Extended Data Figure 4: Greek Islands make differentiation-dependent contacts with other Greek Islands in trans that are stronger than cis contacts with Lhx2/Ebf peaks.

a-b, Heatmap and 3D projection of HiC contacts between a pair of OR gene clusters in cis (a) and trans (b) reveals a local maximum of in situ HiC interactions between Greek Island loci (arrowheads) in mOSNs. c-f, Same as a, b but for immediate neuronal precursors (INPs) and Horizontal Basal Cells (HBCs). g, For chromosome 2, fraction of all HiC contacts made to trans Greek Islands in mOSNs (top), INPs (middle) and HBCs (bottom). h, For each Greek Island, the distribution of HiC contacts, expressed as contacts per billion, made to individual Greek Islands located in trans for HBCs, INPs and mOSNs. Box indicates median, upper, and lower quartiles while whiskers indicate 1.5 * the interquartile range. For each Greek Island, the number of trans Greek Islands is listed. i, (left) Comparison of the total fraction of HiC contacts made by each Greek Islands to intergenic Lhx2/Ebf co-bound peaks present in cis versus Greek Islands present in trans for HBCs, INPs and mOSNs. For each category we compare roughly equal numbers of peaks (number of trans Greek Islands for each Island versus number of cis Lhx2/Ebf sites for each Island, mean+/− standard deviation). (right) Mean fraction of HiC contacts across all Greek islands (two-sided, paired Wilcoxon signed-rank test, n=59). Contacts with trans Greek Islands (red) constitute a higher fraction of HiC contacts than short-range cis (dark blue) or long-range cis (light blue) contacts with intergenic Lhx2/Ebf peaks. All panels present pooled data from 2 independent biological replicates that yielded similar results when analyzed separately.