Supplementary Figure 10: Transcription-factor dynamics at hotspots of topological change.

(a) Compartment switching induced by C/EBPα (B-to-Bα, top) or OSKM (Bα-to-D2, bottom). Line graphs depict average expression changes of genes located in regions that have stably switched. (b) GO annotation of genes (n = 358) that stably switch B-to-A compartment at the Bα-D2 transition. (c) Average gene expression changes of the genes (n = 10) associated with the gene ontology (GO) term ‘Embryo Development’ that stably switch B-to-A compartment at the B-Bα transition. (d) Klf4 binding enrichment (over the genome-wide average) at the 20 switching clusters shown in Fig.2g. Mean values with 95% CI are shown. (e) Percentage of TAD border regions (n = 3,100) bound by Oct4 at each timepoint. (f) Oct4 (left) and Klf4 (right) enrichment kinetics at border regions that are already targeted by these factors at D2 (n = 37 for Oct4, n = 22 for Klf4) or border regions not yet targeted at D2 (n = 147 for Oct4, n = 162 for Klf4). (g) C/EBPα (left) or Oct4 (right) enrichment at border regions bound by indicated transcription factors at the earliest timepoint (n = 123 for C/EBPα, n = 37 for Oct4) or unbound regions (n = 61 for C/EBPα, n = 147 for Oct4). Mean values +/- SD are indicated, as well as individual data points. P values were calculated using a Wilcoxon rank-sum test. (h) Venn diagram showing the overlap between the number of dynamic borders bound by Oct4 (at D2), Klf4 (at D2) and C/EBPα (at Bα). (i) Kinetics of key transcriptional, epigenomic and topological events during somatic cell reprogramming. Light-to-dark color intensity range signifies quantitative differences. Ect., ectopic; chr., chromosome.