Figure 8.

Changes in exon use profiles in SF1-IR and Hrb87F-IR are distinct from those in bru1-IR. (A) Heatmap and hierarchical clustering of log₂FC expression values for all 144 sarcomeric gene exons significantly differentially expressed (DEXSeq p value < 0.01) in either bru1-IR, SF1-IR or Hrb87F-IR. Note the similarity in expression between SF1-IR and Hrb87F-IR and difference to bru1-IR, although all three knockdowns affect myofibril and sarcomere development. Exons are classified as coding (CDS, green), 5’-UTR (pink) or 3’-UTR (magenta) based on Flybase annotation. Black squares denote individual exons from the same gene. For multiple sarcomere genes, different sets of exons are up- and downregulated indicating alternative isoform use. (B) Plot of Pearson’s correlation coefficients of log₂FC values from gene expression and exon use analyses between bru1-IR, SF1-IR and Hrb87F-IR. Coefficient values for comparison of all significant genes (DESeq2 adjusted p value < 0.01) and exons (DEXSeq p value < 0.01) are shown in black, and for comparison of all genes or exons irrespective of significance is shown in blue. (C) Plot of log₂FC values for all 1112 significantly DE exons (DEXSeq p value < 0.01) genome wide (bru-IR exons, green; Hrb87F-IR exons, purple; SF1-IR exons, orange). The number of exons is noted in the top left of each plot region. Gray shaded regions contain exons that are downregulated in the knockdown condition. Note the different regulatory dynamics for individual exons between bru1-IR and SF1-IR or Hrb87F-IR, the similar dynamics in regulation between SF1-IR or Hrb87F-IR and the large number of exons regulated in only one genotype.