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. 2018 Oct;28(10):1494–1507. doi: 10.1101/gr.237180.118

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© 2018 King et al.; Published by Cold Spring Harbor Laboratory Press

This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.

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Figure 5. — The PRC1-dependent nucleosome landscape is linked to, but not explained by, RNA polymerase II activity. (A) A schematic depicting the inhibition of RNA polymerase II (RNA POLII) occupancy using triptolide (TRP). (B) A box plot comparing the median Tn5-tagmented fragment sizes for PcG and non-PcG CGI promoters before and after TRP treatment. (C) A box plot quantifying the NucleoATAC-derived nucleosome occupancy score for PcG and non-PcG CGI promoters before and after TRP treatment. (D) A box plot comparing the median inter-dyad distances for PcG and non-PcG CGI promoters before and after TRP treatment. (E) A Venn diagram for PcG-occupied CGI promoters with significant increases in gene expression in Ring1^−/−;Rnf2^fl/fl and Ring1^−/−;Rnf2^fl/fl;Eed^−/− ATAC-seq before and after tamoxifen (TAM), corresponding to PRC1-null, PRC2-null, and PRC1/2-null (FDR < 0.05; fold change > 2). (F) A bar plot depicting the number of significant RNA-seq expression changes for PcG-occupied CGI promoters. (G) Same as in F, only for ATAC-seq. Changes in ATAC-seq were calculated using the CGI promoter interval. (H) A box plot comparing the change in RNA-seq log₂ fold change (log₂FC) for PcG-occupied CGI promoters with (up-regulated) or without (no change) an increase in gene expression for each cell line and treatment. (I) A box plot comparing the change in median Tn5-tagmented fragment sizes for PcG-occupied CGI promoters with (up-regulated) or without (no change) an increase in gene expression for each cell line and treatment. (J) A box plot quantifying the log₂ fold change (log₂FC) in NucleoATAC-derived nucleosome occupancy for PcG-occupied CGI promoters with (up-regulated) or without (no change) an increase in gene expression for each cell line and treatment. (K) A box plot comparing the difference in median inter-dyad distances for PcG-occupied CGI promoters with (up-regulated) or without (no change) an increase in gene expression for each cell line and treatment.