I discovered that regulatory interactions between miRNAs and their cognate targets were substantially altered by Ago1 in response to Drosophila metamorphosis and ecdysone signaling. We performed cross-linking immunoprecipitation coupled with deep sequencing (CLIP-seq) of endogenous Ago1 protein in both S2 cells in Drosophila, to revealed underlying miRNA-target regulatory axis controlled by ecdysone signaling. We found that coordinated regulation of vacuolar H+-ATPase (V-ATPase) subunits by miR-8-3p is involved in Drosophila metamorphosis by controlling the ecdysone biosynthesis. Furthermore, I also have demonstrated that another novel ecdysone signaling responsible miRNA, miR-252-5p targets Abelson interacting protein (Abi) and mushroom bodies tiny (mbt) to regulate cell cycle progression and animal growth for both S2 cells and Drosophila, respectively.