Extended Data Fig. 5: Greek islands and LHX2 are required for OR compartmentalization in developing OSNs.

a, Pairwise Hi-C contacts between all pairs of Greek islands ordered by genomic position in control (left) and Greek island triple KO (right) mOSNs. The 50-kb regions containing the deleted Greek islands are marked with arrowheads. Plotting the log₂[fold difference] in Hi-C contacts (right) reveals that consistent strong reductions are observed for the deleted islands. Colour bar depicts chromosome. b, c, The genomic regions exhibiting the most significant reductions in Hi-C contacts with trans OR Greek islands (b) or trans OR clusters (c), in triple KO mOSNs relative to control mOSNs, are mostly located within the three OR clusters containing the deleted Greek islands (two biological replicates per condition, see Methods). d, Genetic and experimental strategy for early Lhx2 deletion. Tamoxifen induction with Krt5-creER deletes Lhx2 in HBCs and then methimazole treatment ablates INPs and mOSNs, leading to regeneration from Lhx2-deleted HBCs. e, Fluorescent labelling of the HBC-derived cells upon methimazole induction reveals two major populations, bright and dim. f, RNA-seq shows that the dim population expresses markers of INPs and mOSNs; the bright population expresses markers of HBCs. Counts are normalized by row. g, Three-dimensional projection of Hi-C contacts between OR clusters located on different chromosomes in control mOSNs, INPs, early Lhx2 KO cells and late Lhx2 KO cells (from left to right). A Hi-C hotspot between interacting Greek islands is observed only in control mOSNs (arrowhead). In addition, a strong reduction in the surrounding OR–OR contacts relative to mOSNs or INPs is observed in the early Lhx2 KO cells. h, Circos plots depicting the strongest 1,000 interchromosomal interactions genome-wide at 1-Mb resolution in (left to right) mOSNs, INPs, early Lhx2 KO cells, and late Lhx2 KO cells. Red lines represent OR–OR contacts and black lines non-OR–non-OR contacts. Line thickness increases with contact frequency. Chromosome numbers depicted at the periphery of the circle. i, Genetic strategy for late Lhx2 deletion and fluorescent marking of Lhx2 KO mOSNs. j, Left, for each Greek island, the fraction of total Hi-C contacts made to other Greek islands located in cis at short range (<5 Mb apart, grey), long range (>5 Mb apart, blue), and in trans (red). Top, control mOSNs; bottom, late Lhx2 KO cells. Right, the effect of late Lhx2 KO on the mean fraction of Hi-C contacts across all Greek islands (two-sided, paired Wilcoxon signed-rank test, n = 59).