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. 2019 Jan 21;10:348. doi: 10.1038/s41467-018-08255-x

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© The Author(s) 2019

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 — BAP1.com promotes transcription independently of an antagonism with the PRC2 complex. a Heatmaps showing H2AK119ub1, H3K27me3, and H3K4me3 distribution in a −5/ + 5 kb window around the transcription start site (TSS) of genes downregulated in BAP1 KO cells in wild-type and BAP1 KO cells. Corresponding average profiles are plotted on top of each heatmap. b Western blot analysis of BAP1 and EZH2 in single and double BAP1/EZH2 KO cells. HDAC1 is used as a loading control. c Dot plot showing proliferation of wild-type cells and two independent clones of BAP1/EZH2 dKO cells. n = 3. d Heatmap of gene expression (Z-scores) in the different genotypes. Top: BAP1-only-regulated genes, and bottom: BAP1- and EZH2-regulated genes, TSS = transcription start site. e Box-plots (median, lower, and upper quartiles, lowest and highest values) of log2 transcript per million (TPM) expression values of BAP1-only-regulated genes (top) and BAP1/EZH2-regulated genes⁶¹ in the different conditions as indicated. Result of the Mann–Whitney test on the EZH2 KO versus wild-type comparison is indicated. f Plot showing average enrichment of H2AK119ub1, H3K27me3, and H3K4me3 in a −5/ + 5 kb around the TSS for BAP1-only-regulated genes (top) and BAP1/EZH2-regulated genes⁶¹. g Example snapshots of H2AK119ub1, H3K27me3, and H3K4me3 enrichment in WT and BAP1 KO cells at a BAP1-only-regulated gene and a BAP1/EZH2-regulated gene (middle). Expression values of the corresponding genes across WT, EZH2, BAP1, and BAP1/EZH2 KO conditions as detected in corresponding RNA-seq data are shown on the right. Horizontal bars indicate the mean expression