Extended Data Fig. 7: Effects of conditional Ldb1 deletion on Greek island interactions and OR expression. | Nature

Extended Data Fig. 7: Effects of conditional Ldb1 deletion on Greek island interactions and OR expression.

From: LHX2- and LDB1-mediated trans interactions regulate olfactory receptor choice

Extended Data Fig. 7

a, Schematic of the genetic strategy used to generate Ldb1 KO mOSNs that are fluorescently labelled. b, In Ldb1fl/fl;OMP-cre mice, LDB1 (green) is lost from mOSNs but retained in basal immature cells. Nuclei are stained with DAPI (magenta). Scale bar, 20 μm. Similar results were obtained from three independent experiments. c, Hi-C contacts between a pair of OR clusters located on different chromosomes in control (top) and Ldb1 KO (bottom) mOSNs. A Hi-C hotspot between interacting Greek islands in control mOSNs (arrowheads) is absent in Ldb1 KO OSNs. d, Three-dimensional projection of the same OR cluster pair in control and Ldb1 KO OSNs. e, Trans interactions of each Greek island (n = 59) with the other Greek islands as fraction of the total Hi-C contacts in mOSNs versus Ldb1 KO cells. Greek islands that changed more than twofold are red. f, For each Greek island, the mean number of cis long-range (left) and trans (right) Hi-C contacts per billion made to every non-OR sequence (at 50-kb resolution), intergenic LHX2- and EBF-bound peak (outside OR clusters), or Greek island. Boxes indicate median, upper and lower quartiles; whiskers indicate 1.5 × the interquartile range. g, As in e but for trans contacts between OR gene clusters (n = 67). Clusters that changed more than 1.5-fold are red. h, Circos plots depicting the strongest 1,000 interchromosomal interactions genome-wide at 1-Mb resolution in control mOSNs (left) and Ldb1 KO mOSNs (right). 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, Transcript levels of Greek island-binding factors in RNA-seq data from control mOSNs and Ldb1 KO mOSNs. Transcript levels of Ebf3 are reduced approximately twofold (P = 0.031 for greater than 1.5-fold change, DESeq2 normalized Wald test with n = 5 for control mOSNs and n = 4 Ldb1 KO). The expression of other factors is not significantly different between conditions.

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