Fig. 3: Lola-I promotes tissue-specific gene expression through an effect on the promoter.
From: Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development
a Left panel: Boxplot of bulk RNA-seq data show that Lola-I targets are down-regulated in lola-I mutants compared to wild-type (14–17 h AEL), while control genes show overall similar expression levels. This confirms that Lola-I mediates its effect by directly binding to target promoters, and not by indirect effects that would affect all genes (Wilcoxon two-sided test, lolaORC4/ORC4: *P = 1.8e−11, lolaORC4/ORE50: *P < 2e−16). Right panel: Boxplot of bulk RNA-seq data show that genes associated with distal Lola-I binding sites are not significantly affected in lola-I mutants compared to wild-type (14–17 h AEL), while genes with Lola-I binding at the promoter (with or without distal binding) are reduced in expression, showing that Lola-I largely mediates its effect through binding promoters. b scRNA-seq analysis of wild-type and lola-I mutant embryos at 14–14.5 h AEL suggests that Lola-I is required for both tissue-specific expression (left) and basal expression levels in other tissues (right) at target genes (defined by >2-fold loss in Pol II occupancy in mutant embryos). Expression, shown as the fraction of cells with detectable expression, is reduced in lola-I mutant embryos compared to wild-type (Wilcoxon two-sided test, expressing tissue: *P = 1.1e−05, other tissue: *P = 0.00578). The same trend is observed for the median expression (Supplementary Fig. 3c). c scRNAseq expression data for the Lola-I target gene Gip is shown for each cell (red and gray dots) isolated from wild-type (left) or lola-I mutant embryos (right). A violin plot of the data is laid on top. In wild-type embryos, Gip is expressed at high levels in crystal cells (marked in red by the expression of the PPO2 gene), but also shows basal levels of expression in the majority of cells where Gip is not expected to be expressed. In lola-I embryos, both the specific expression and the basal expression are reduced. Box plots show the median as the central line, the first and the third quartiles as the box, and the upper and lower whiskers extend from the quartile box to the largest/smallest value within 1.5 times of the interquartile range.
