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. 2020 Aug 3;27(9):836–845. doi: 10.1038/s41594-020-0466-9

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© The Author(s), under exclusive licence to Springer Nature America, Inc. 2020

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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Extended Data Fig. 8 — a, Waterfall dependency plots for RING1B, PCGF3, PCGF5 and KDM2B genes across n = 387 cell lines in Project DRIVE Dataset (Novartis). b, CERES dependency scores (fitness dropout) derived from genome-scale fitness screens performed using CRISPR-Cas9-based methods (Achilles, Broad Institute; https://depmap.org/portal/achilles/). Difference is the score calculated between SYO1, Yamato-SS, SCS241 (SS18-SSX + ) cells and SW982 cells (negative for fusion, histologic mimic). Blue, enriched for dependency. mSWI/SNF, PRC1, PRC2 members are shown. c, CERES and DEMETER Dependency scores for SSX1 and SS18 genes for CRISPR-Cas9 and RNAi datasets, respectively. Synovial sarcoma cell lines are indicated in pink; all other cell lines are represented in gray. d, CERES and DEMETER Dependency scores for SSX1 and SS18 genes for CRISPR-Cas9 and RNAi datasets, respectively. Synovial sarcoma and soft tissue (SS cell lines) exhibit preferential dependency. (Project DRIVE; https://oncologynibr.shinyapps.io/drive/). SS cell lines containing the SS18-SSX fusion oncoprotein are highlighted in red. e, H2AK119Ub and RING1B ChIP-seq tracks over selected loci, aligned with SS18 (BAF) localization in SYO1 cells treated with shScramble or shSS18-SSX. f, MBP-SSX1 (78aa) pull-down experiments indicate capture of histones, and specifically, H2AK119Ub species. g, Streptavidin-based pull-down experiments (n = 4 independent replicate experiments) using endogenous, fully-assembled HA-SS18- or HA-SS18-SSX-bound BAF complexes incubated with biotinylated WT nucleosomes (unmodified) or H2AK119Ub-modified nucleosomes. SMARCA4 and Histone H3 immunoblots are shown. h, Representative silver stain of the WT SS18 complexes and SS18-SSX fusion complexes isolated using ammonium sulfate nuclear extraction protocol. Identified proteins are labeled. i, Pull-down experiments performed using GST-SSX incubated with unmodified or a series of modified recombinant mononucleosomes, or endogenous mononucleosomes (mammalian, purified via MNase digestion from HEK-239T cells). j, Quantitative densitometry performed on experiment in Extended Data Fig. 8i. Uncropped gel images for all relevant panels are presented in Supplementary Figure 1.