Fig. 6: Transcription factors responsible for the regulatory activity of NPE and FPE.

a PLAC-seq data showing the interaction of the Myc promoter with H3K4me3-, H3K27Ac- and Pol2-positive regions in the whole Myc regulatory region (data from ref. ⁴³ downloaded from the 3D genome browser⁶⁸ http://3dgenome.fsm.northwestern.edu/). b PLAC-seq data showing the interaction of the Myc promoter with H3K27Ac- and Pol2-positive regions and ChIPseq data for pluripotency factors in the regulatory region containing the putative NPE and FPE. Above the line that represents the genome, green color segments indicate H3K4me3 interactions with the Myc promoter, red color segments indicate interactions with H3K27-positive regions, and yellow color with both. Below, the ChIPseq meta-analysis is shown for ESCs and EpiSCs. ChIPseq data are from published studies (data retrieved from the ChIP Atlas web browser⁴² https://chip-atlas.org/peak_browser). The height of the bars is proportional to the number of independent studies that detect binding for each factor. c Enlargement of the regions in NPE and FPE that bind Pluripotency TFs. The numbers to the right of the bars indicate the number of independent studies that detected the interaction. d mapping of pluripotency TF DNA-binding motifs coinciding with the ChIPseq interactions and indication of the CRISPR deletions affecting these motifs. e Quantification of the percentage of activity that Myc^GFP/GFP ESCs carrying TF binding motif deletions show in comparison with control Myc^GFP/GFP ESCs in different culture conditions. See Fig. S10 for details on the biological replicates, number of cells analyzed, and exact P-values. Ordinary one-way ANOVA with Šídák’s multiple comparisons test; ns: P-value > 0,05; **P-value < 0,01; ***P-value < 0,001. Source data for all graphs are available from the Source Data file and raw data from Figshare (see “Data availability” section).