1. Volume 10, Issue 10, Pages 1274-1292 (October 2017)
H2A.Z Represses Gene Expression by Modulating Promoter Nucleosome Structure and Enhancer Histone Modifications in Arabidopsis 
Xiaozhuan Dai, Youhuang Bai, Lihua Zhao, Xianying Dou, Yanhui Liu, Lulu Wang, Yi Li, Weimin Li, Yanan Hui, Xinyu Huang, Zonghua Wang, Yuan Qin 
Molecular Plant 
Volume 10, Issue 10, Pages (October 2017)
DOI: /j.molp
Copyright © 2017 The Author Terms and Conditions

2. Figure 1 H2A.Z Is Enriched at Promoters and Enhancers.
(A) The peak counts in wild-type (WT).
(B) Peak annotation in WT.
(C) Venn diagrams for promoters and enhancers occupied by H2A.Z (black) and either H3K4me3 (green) or H3K27me3 (red). Significant levels for the elements in common determined by Fisher's exact test: **p <
(D) Chromatin mark combinations associated with the 10 chromatin states. Each row shows the specific combination of marks associated with each chromatin state and the frequencies between 0 and 1 with which they occur.
(E) The emission probability parameters of the hidden Markov model (HMM) learned across the genome during model training. The darker the color, the higher the probability of a given chromatin state occurring.
(F) The relative percentage of the genome represented by each chromatin state (first column) and the relative fold enrichment for different genome features (other columns).
(G) The expression level of putative target genes (the most proximal genes flanking each enhancer) for H2A.Z-bound and non-H2A.Z-bound enhancers. The p value was calculated by the Kolmogorov–Smirnov test.
(H) The expression level of putative target genes for H3K27me3-bound enhancers with H2A.Z (w/) and those without H2A.Z (w/o). The p value was calculated by the Kolmogorov–Smirnov test.
Molecular Plant  , DOI: ( /j.molp )
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3. Figure 2
H2A.Z Is Globally Localized to Promoters of Inactive Genes in Arabidopsis.
(A) Most H2A.Z peaks are located within promoters. The fraction of 23 190 H2A.Z peaks present with promoter (blue) and non-promoter (red) regions is shown.
(B) The fraction of the 27 027 promoter regions containing (blue) or not containing (red) H2A.Z peaks is shown.
(C, D, F, and G) Relationship of normalized, average tag density at promoter regions to expression levels. All expressed genes (FPKM ≥1) were sorted into four equal-sized groups according to their mRNA expression values (FPKM). 0–25% stands for the highest expressed genes; 25–50% and 50–70% are the medium expressed genes; 75–100% represents the lowest expressed genes. The x axis is the genomic coordinate and the y axis is the enrichment of specific chromatin marks (H2A.Z, H3K27me3, H3K4me3, and Pol II).
(E) The expression level of H2A.Z-bound or non-H2A.Z-bound promoters relative to all expressed genes. The p value was calculated by the Kolmogorov–Smirnov test.
Molecular Plant  , DOI: ( /j.molp )
Copyright © 2017 The Author Terms and Conditions

4. Figure 3
Bayesian Mixture Models Fit and Classification for Wild-Type and arp6 Datasets.
(A) The gray histograms show the empirical distribution of the Z score at different scales for H2A.Z. The histograms are overlaid with the mixture density and the densities of the single components.
(B) The observed Z values are plotted against their classification in the mixture model. More transcripts were classed into the negative (560) than into the positive component (172), indicating a negative correlation between H2A.Z and gene transcription.
(C) The same as (A) for H3K27me3.
(D) The observed Z values are plotted against their classification in the mixture model. More transcripts were classed into the negative (392) than into the positive component (75), indicating a negative correlation between H3K27me3 and gene transcription.
(E) The same as (A) for H3K4me3.
(F) The observed values Z are plotted against their classification in the mixture model. More transcripts were classed into the positive (509) than into the negative component (42), indicating a negative correlation between H3K4me3 and gene transcription.
Molecular Plant  , DOI: ( /j.molp )
Copyright © 2017 The Author Terms and Conditions

5. Figure 4
The Genome-wide Changes in H2A.Z, Pol II, H3K4me3, H3K27me3, and Nucleosome Occupancy Caused by arp6 Mutation.
(A) Profiles of H2A.Z in WT and arp6 mutant.
(B) Profiles of nucleosome occupancy in WT and arp6 mutant.
(C) Nucleosome occupancy profiles of genes associated with or without an H2A.Z peak. Peaks represent nucleosomes, and valleys represent linker regions.
(D) The expression level of two groups of the H2A.Z-bound genes classified by the nucleosome occupancy level (RPM ≥1) at −1 nucleosome loci. The “high” in the x axis stands for the gene group with higher nucleosome occupancy, and “low” represents the gene group with lower nucleosome occupancy.
(E) The expression level of two groups of H2A.Z-bound genes classified by nucleosome occupancy (RPM ≥1) at +1 nucleosome loci.
(F) Profiles of Pol II in WT and arp6 mutant.
(G) Profiles of H3K4me3 in WT and arp6 mutant.
(H) Profiles of H3K27me3 in WT and arp6 mutant.
(I) The enrichment signals of H2A.Z, H3K4me3, H3K27me3, Pol II, and nucleosome occupancy in WT and arp6 mutant. The y axis scale for (iii) is the H2A.Z enrichment level in arp6 mutant subtracted from that in WT.
Molecular Plant  , DOI: ( /j.molp )
Copyright © 2017 The Author Terms and Conditions

6. Figure 5
The Dynamic Changes in H2A.Z, Pol II, H3K4me3, H3K27me3, and Nucleosome Occupancy Caused by the arp6 Mutation.
(A) The percentages of H2A.Z, H3K4me3, H3K27me3, and Pol II binding sites that showed a significant increase (blue), decrease (orange), or no change (gray) in apr6.
(B) The feature distributions on the whole genome of these increase or decrease binding sites.
(C) Heatmap of ChIP-seq and MNase-seq signals over transcription start sites (TSS) in Arabidopsis. Each row represents the normalized ChIP-seq enrichment over one transcript. Enrichment is calculated by first scaling arp6 mutant and wild-type signals to reads per million mapped reads and then subtracting the wild-type signal from the mutant signal. Red equates to increased signals in the arp6 mutant compared with wild-type; blue is the reverse.
Molecular Plant  , DOI: ( /j.molp )
Copyright © 2017 The Author Terms and Conditions

7. Figure 6
Correlation Analysis of H2A.Z, Nucleosome Occupancy, H3K4me3, H3K27me3, and Pol II with Gene Responsiveness.
(A–E) Enrichment of H2A.Z, nucleosome occupancy, H3K4me3, H3K27me3, and Pol II in genes showing reduced H2A.Z enrichment and upregulated expression level in arp6, divided into three subgroups according to the change in their expression (log2 fold change).
Molecular Plant  , DOI: ( /j.molp )
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8. Figure 7
Altered H2A.Z Level in arp6 at Enhancers Is Associated with Modified Histone Modification Status.
(A–D) H2A.Z, nucleosome occupancy, H3K4me3 and H3K27me3 density in WT and arp6 for the H2A.Z-bound enhancers that show decreased H2A.Z enrichment in arp6 compared with WT.
(E) The expression levels of putative target genes of these H2A.Z-bound enhancers with decreased H2A.Z enrichment in arp6 compared with WT.
(F–I) The H2A.Z and histone modification density in WT and arp6 for the enhancers whose putative target gene expression levels increased (fold change ≥2) in arp6 compared with WT.
Molecular Plant  , DOI: ( /j.molp )
Copyright © 2017 The Author Terms and Conditions

9. Figure 8
Proposed Model of H2A.Z Coordinating Nucleosome Accessibility and Histone Modifications to Regulate Genes Expression.
(A) A diagram showing the coordinated action of H2A.Z, nucleosome accessibility, and histone modifications in repressing gene expression in WT. In WT, SWR1-mediated H2A.Z deposition at +1 nucleosome results in a closed +1 nucleosome structure, which may prevent the access of a transcriptional activator and prevent Pol II transit. H2A.Z at −1 nucleosome is associated with an open −1 nucleosome structure, which may facilitate the access of a transcriptional repressor. At enhancers, H2A.Z associates with H3K27me3 to repress enhancer activity likely by repressing the enrichment of H3K4me3.
(B) A diagram showing the coordinated action of H2A, nucleosome accessibility, and histone modifications in promoting gene expression in arp6. In the arp6 mutant, the H2A containing +1 nucleosome is associated with reduced nucleosome occupancy, which may facilitate the access of activator and reduce the high energy barrier of +1 nucleosome, and the H2A containing −1 nucleosome is associated with increased nucleosome occupancy, which may inhibit the access of repressor, thus activating gene expression. Upregulated genes in the arp6 mutant are accompanied by slightly increased levels of H3K4me3 at –1 nucleosome and significantly reduced levels of H3K27me3 at +1 nucleosome. At enhancers, the arp6-reduced H2A.Z enrichment is associated with dramatically increased H3K4me3 levels, which may result in activation of enhancer activity.
Molecular Plant  , DOI: ( /j.molp )
Copyright © 2017 The Author Terms and Conditions