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. 2020 Oct 8;11:5061. doi: 10.1038/s41467-020-18900-z

Fig. 3. JMJD3-induced H3K27me3 demethylation precedes transcription activation.

Fig. 3

a RNA-seq heatmap of genes significantly (q value < 0.1, fold-change >1.5) upregulated upon JMJD3 OE or downregulated by shJmjd3 #2 at days 5 and 10. These genes were divided into PSC-enriched, transiently activated, and MEF-enriched according to expression pattern in MEFs, PSCs, and OSKM-reprogramming. Left controls: P2 MEFs transduced with Empty or JMJD3, P2 WT, and Jmjd3 cKO MEFs. Right controls: our own dataset for OSK-iPSCs and PSCs including iPSCs and ESCs from a published dataset (GSE93027). b Heatmaps showing the fold change of selected epithelial and mesenchymal genes upon JMJD3 OE or knockdown compared to the controls. c Heatmaps showing the fold change of selected early-activated and late-activated pluripotency genes upon JMJD3 OE or knockdown compared to the controls. Genes with asterisk have H3K27me3 demethylation at day 5 of reprogramming. d H3K27me3 global density pileups (upper panels) and tag density heatmaps (lower panels) of all H3K27me3 peaks in WT and Jmjd3 KO P2 MEFs transduced with OSKM and Empty or JMJD3 in medium with Vc at days 5 and 10. e Tag density pileups of H3K27me3 in WT (solid line) and Jmjd3 KO (dashed line) P2 MEFs transduced with OSKM and JMJD3 (green) or Empty (red) at day 5. -/+10 kb windows of regions around the TSS and TTS (left panel), gene desert (middle panel), and within ESC-specific enhancers34 (including typical enhancers and super-enhancers; right panel), are shown. f Violin plots of H3K27me3 levels at TSS and enhancers of PSC-enriched genes that upregulated by JMJD3 OE at day 5 (upper left panels) or only at day 10 in the indicated samples (upper right panels). Numbers in the brackets are gene number for each time point. The lower two panels are reanalysis of the dataset by Chronis et al.34 (GSE90895). 48 h, 48 hours. g Tag density pileups of H3K27me3 in WT and Jmjd3 KO P2 MEFs transduced with OSKM and Empty or JMJD3 in medium with Vc at day 5 at binding sites of OSKM in ESCs (from GSE11431).