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. 2018 May 29;7:e37084. doi: 10.7554/eLife.37084

Figure 5. FBXL19 targets CDK8 to promoters of silent developmental genes in ES cells.

(A) Gene ontology analysis of genes associated with a decrease in CDK8 binding (n = 673).(B) A boxplot showing expression levels (log2FPKM) of CDK8-bound genes in wild-type ES cells. CDK8-associated genes are divided based on CDK8 binding in Fbxl19ΔCXXC ES cells: all CDK8-bound (n = 15161), reduced CDK8 (n = 673, ↓), and increased CDK8 binding (n = 255, ↑). p-values were calculated using a Wilcoxon rank sum test. (C) A boxplot showing the change in gene expression (log2 fold change) observed by 4sU RNA-seq of CDK8-associated genes (as in B) following RA treatment. p-values were calculated using a Wilcoxon rank sum test. (D) A boxplot comparing gene expression levels (log2FPKM) of all (n = 19310) and FBXL19-bound (FBXL19+, n = 11368) genes separated by low (all genes n = 7417; FBXl19+ genes n = 2031) and high expression levels (all genes n = 11893, FBXl19+ genes n = 9337) in ES cells (based on Figure 5—figure supplement 1B). (E) A boxplot showing CDK8 enrichment at all and FBXL19-bound genes separated by expression level as in (D). (F) A boxplot showing change in CDK8 binding at the TSSs of all and FBXL19-bound genes divided by expression level as in (D). p-values were calculated using a Wilcoxon rank sum test.

Figure 5.

Figure 5—figure supplement 1. FBXL19 targets CDK8 to promoters of silent developmental genes in ES cells.

Figure 5—figure supplement 1.

(A) Metaplots showing enrichment of H3K27me3 (left) and H3K4me3 (right) ChIPseq signal at all (top), reduced (↓) and increased (↑) CDK8 peaks. (B) Heatmaps showing enrichment of CDK8, H3K27me3 and H3K4me3 ChIPseq signal at H3K27me3 peaks (n = 5588) divided by overlap with CDK8 peaks (CDK8 +n = 3637, CDK8- n = 1950) sorted by decreasing H3K27me3 signal. Distance from the peak center is shown. (C) Volcano plots showing alterations in expression (log2 fold change) comparing ES cells and RA-treated cells. Genes that rely on FBXL19 for normal CDK8 binding in the ES cells state are plotted. Top: reduced levels of CDK8 (red, n = 673 of which 203 genes are significantly induced by RA and 55 genes are ES-specific). Bottom: increased levels of CDK8 (green, n = 255 of which 28 genes are significantly induced by RA and 26 genes are ES-specific). (D) Genes for Figure 5D–F were separated into two categories (low and high expression) based on FPKM value cut-off represented by the dashed line. (E) Gene ontology analysis of the genes associated with unchanged CDK8 levels in FBXL19ΔCxxC ES cells (n = 14767).