Supplementary Figure 6: E2 stimulation results in dynamic proximity of MegaTrans enhancers in chromosome 21.
From: Phase separation of ligand-activated enhancers licenses cooperative chromosomal enhancer assembly
a. Effects of E2 on the proximity of indicated MegaTrans enhancer loci. Arrowhead points to the pair of loci in proximity. Image representative of at least 200 nuclei examined in independent experiments b. Comparison of cumulative distribution of distances between indicated MegaTrans enhancers demonstrate that 3D distances between these loci are reduced in response to E2 stimulation. c. Data from DNA FISH targeting genomic regions that showed or did not show induced proximity with E2 treatment. CP = Control Probes targeting non-ERα bound genomic regions. Numbers on the box plots represent median distance. Data are median ± interquartile range. P-value was calculated using Wilcoxon rank sum test with continuity correction. (b,c) Data pooled from total of at least 150 nuclei examined in replicates d. Relationship between median spatial distance and genomic distance for all pairs of TADs on Chr.21 in IMR90 cells, calculated using published data70. The solid line is the best-fit of a power-law function with scaling exponent S. This function was used to predict the expected median spatial distance between any two probed genomic loci in the basal condition. A cut-off distance equal to 40% of the predicted median distance for any two given loci was arbitrarily used to define the spatial proximity of those loci. For example, since the predicted median distance between the TFF1 and NRIP1 loci in IMR90 cells was 1.5 µm, the cut-off distance was taken to be 1.5 x 0.4 = 0.6 µm (600 nm). See Methods for more details.
