Figure 1.
Patterns of nucleosome positioning around DHSs in the rice genome.
The nucleosome positioning profiles were shown around the DHSs located in (A) proximal promoters (within 200 bp upstream of a TSS); (B) distal promoters (200–1000 bp upstream of a TSS); (C) within genes; (D) downstream regions of genes (within 200 bp downstream of gene transcription); (E) intergenic regions and (F) 10,000 randomly selected genomic regions. Y-axes show normalized reads (read number in per bp genome in per million reads) within 1 kb upstream and downstream around the DHSs. Ellipses indicate the nucleosomes within (grey) and outside (black) of DHSs. Arrows in (A–D) indicate the direction of gene transcription. Single-end MNase-seq reads were used in mapping nucleosome positioning.
Figure 2.
Phased nucleosome arrays flanked TSSs of rice genes.
(A) Nucleosome positioning profile associated with active genes. Phased nucleosome arrays are detectable after the TSSs. (B) Nucleosome positioning profile associated with non-expressed genes. Phased nucleosome arrays are detected on either side of the TSSs. (C) Distribution of DHS length for five different DHS categories. Note: the length of DHSs associated with proximal promoters (black line) are more variable than the lengths of other DHSs. (D) Heatmap of nucleosome positioning associated with active genes. Left panel: All expressed genes were sorted by the length of DHSs located in proximal promoters. The 5′ ends of the MNase-seq reads were mapped within 1 kb upstream and 1 kb downstream of the TSS of each gene to show the boundaries of nucleosomes core and linker. The red line on the left heatmap indicates the boundaries of DHSs. With the same order of the genes as in the left panel, the 5′ ends of DNase-seq reads (middle panel) and the fragments per kilobase of exon per million fragments mapped (FPKM) value log10 transformation (right panel) were mapped to show the DNase I sensitivity and the expression level of each gene, respectively.
Figure 3.
Association IPA1-binding sites with phased nucleosomes.
An example of phased nucleosome arrays that flank an intergenic IPA1-binding site on rice chromosome 8. This binding site is overlapped with a DHS (red arrow). The distribution of MNase-seq data (dyad density calculated from paired-end reads by NucleR) and DNase-seq data (density calculated by F-seq) were used to present the nucleosome and DHS positions. Phased nucleosomes and DHS regions were also schematically marked.
Figure 4.
Nucleosome positioning profiles associated with DHSs with different lengths in proximal promoters.
(A) DHSs in 320–480 bp. (B) DHSs in 200–320 bp. (C) DHSs in 140–200 bp. (D) DHSs in 80–140 bp. (E) DHSs in 20–80 bp. Y-axes show normalized reads of DNase-seq and MNase-seq. Zero on the X-axis indicates the boundary of DHSs toward short arm of the chromosomes. Black ellipses indicate the inferred nucleosomes. Grey ellipses indicate -1 nucleosomes within DHSs. Black vertical lines in (d, e) indicate the left and right boundaries of the DHSs inferred by DNase-seq reads.
Figure 5.
Boxplots of estimated lengths of linkers (A) and spacing (B) between the phased nucleosomes mapped close to DHSs.
"***","**","*" indicated p<0.001, p<0.01, p<0.05, respectively, for the comparison of linker length/spacing between intergenic region and either regions within genes (“gene”) or in proximal promoters (“200 bp”).
Figure 6.
Patterns of nucleosome positioning around DHSs in the human genome.
DHSs (data from CD4+ T cell line) were also divided into five different categories based on their genomic locations: (A) proximal promoters (within 200 bp upstream of a TSS); (B) within genes; and (C) intergenic regions. Y-axes show normalized MNase-seq reads (read number in per bp genome in per million reads). Zero on the x-axes indicates the most sensitive site of the aligned DHSs. Ellipses indicate phased nucleosomes with H2A.Z. Arrows in (A, B) indicate the direction of gene transcription.