Figure 3.

M1BP RNAi leads to widespread gene deregulation that is largely prevented through ZKSCAN3 co-expression. (A) Weighted Venn diagram representation of RNA-seq-identified L3F differentially expressed genes (DEGs) upon M1BP RNAi knockdown and DEGs in M1BP RNAi;ZKSCAN3 co-expressing fat body cells highlighting that more than two-thirds (1026) of M1BP RNAi-induced DEGs are prevented by ZKSCAN3 co-expression. Scatter plot of log2 fold changes in gene expression upon M1BP RNAi (ordinate) and M1BP RNAi;ZKSCAN3 (abscissa) co-expressing L3F fat body cells. Differential gene expression analyses identifying DEGs in both conditions are marked in red, genes prevented from being differentially expressed upon M1BP RNAi through ZKSCAN3 co-expression are shown in green and DEGs present in only M1BP RNAi;ZKSCAN3 fat bodies are shown in orange. Genes not differentially expressed in any condition are in grey. (B) Average transcripts per million (TPM) from biological replicate RNA-seq counts for all autophagy-related genes (Atg) show significant upregulation of numerous Atg genes upon M1BP RNAi that is prevented by ZKSCAN3 co-expression. Error bars represent standard deviation of mean replicate values. (C) Reactome pathway enrichment analysis³⁶ identified the “Autophagy Reactome” pathway as significantly enriched with 30% of pathway entities being upregulated upon M1BP RNAi and the “Metabolism Reactome” as significantly enriched with 23% of pathway entities being downregulated upon M1BP RNAi. In both cases, the majority of deregulated pathway genes are restored to wild type values upon ZKSCAN3 co-expression leading to the absence of pathway enrichment. The pathway illustrations (CC BY 4.0 license) as provided by the Reactome analyses³⁶ significantly affected within each of the reactomes are shown in red while not significant pathways are shown in grey.