Figure 5

Reduced Gene Expression in Sox2 MUT NSCs Correlates with Loss of Long-Range Interactions

(A) Distribution of expression values (TPM) of genes with TPM >0. Blue, WT NSCs; orange, MUT NSCs. From left to right: all genes; genes whose promoter is a node (P-P, P-E interactions); genes whose promoter is connected to an enhancer (P-E interactions); genes with SOX2-positive P-E interactions.

(B) Distribution of expression values (y axis) of genes according to the number and type of element (enhancer or promoter anchors) interacting with the gene promoter (x axis) in wTR1, wTR2, and wTR3. Top: interactions with enhancers. Bottom: interactions only with promoters. The number of genes involved is shown in each diagram inside the box along the x axis.

(C) Distribution of the fold ratio values for all genes with TPM >0 defined as log2 (TPM_WT/TPM_MUT). It confirms results shown in (B): the fold ratio is shifted toward positive values (i.e., a majority of genes have expression in WT higher than in MUT NSCs).

(D) Coassociation scores (histograms, -log₁₀p) calculated for genes (TPM >5) showing either reduced gene expression in MUT NSCs (red), or no relevant change (green), and the indicated categories of interactions detected in wTR1, wTR2, and wTR3 (see STAR Methods). DOWN_MUT, genes showing statistically significant expression reduction; DOWN_MUT NO_SIGN, genes showing moderate expression reduction; OTHERS, all other genes. The types of interactions are shown on the right; data for “SOX2 promoter target” are not significant.

See also Tables S5 and S8.