Fig. 5: The genomic locus of Gm26793 forms inter-chromosomal interaction with Cubn.

a Venn diagram showing the workflow for the screening of potential Gm26793 targets by the integrative analyses of RNA-seq and 4C-seq data. b Circos plot showing inter- and intra-chromosomal connectivity associated with the genomic region of Gm26793. Line colors represent up- (red) and down-regulation (blue) of annotated genes. c Dot plot summarizing genes with both significant Gm26793-interacting hits revealed by 4C-seq and obvious expression changes between WT and GKO cells based on transcriptomic data. Genes are ranked by the fold change of expression. d, e Western blotting results reporting the aberrant activation of CUBN in GKO cells during EB (d) and XEN (e) differentiation. f, g The expression recovery of mesoderm-associated genes on day 6 of EB differentiation (f) and PrE-related genes on day 7 of XEN differentiation (g) upon Cubn knockdown in GKO cells. h, i Heatmap showing the transcriptomic recovery of GKO samples on XEN-D7 upon Cubn knockdown. Expression recovery of representative up- and down-regulated genes are listed in i. j, k Representative images describing the rescue of protein distribution during EB (left) and XEN (right) differentiation. Scale bars, 50 μm and 75 μm. Quantification of the data is shown in k. l, m dCas9-mediated living cell imaging showing the spatial separation of the Gm26793 (Red probe) and Cubn (Green probe) loci upon GKO region deletion in mESCs. The increase in 3D-distance between Gm26793 and Cubn loci is presented in m as mean ± SD (WT, n = 37 cells; GKO, n = 65 cells). One-way ANOVA analysis with Tukey’s test is used in f, g, k and data are shown as means ± SEM; Student’s t-test analysis is used in m; *P < 0.05, **P < 0.01, ***P < 0.001.