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Results: 5

1.
Figure 1

Figure 1. Positioning of boundary nucleosomes within open chromatin.. From: Regulation of the Boundaries of Accessible Chromatin.

(A) Superposition of in vivo and in vitro nucleosomes, and FAIRE read density across the boundaries of promoter-associated (left) or non-associated (right) open chromatin in yeast. (B) Superposition of in vivo and in vitro nucleosomes, and FAIRE read density across the boundaries of promoter-associated (left) or non-associated (right) open chromatin in human.

Xiaoran Chai, et al. PLoS Genet. 2013 September;9(9):e1003778.
2.
Figure 3

Figure 3. Histone modifications and H2A.Z occupancy across open chromatin in human.. From: Regulation of the Boundaries of Accessible Chromatin.

Shown is the body of open chromatin, which is divided into ten bins, along with 1(A) Pattern of H3K27ac, H3K4me2, H3K4me3, and H3K9ac. (B) Pattern of H3K4me1, H3K79me2, H3K9me3, and H4K20me1. (C) Pattern of H3K27me3 and H3K36me3.

Xiaoran Chai, et al. PLoS Genet. 2013 September;9(9):e1003778.
3.
Figure 2

Figure 2. Boundary nucleosome positioning within open chromatin.. From: Regulation of the Boundaries of Accessible Chromatin.

(A) Superposition of in vivo and in vitro nucleosomes surrounding the in vivo TFBSs (black curve) and sequence-predicted Transfac TFBSs (gray curve). (B) Number of DHS tags mapped to the region centered on the in vivo TFBSs (black curve) and sequence-predicted Transfac TFBSs (gray curve). (C) Chromatin structure in GM12878 at a genomic locus (chr2:232,378,500–232,379,800). Shown from top to bottom are tracks for open chromatin density (two replicates), chromatin states (red: active promoter, yellow: weak enhancer, and orange: strong enhancer), nucleosome density (blue box: boundary nucleosomes), histone modifications (density shown on the gray scale with dark indicating dense modifications), and TF binding locations (binding affinity shown on the same gray scale as above).

Xiaoran Chai, et al. PLoS Genet. 2013 September;9(9):e1003778.
4.
Figure 5

Figure 5. Effects of chromatin border regulation on nearby gene expression.. From: Regulation of the Boundaries of Accessible Chromatin.

(A) FAIRE density in the BY4716 (BY) and RM11_1a (RM) strains for accessible chromatin located upstream of the tss of the TAT1 gene is shown above the positioned nucleosomes (black bars) identified based on nucleosome density (light green below). The FAIRE region was supported by DNase I-based protein-binding footprints (blue tick) and the regulatory code track at the bottom displaying the location of TFBSs (black ticks). The left-side border of the FAIRE peak (orange box) was associated in cis with local genotypes, which were also associated with the expression level of TAT1. (B) The gene expression level in strains with the RM genotype and BY genotype. (C) The distance of the left-side border in each strain with the RM or BY genotype relative to that in the BY4716 strain. (D) Correlation between the gene expression level of TAT1 and the boundary-to-boundary distance of the left border of the FAIRE peak across the 96 strains.

Xiaoran Chai, et al. PLoS Genet. 2013 September;9(9):e1003778.
5.
Figure 4

Figure 4. Local changes of yeast open chromatin upon genetic perturbation.. From: Regulation of the Boundaries of Accessible Chromatin.

(A) We identified 4,897 open chromatin loci in BY4716 and aligned them by the 5′ end, center, and 3′ end, and then mapped the relative locations of nearby open chromatin loci in the other 95 strains. The center is defined as the middle point between the 5′ and 3′ boundaries. The number of strains (0∼95) that matches its boundary or center within a given distance from the homologous boundary or center in BY4716 was obtained and the frequency of the overlappings is represented as color gradient according to the distance shown at the bottom of each heat map. The rows of each heat map correspond to each of the 4,897 chromatin sites in BY4716. (B) The average frequency of mapped locations as a function of the distance to the center or to the end of the homologous site in BY4716. (C) The average frequency of mapped locations according to the in vitro nucleosome score as a function of the distance to the center or to the end of the homologous site in BY4716.

Xiaoran Chai, et al. PLoS Genet. 2013 September;9(9):e1003778.

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