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. 2020 Feb 28;11:1112. doi: 10.1038/s41467-020-14916-7

Fig. 5. DM subregions are most specifically demarcated by high levels of ESRRB binding.

Fig. 5

a Transcription factor (TF) motif enrichment in PU, DM and INT subregions, and gene expression of corresponding TFs in ESCs (serum/LIF) and EpiSCs25. b Motifs and statistical enrichment (hypergeometric test, BH adjusted) for TFs shown in a. c Heatmap showing the relative enrichment levels (median log2 fold change of ChIP-seq signal (RPKM + 1) over input signal (RPKM + 1)) at SE subregions in ESCs for TFs, co-regulators and chromatin accessibility (ATAC-seq). d Heatmap showing relative enrichment levels (calculated as in c) at SE subregions in ESCs for ESRRB, SOX2 and STAT3-independent ChIP-exo datasets. Enrichment scores for each feature are scaled by dividing by the mean enrichment score for that feature across all subregions. See Supplementary Data 1 for dataset accession numbers. e Expression changes (RT-qPCR) relative to control ESCs of selected class I (Oct4, Smarcad1, Otx2, Lefty1, Klf13, Med13l, Tet1 and Nanog) and class II (Tfcp2l1, Klf2, Klf4, Klf5, Tdh, Tbx3, Tet2 and Esrrb) SE-associated genes in Esrrb-depleted (−/−) and Nanog−/− ESCs. Medians are indicated by bars. Mann–Whitney test was used to compare class I (light green) and class II (pink) expression behaviour. f Expression changes (RT-qPCR) in WT or MutAF-2 transfected Esrrb−/− ESCs relative to empty vector are shown for selected class I and class II SE-associated genes as in a. Data represent three independent experiments (n = 3). g CpG methylation at different CpG positions (asterisks) within DM (magenta) and INT (grey) subregions of the Klf4-associated SE in Esrrb−/− (blue) and control (f/f; grey) ESCs and corresponding converted EpiSCs (c-EpiSCs; red and orange, respectively), as well as in control ESCs cultured in 2i/LIF (2i; black dashed). The profile of Esrrb−/− ESCs was not analysed in 2i/LIF due to loss of cell viability as previously reported50. Data are means ± s.e.m. of three independent experiments (n = 3). Source data are provided as Supplementary Data 10.