Fig. 6: Six3 contributes to the robust insulation of the Six3 and Six2 regulatory domains through promoter competition. | Nature Communications

Fig. 6: Six3 contributes to the robust insulation of the Six3 and Six2 regulatory domains through promoter competition.

From: Cooperative insulation of regulatory domains by CTCF-dependent physical insulation and promoter competition

Fig. 6

A Genomic rearrangements generated in mESC within the Six3/Six2 locus: Δ6XCTCF; Six3−/−; Δ6XCTCF: Six3−/−; Δ4XCTCF; Δ4XCTCF:Six3−/−. B, C Six3 and Six2 expression was measured by RT–qPCR in NPC homozygous for the indicated re-arrangements using the following number of biological replicates: WT −16 replicates (same as in Fig. 5C, D); Δ6XCTCF −19 replicates using a previously characterized clonal line63 (same as in Fig. 5C, D); Six3−/− −16 replicates using three clonal lines; Δ6XCTCF:Six3−/− -15 replicates using three clonal lines. D Capture-C experiments in WT, Δ6XCTCF, Six3−/− and Δ6XCTCF:Six3−/− NPC using Six3 SE as a viewpoint. Average Capture-C signals of the two replicates performed for each cell line are shown around the Six3/Six2 locus individually (upper tracks) or after subtracting the WT signals (lower tracks). E Average Capture-C signals were measured around Six2 (highlighted in yellow in (D); chr17:85674267-85698254 (mm10)) and within five 30 Kb control regions (Ctrls) located within the Six3 TAD (red asterisks in (D) indicate the midpoint of the controls regions (mm10): chr17:85388601-85418601; chr17:85338601-85368601, chr17:85288601-85318601, chr17:85238601-85268601, chr17:85188601-85218601). Capture-C signals are shown for the Δ6XCTCF, Six3−/− and Δ6XCTCF:Six3−/− NPC as log2 fold-changes with respect to WT NPC. F, G Six3 and Six2 expression was measured by RT–qPCR in NPC homozygous for the indicated genomic re-arrangements using the following number of biological replicates: WT −16 replicates (same as in Fig. 5C, D); Six3−/− −16 replicates using three different clonal lines (same as in Fig. 6C); Δ4XCTCF −12 replicates for Six3 and 11 replicates for Six2 using three different clonal lines; Δ4XCTCF:Six3−/− −12 replicates using three different clonal lines. Expression differences among cell lines were calculated using two-sided non-paired t-tests (NS (not significant): fold-change < 2 or p > 0.05); ND (not detectable)). In (B, C, F, G) box plots, the upper and lower parts of the box are the upper and lower quartiles, respectively, the horizontal line that splits the box in two is the median and the upper and lower whiskers indicate the maximum and minimum, respectively. Source RT-qPCR data are provided as a Source Data file.

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