Supplementary Figure 10: Looping efficiency analysis highlights the effect on the endogenous Klf4-SE loop after engineering a loop with 24h blue light illumination.

(a) Zoomed-in 5C heatmaps representing the endogenous loop between pluripotency-specific Klf4 SE and Klf4 gene (chr4:55,447,136–55,583,136). The blue box represents the 4C viewpoint at Klf4 promoter in (b-c) and Figure 3g. The green box indicates the 4C viewpoint at Klf4 SE in (b, c) and Figure 3g. See Supplementary Figure 1 for details of the plasmid combinations used. (b) Classic 4C looping efficiency plots. The line graphs represent normalized interaction frequency of the Klf4 promoter (brown vertical line) for five biological replicates in LADL + blue light (blue line), LADL + dark (black line) and additional controls in each replicate as listed: Empty target control in dark (grey line) included in replicates 1, 3 and 4; Empty anchor control + dark (grey line) and + blue light (light blue line) included in replicate 2; and one-sided guide control +dark (light gray line) and + blue light (light blue line) included in replicate 3. The single pixel of interest (endogenous Klf4-SE loop) at the SE is shaded in yellow. (c) Strip charts show the % looping efficiency of the (left) Klf4 promoter interactions at the SE and (right) SE interactions at Klf4 promoter for each condition in all five replicates after 24h of blue light illumination. Values derived from the pixel at the intersection of green and blue boxes as shown in panel (a). Red bars indicate medians of each condition.