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. 2020 Apr 7;9:e55159. doi: 10.7554/eLife.55159

Figure 5. Cap-G knockdown in neurons display severe misregulation of gene expression.

(A) Volcano plots showing differentially expressed genes in elav-KD and nSyb-KD respectively. Significant differential expression marked in red by a Log2 fold change > 1 or <-1 and FDR < 0.05. Control genotypes are elav-GAL4; UAS-deGradFP and nSyb-GAL4; UAS-deGradFP for elav-KD and nSyb-KD respectively. (B) Pie charts showing tissue of origin expression data for upregulated genes in Cap-G KD datasets taken from FlyAtlas. The majority of genes are not normally expressed in the CNS but in alternative tissues. (C) Venn diagrams showing significant overlap between Up/Down regulated genes and Cap-G DamID peaks for elav and nSyb neurons respectively, Fisher’s exact test (p<1×10−20). (D) Heatmap of overlapping differentially expressed genes between elav-KD and nSyb-KD. (E) Enriched Gene Ontology analysis of downregulated genes from elav-KD shows mostly neuron-specific terms. (F) Example of differentially expressed genes directly bound by Cap-G in elav-KD (all three replicates displayed).

Figure 5.

Figure 5—figure supplement 1. Analysis of RNA-seq data.

Figure 5—figure supplement 1.

(A-B) MA plot of RNAseq datasets for elav-KD and nSyb-KD respectively showing mean of normalised counts and log2 fold change values, significant genes marked in red. (C-E) Enriched GO terms analysis for differentially expressed genes, gene enrichment ratio shown, circle size correlates with number of genes detected and colour with p-adjust value. (C) Upregulated genes in elav-KD showing generic, non-CNS specific terms GO terms. (D) Upregulated genes in nSyb-KD showing generic, non-CNS specific terms. (E) Downregulated genes in nSyb-KD showing metabolic-related GO terms.