outside of core binding sites. Published by Cold Spring Harbor Laboratory Press.
    Genome Research 03/2015; 25:1018-1029. DOI:10.1101/gr.185033.114 · 14.63 Impact Factor
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    • "Therefore, understanding the cause of nucleosome formation is important to uncover gene regulatory and cellular mechanisms. With the technological advancement in large-scale nucleosome occupancy measurement [9] [10] [11] [12] [13] [14], genome-scale data concerning nucleosome occupancy has become publicly available in multiple species, including human and yeast [15] [16] [17] [18]. Dozens of computational methods have been developed to utilize these data to model and predict nucleosome occupancy. "
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    ABSTRACT: The identification of important factors that affect nucleosome formation is critical to clarify nucleosome-forming mechanisms and the role of the nucleosome in gene regulation. Various features reported in the literature led to our hypothesis that multiple features can together contribute to nucleosome formation. Therefore, we compiled 779 features and developed a pattern discovery and scoring algorithm FFNs (Finding Features for Nucleosomes) to identify feature patterns that are differentially enriched in nucleosome-forming sequences and nucleosome-depletion sequences. Applying FFN to genome-wide nucleosome occupancy data in yeast and human, we identified statistically significant feature patterns that may influence nucleosome formation, many of which are common to the two species. We found that both sequence and structural features are important in nucleosome occupancy prediction. We discovered that, even for the same feature combinations, variations in feature values may lead to differences in predictive power. We demonstrated that the identified feature patterns could be used to assist nucleosomal sequence prediction.
    Genomics 08/2014; 104(2). DOI:10.1016/j.ygeno.2014.07.002 · 2.28 Impact Factor
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