Fig. 9
Pioneering activity of mPouV/Sox3 initiates extensive chromatin remodelling, such as the chromatin looping of distal pCRMs with promoters. a Used approach to reveal the effect of mPouV/Sox3 on chromatin conformation between 30 promoters and distal pCRMs (next-generation capture-C; n = 3 biologically independent samples) at the MBT. b Bar graph shows the number of normalised promoter contacts (mean + s.d.; n = 3 biologically independent samples) derived from non-redundant capture-reporter FLASH88 reads (Supplementary Fig. 12b) for each promoter captured with one or two probes under control condition (Supplementary Data 10). c Violin plots compare the number of promoter contacts with accessible pCRMs between uninjected and mPouV/Sox3 LOF embryos. The comparison is stratified into pCRMs with stable and lost accessibility upon mPouV/Sox3 LOF and shown for both all and affected (FDR ≤10%) promoter contacts. Wilcoxon tests and effect size estimates: *p = 5 × 10–5 and reffect = 0.12 (small effect); **p = 5 × 10−30 and reffect = 0.34 (medium effect); and ***p = 5 × 10−10 and reffect = 0.78 (large effect). d Superimposed line tracks show promoter contact frequencies, chromatin accessibilities and DNA occupancies of various chromatin components (Smad2, β-catenin, H3K4me1 and RNAPII) at the cdc25b gene locus between control (uninjected) and mPouV/Sox3 LOF embryos. The RNA track is split into a high (0–12) and low (0–0.01) expression window. Note that the low-expression window shows that locally transcribed non-coding super-enhancer RNA depend on mPouV/Sox3 as well as the gene cdc25b. Heat maps (p∆) below each superimposed line plot show the statistical significance (Wald test) of changes caused by mPouV/Sox3 LOF. The footer highlights the occurrences of canonical POU/SOX motifs (black filled rectangles) at accessible pCRMs (±50 bp from the accessibility centre) and one strongly affected pCRM with an arrowhead. Asterisks on the p∆ heat map mark significant (FDR ≤10%) reductions to pCRM accessibility. pCRMs are boxed in and their frequency of contacts with the cdc25b promoter are illustrated with an arc of varying strength. Boxes of affected pCRM and arcs of promoter contacts are coloured orange
