A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome.

By Travis N. Mavrich, I. Ioshikhes, Bryan J. Venters, Cizhong Jiang, L. Tomsho, Ji Qi, Stephan C. Schuster, I. Albert, B. Franklin Pugh. Genome Research, 2008

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Most nucleosomes are well-organized at the 5' ends of S. cerevisiae genes where "-1" and "+1" nucleosomes bracket a nucleosome-free promoter region (NFR). How nucleosomal organization is specified by the genome is less clear. Here we establish and inter-relate rules governing genomic nucleosome organization by sequencing DNA from more than one million immunopurified S. cerevisiae nucleosomes (displayed at http://atlas.bx.psu.edu/). Evidence is presented that the organization of nucleosomes throughout genes is largely a consequence of statistical packing principles. The genomic sequence specifies the location of the -1 and +1 nucleosomes. The +1 nucleosome forms a barrier against which nucleosomes are packed, resulting in uniform positioning, which decays at farther distances from the barrier. We present evidence for a novel 3' NFR that is present at >95% of all genes. 3' NFRs may be important for transcription termination and anti-sense initiation. We present a high-resolution genome-wide map of TFIIB locations that implicates 3' NFRs in gene looping.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/15e974d11a249f32b982ee81ca0e023c268aa020

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Citations in the corpus

Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals (2008, background): “Our results thus suggest that relatively large open chromatin regions can be accurately predicted simply by the presence of Poly(dA:dT) elements, consistent with the suggestion that boundaries such as Poly(dA:dT) elements account for many aspects of the in vivo nucleosome organization [9,12].”
Epigenetics in alternative pre-mRNA splicing (2011, neutral): “In S. cerevisiae, the 3 0 region near the polyadenylation site is depleted of nucleosomes (Mavrich et al., 2008), and in human T cells nucleosome density dips noticeably within 200 nt of the canonical polyadenylation signal (Spies et al., 2009).”
The ISW1 and CHD1 ATP-dependent chromatin remodelers compete to set nucleosome spacing in vivo (2016, neutral): “Consistent with previous observations (9,13,17,39), the global average spacing in wild-type cells is 166 bp with a standard deviation of 0 bp, based on the average values from two biological replicate experiments (n = 2) (Supplementary Table S2).”
Genomic nucleosome organization reconstituted with pure proteins (2016, background): “NPSs have strand-specific 10 bp periodicities of AA dinucleotides concentrated near nucleosome 5’ ends (Ioshikhes et al., 2006; Mavrich et al., 2008).”
Mechanisms and consequences of alternative polyadenylation (2011, neutral): “Significantly, the 30 region near the poly(A) site was shown to be depleted of nucleosomes (Mavrich et al., 2008; Shivaswamy et al., 2008; Spies et al., 2009).”
Global mapping of protein-DNA interactions in vivo by digital genomic footprinting (2009, background): “These results emphasize the heterogeneous nature of factor binding and consequent control of gene expression, requiring gene-level analyses of factor occupancy.”