Extended Data Fig. 2: The transcriptomic landscape of TKO EpiLCs and genomic composition of SWRs.
From: DNA methylation shapes the Polycomb landscape during the exit from naive pluripotency
a. Heatmaps showing expression levels (RPKM) of naïve (Klf4, Tbx3, Zfp42/Rex1, Fgf4 and Prdm14) and formative/primed (Pou3f1, Sox3, Etv5, Cdh2 and Fgf5) pluripotency markers in vitro and in vivo (inner cell mass cells of E3.5 and E4.0 blastocysts, and E5.5 and E6.5 epiblasts). For each in vitro and in vivo dataset, the scale bar for each gene is set independently to the maximum expression of that gene in WT and TKO samples. b. Principal Component Analysis (PCA) plot showing transcriptomic similarities between naïve ESCs with the inner cell mass cells of the blastocyst, and between EpiLCs with epiblasts. Both groups are arbitrarily circled by a dotted line. D0: ESCs; D2, D4, D7: EpiLCs; Oo.: oocyte; 1C: zygote; E2C: early 2-cell embryo; 2C: 2-cell embryo; L2C: late 2-cell embryo; 4C: 4-cell embryo; 8C: 8-cell embryo; Mo.: morula-stage embryo; ICM: inner cell mass cells of the blastocyst; TE: trophectoderm cells of the blastocyst; E5.5-, 6.5-, 7.5-: embryonic days; Epi: epiblast; ExE: extraembryonic ectoderm; Endo.: endoderm; Meso.: mesoderm; Ecto.: ectoderm; Prim. Str.: primitive streak. c. Pie charts showing the genomic distribution of H3K27me3 domain classes SWitch Regions (SWRs), ESC-Specific Regions (ESRs) and COnstitutive Regions (CORs). A fourth pie chart showing the total area of each genomic compartment is included. d. Motif analysis showing enriched motifs in the putative PRC binding sites within SWRs using ESRs as control sequences and two motif analysis algorithms.
