Extended Data Fig. 6: TET1 regulates actively transcribed genes in liver organoids.

a-d, DamID-sequencing was performed in EpCAM⁺ sorted ductal cells derived from already established liver organoids (3 independent experiments). Only TET1-Dam peaks identified in all 3 experiments were considered for further analyses. a, Scheme of DamID-seq protocol. b, Heatmaps showing TET1 peaks identified by DamID-seq (left panels) and H3K4me3 peaks identified by ChIP-seq (right panels). Heatmaps are centred in the middle of the peak (0) and show a genomic window of ± 10 kb. Top heatmaps represent common peaks between TET1 and H3K4me3 (2848 peaks) while bottom heatmaps represent TET1-specific peaks (2254 peaks). c, Pie-chart indicates the percentage of genomic distribution of TET1-Dam peaks. d, GO and statistical analyses of biological processes among TET1-Dam targets in liver organoids were performed using DAVID 6.8. n, number of genes. e, 5hmC and 5mC levels determined by MeDIP and hMeDIP followed by qPCR on the indicated genomic region surrounding Lgr5 TSS in WT (black), Tet1^hypo/hypo (blue) and hypo-OE (red) organoids. Graphs represent mean of n = 3 independent experiments. Student’s two tailed was performed comparing samples to WT. *, p < 0.05; ** = p < 0.01 f, TET1 ChIP-qPCR at Lgr5 TSS (left panel) and Lgr5 mRNA levels (right panel) in WT, Tet1^hypo/hypo and hypo-OE organoids. Graphs represent mean ± SD of n = 3 independent experiments. Student’s two tailed t-test statistical analyses were performed versus WT. **, p < 0.01 g, Sorted EpCAM⁺ cells from WT livers were cultured in organoid culture conditions and harvested for DNA, chromatin and mRNA expression analyses at the indicated time points. Graphs represent mean of n = 3 independent experiments. Student’s two tailed t-test analyses were performed versus t = 0 h *, p < 0.05; ** = p < 0.01; *** = p < 0.001.

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