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. Author manuscript; available in PMC: 2016 Jul 2.
Published in final edited form as: Mol Cell. 2015 Jun 4;59(1):75–88. doi: 10.1016/j.molcel.2015.05.009

Figure 4. A unique signature of H2A.Z occupancy at H2A.Z.2-regulated genes.

Figure 4

(A) Pie chart displaying the percentages of H2A.Z peaks occupying promoters, gene bodies and distal regions. Promoters: −3Kb < TSS < +1Kb; Gene bodies: from +1Kb > TSS to TES; all other regions defined as distal. (TSS: Transcription Start Site; TES: Transcription End Site).

(B) Correlation of H2A.Z signals at the promoter or gene body with mRNA expression levels. Genes were divided by expression level into high (top 25%), medium (middle 50%) and low (bottom 25%) from RNA-sequencing data. Fold enrichment profiles (sliding 100 bp window) and boxplots were calculated around the TSS (−3kb, +3Kb) and over the gene body (TSS to TES) for each group; Mann Whitney test (two-tailed).

(C) Venn diagrams displaying H2A.Z.2 downregulated genes and H2A.Z bound genes by ChIP-seq in SK-mel147. Class I (downregulated in H2A.Z.2 knock down and bound by H2A.Z, red); Class II (bound by H2A.Z but unaffected by H2A.Z.2 knock down, light blue); Class III (downregulated by H2A.Z.2 knock down but not bound by H2A.Z, purple); Class IV (11,003 genes that are not downregulated by H2A.Z.2 knock down and not bound, grey).

(D) ChIP Enrichment Analysis tool (ChEA2) analysis of Class I, Class II and Class III genes (as defined and color coded in panel A). The ChEA2 database contains ChIP-seq data of 200 transcription factors from 221 publications for a total of 458,471 TF-target interactions (Kou et al., 2013). Transcription factors are ranked by ChEA combined score.

(E) H2A.Z occupancy at the promoter and gene body of the four classes of genes defined in (C), in SK-mel147 cells. Profiles and boxplots represent fold enrichment over input. Mann Whitney test (two-tailed).

(F) Captures of the UCSC genome browser (GRCh37/hg19) showing the ChIP-seq profiles for H2A.Z for genes belonging to each of the classes defined in (C). RefSeq annotated genes are displayed on top.

(G) Boxplot representing expression levels (FPKM) for each gene class as in (C), in primary melanocytes and in SK-mel147. Mann Whitney test (two-tailed). Two-way ANOVA.

(H) H2A.Z occupancy at the promoter and gene body of the four classes of genes defined in (C) in primary melanocytes (as in (C)).