Fig. 5.

Oct4^defSox2 targets pluripotency enhancers but eventually derails. a Heat maps of ChIP-seq reads at days 1 and 5 for Oct4, Oct4^defSox2 and Sox2 in Oct4-SK (top panels) or Oct4^defSox2-SK (bottom panels) cocktails centered at Oct4 constitutively bound occupancy trajectories (‘110’ and ‘111’) containing SoxOct motifs (left panels) or MORE motifs (right panel). A cartoon on the left summarizes the results. b ChIP-seq reads at day 5 for Oct4 and Oct4^defSox2 for Oct4 late bound occupancy trajectories ‘010’ and ‘011’ at SoxOct (top) or MORE (bottom) locations. c Heatmap of Oct4, Oct4^defSox2 and Sox2 ChIP-seq signals at days 1 and 5. Rows are Sox2 ChIP-seq peaks called in the Oct4-SK condition containing SoxOct motifs at day 1 (left panel) and day 5 (right panel). ChIP-seq signal heatmaps in a, b and c are normalized using EAseq (DNA fragments per kilobase pairs (kbp) per million (M) reads) and shown for 2 kb genomic intervals centered on midpoints or motifs. d Genome browser tracks of selected Oct4, Oct4^defSox2 and corresponding Sox2 ChIP-seq peaks are shown at different days of reprogramming. The nearest genes and motif under the peaks are mentioned on the top. Genomic coordinates for the summits are listed in Supplementary Table 4. e Phase-contrast images of conditional Oct4-knockout ZHBTc4⁴³ ESCs rescued with wild-type Oct4 or Oct4^defSox2 after culturing for 6 days in the presence of Dox (passage 1). Scale = 100 μm. f Fluorescence images of ZHBTc4 ESCs rescued with wild-type Oct4 or Oct4^defSox2 after 6 passages in the presence of Dox. Scale = 100 μm. The antibodies list is in Supplementary Table 11. g qRT-PCR analysis of selected gene expression of ZHBTc4 ESCs rescued with wild-type Oct4 or Oct4^defSox2 after 6 passages in the presence of Dox. The expression is relative to untransduced control induced with Dox for 7 days. Rpl37a was used as a house keeping gene. Individual data points are shown as black jitter plots (n = 3, technical replicates). The primers for Oct4 CDS (coding DNA sequence) and other markers are mentioned in Supplementary Table 10 and Source data are provided as a Source Data file