Figure 6.

TF activity and RNA-seq integration identifies Chi3l1-activated MAZ as regulator of stemness in GSCs. A, Left, MA plot exhibiting differentially accessible sites following Chi3l1 exposure. Right, the corresponding motif enrichment at promoters with accessibility gain. B, Venn diagrams depicting TF activity consensus across the three TF activity platforms (DAStk, HINT-ATAC, and TOBIAS). C, Barcode plot encoding TF activity enrichment at MAZ motifs in Chi3l1-treated samples versus controls (P = 2.3E-05) using DAStk. D, HINT-ATAC aggregates footprint signal at MAZ motif in control versus treated samples (P = 0.06). E, Top plots show aggregate signals of TF binding across conditions (left, control; right, Chi3l1). Heatmaps depicting individual binding site signals show greater signal enrichment for bound sites compared with nonbound sites. Chi3l1 sample experienced an increase in bound site relative to control. F, Read count plot showing that MAZ is knocked down in siMAZ (siRNA) RNA-seq. G, Volcano plot displays differential gene expression following MAZ knockdown. NS, nonsignificant; up, upregulated in siMAZ; down, downregulated in siMAZ. H and I, Volcano plots depict differentially expressed genes following siMAZ [genes activated by MAZ (H) or repressed by MAZ (I)]. Green points emphasize differentially expressed genes with MAZ footprint/binding within their promoters. J, The activated or repressed genes by MAZ were queried for pathway enrichment. K and L, Examples depicting footprints within the promoters of MAZ-activated FOXO3 and MAZ-repressed ADAMS9. Footprints coincide with sites with (i) high binding scores and (ii) loss of signal within highly accessible sites that is characteristic of ATAC footprints. M, Knockdown of MAZ expression in GSCs rescues the activation of self-renewal induced by Chi3l1.