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Fig. 4 | Epigenetics & Chromatin

Fig. 4

From: Individual retrotransposon integrants are differentially controlled by KZFP/KAP1-dependent histone methylation, DNA methylation and TET-mediated hydroxymethylation in naïve embryonic stem cells

Fig. 4

5hmC accumulates at upregulated TEs upon KAP1 removal. a Boxplot of 5hmC enrichment fold change between Kap1 knockdown and control sample on genes or TEs separated in upregulated (brown), downregulated (blue) or stable (green) according to their behaviour upon Kap1 knockdown as measured by RNA-seq (5 days post-transduction). Number of elements in each subgroup is shown below in each box. Wilcoxon test, ***p < 0.001. Data are averaged from three independent RNA-seq experiments. b Correlation plots between fold change in RNA levels and 5hmC enrichment upon Kap1 knockdown for IAPEz (left) and MERVL (right) integrants. Elements in each family are divided in KAP1-bound (orange) and not bound (grey). Regression line is traced in green for bound elements and black for not-bound elements. IAPEz: bound pval = 0.0, Spearman correlation coefficient = 0.3, not bound pval = 0.44, Spearman correlation coefficient = 0.2. MERVL: bound pval = 0.926, Spearman correlation coefficient = 0.0216, not bound pval = 0.4, Spearman correlation coefficient = 0.03. a Percentage of KAP1-bound L1 elements from indicated subfamilies in mESCs, arranged from the oldest to the youngest as previously described [65]. KAP1 binding was determined by ChIP-Seq, plotting either uniquely or multiply mapped reads. Data are averaged from two independent ChIP-seq experiments. Myr: Million years. b Boxplot of 5hmC enrichment on indicated KAP1-bound L1 elements in wild-type and Kap1 knockdown cells. Wilcoxon test, *p < 0.05, **p < 0.01, ***p < 0.001. Data are averaged from two independent hMeDIP-seq experiments. c Correlation plots between fold change in RNA levels and 5hmC enrichment upon Kap1 knockdown for L1Md_A and L1Md_T elements. Elements in each family are divided in KAP1-bound (orange) and not bound (grey). Regression line is traced in green for bound elements and black for not-bound elements. L1Md_A: bound pval = 0.0, Spearman correlation coefficient 0.26, not bound pval = 0.69, Spearman correlation coefficient = 0.01. L1Md_T: bound pval = 0, Spearman correlation coefficient = 0.3, not bound pval = 0.0, Spearman correlation coefficient = 0.08. e Boxplot of 5hmC enrichment on L1MdT KAP1-bound and enriched for the indicated histone mark, in wild-type and Kap1 knockdown cells. Wilcoxon test, *p < 0.05, **p < 0.01, ***p < 0.001. Data are averaged from two independent hMeDIP-seq experiments

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