Bioinformatic analysis of the mid-third instar transition in <i>Drosophila melanogaster</i>

In the fruit fly, Drosophila melanogaster, a relatively uncharacterized developmental timepoint termed the mid-third instar transition (MIT) occurs during the third and final larval stage. While there are no obvious morphological changes that occur during the MIT, widespread changes in gene expression are thought to prepare the organism to enter metamorphosis. How these massive changes in gene expression are regulated and how they alter larval behaviour and physiology are unclear. Here, we examine tissue and developmental stage-specific transcriptome data generated as part of the ModEnCODE project to better understand how changes in gene expression at the MIT alter physiology in preparation for metamorphosis. Analysis of enriched binding motifs suggests that regulation of MIT genes is complex but is likely mediated, at least in part, by ecdysone. Our results also suggest that gene expression changes at the MIT likely prepare the larva for metamorphosis in numerous ways, including altering metabolism to help meet energetic demands, increasing glue protein production allowing pupae to adhere to surfaces and preparing the immune system to control the spread of microbes during histolysis of larval tissues. At the same time, changes in imaginal tissues support the proliferation and differentiation of cells characteristic of the metamorphic moult.