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. 2018 Sep 14;9:3759. doi: 10.1038/s41467-018-06247-5

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© The Author(s) 2018

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 4 — ZZZ3 is required for ATAC-mediated H3K9 acetylation and gene activation. a Heatmaps of the ZZZ3, Flag-YEATS2, H3K4ac, H3K9ac, and H3K4me3 ChIP-seq signals centered on ZZZ3 binding sites in a ± 5-kb window. Loci were classified as ZZZ3 peaks enriched with active promoter marks and others without active promoter marks. The color key represents the signal density. b Representative genome-browser views of ZZZ3 (red), YEATS2 (blue), H3K4me3 (purple), H3K4ac (cyan), and H3K9ac (green) ChIP-seq signals. TSS is indicated by an arrow. c qPCR analysis of Flag-ZZZ3 ChIP on gene promoters in cells stably expressing Flag-tagged WT ZZZ3 or the indicated point mutants. d Heatmap of the normalized ZZZ3 ChIP-seq signal densities in control (shNT), ZZZ3 KD (shZZZ3) cells, and KD cells ectopically expressing shRNA-resistant WT ZZZ3 or the indicated mutants. The signal is centered on ZZZ3 binding site in a ± 3-kb window. e Heatmap representation of differentially expressed genes in cells as in d from two biological replicates of RNA-seq experiments. Fisher’s exact test was used to define differentially expressed genes (q < 0.01). The color key represents normalized Log2 expression values. f qRT-PCR analysis of the expression of the indicated ribosomal protein genes in control (shNT), ZZZ3 KD (shZZZ3) cells, and KD cells ectopically expressing shRNA-resistant WT ZZZ3 or the indicated mutants. g qPCR analysis of H3K9ac ChIP on a promoter of the indicated ribosomal protein genes in cells as in f. Error bars represent s.e.m. of three biological replicates. ^∗p < 0.05; ^∗∗p < 0.01 (two-tailed unpaired Student’s t-test)