A high-resolution atlas of nucleosome occupancy in yeast

By William Lee, Desiree Tillo, Nicolas L. Bray, R. Morse, Ronald W. Davis, Timothy R. Hughes, Corey Nislow. Nature Genetics, 2007

907 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/1536f349e4b2d71ec86a2e0022c78a45e21c1808

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Citations in the corpus

Zelda is differentially required for chromatin accessibility, transcription factor binding, and gene expression in the early Drosophila embryo (2015, background): “species (Lee et al. 2007; Schones et al. 2008; Weiner et al. 2010; Thomas et al. 2011; Valouev et al. 2011).”
G+C content dominates intrinsic nucleosome occupancy (2009, methodology): “In order to further benchmark our model, we compared the performance of the 14 feature model with published models[2,8,22-26,29,31,32] on other in vitro and in vivo nucleosome occupancy data sets, using Pearson correlation between predicted and actual data.”
Global mapping of protein-DNA interactions in vivo by digital genomic footprinting (2009, background): “Whereas ChIP requires that each DNA-binding protein ﬁrst be interrogated by genome-wide location analysis and can be carried out for only one protein at a time, DNase I footprinting addresses all factors simultaneously in their native state and detects regions of direct binding with nucleotide…”
Structure and mechanism of the chromatin remodelling factor ISW1a (2011, background): “This result confirms three expectations from our model: (1) ISW1a would be oriented on this dinucleosome substrate, most probably through Ioc3 CLB interaction with the 29-bp extension; (2) the I/E-nucleosome would be static; and (3) the I-nucleosome would be mobile through association with the Isw1 ”
Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals (2008, methodology): “Consistent with this hypothesis, microarray-based maps of yeast [5,9] and human [24] Figure 4.”
How a protein searches for its site on DNA: the mechanism of facilitated diffusion (2009, background): “(D) An example of experimentally observed nucleosome structure [52].”
Inaugural Article: DNA transposon Hermes inserts into DNA in nucleosome-free regions in vivo (2010, neutral): “Like the regions of preferred Hermes insertion in vivo, NFRs (also often termed nucleosome-depleted regions) are present upstream and downstream of genes in vivo (15) and, indeed, we find that Hermes inserts in vivo preferentially into NFRs (Fig.”
A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. (2008, methodology): “Similar results were observed genome-wide relative to transcriptional start sites in yeast (Yuan et al. 2005; Albert et al. 2007; Lee et al. 2007; Whitehouse et al. 2007; Shivaswamy et al. 2008; Yuan and Liu 2008) as well as in human promoters (Lin et al.”
Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood (2008, background): “Because nucleosome occupancy throughout the eukaryotic genome is not necessarily uniform and depends on factors such as function, expression, or sequence of the region (30, 43), the representation of sequences from different loci in cell-free maternal plasma may not be equal, as one usually expects ”