Fig. 4

OCT4-binding dynamics distinguish several classes of gene regulatory elements. a Heatmap of 31,555 high-confidence OCT4-binding peaks that show dynamic changes over undirected differentiation (2-fold change between any two timepoints). Dynamic peaks were sorted based on OCT4 enrichment at 0, 48, and 96 h, separating them into pluripotency (n = 16,229) or differentiation (n = 15,326) associated peaks. RPKM: Reads per kilobase per million. Each timepoint consists of two replicates. b Heatmap of the statistical overlap between transcriptionally dynamic genes and genes associated with either with pluripotency or differentiation peaks. P value is calculated by the hypergeometric test and displayed in log₁₀. c Venn diagram of OCT4 peaks from iPSCs (0h; gray), the 96 h differentiated cells (orange), and cells exposed to dox for 48 h after 48 h of differentiation (light blue, 48 h + 48 h dox). Most pluripotency-associated OCT4 targets are not shared with the 96 h or 48 h + 48 h dox timepoints (pluripotency-exclusive: “exclusive”, n = 9293 of 16,229 0 h peaks). A subset of pluripotency-associated sites (pluripotency-reaccessed: “reaccessed”; n = 3,550) are accessed by OCT4 in the 48 h +48 h dox sample (see also Supplementary Fig. 3a). RPKM Reads per kilobase per million. d Composite plots of OCT4 occupancy (black) and chromatin state at 0, 48, and 96 h differentiation timepoints for exclusive (top) and reaccessed (bottom) OCT4 targets. Chromatin state includes: H3K4me2, yellow; H3K27ac, dark red; and chromatin accessibility as measured by ATAC-seq, blue. Lines represent the median enrichment for each set within ±2 kb of the peak center. Each time-point consists of two replicates. e Genome browser tracks of OCT4 enrichment at the Zfp281 locus. Top: OCT4 enrichment over differentiation (black). Bottom: selected chromatin dynamics (H3K4me2, yellow; H3K27ac, red; ATAC, blue). f. P value heatmap of the statistical overlap between genes that are induced, repressed, or unchanged (unresponsive) upon OSKM induction after 48 or 96 h differentiation, and genes closest to each of the three dynamic peak classes. Peaks were assigned to nearest protein-coding gene, with no upper bound on distance. P value for overlap significance is calculated by the hypergeometric test