Comparative Time-Course RNA-Seq Analysis of Abdominal Muscle cell Remodeling in Drosophila with or without Autophagy
Differentiated muscle cells contain myofibrils and well-organized organelles, enabling powerful contractions. Muscle cell reorganization occurs in response to various physiological stimuli; however, the mechanisms underlying this remodeling remain enigmatic due to the lack of a genetically trackable system. Previously, we reported that a subset of larval muscle cells is remodeled into adult dorsal internal oblique muscle (DIOM) cells through an autophagy-dependent mechanism in Drosophila. To elucidate the underlying mechanisms of this remodeling, we performed a comparative time-course RNA sequencing (RNA-Seq) analysis of isolated DIOM cells with or without autophagy. As a control, we analyzed DIOM cells expressing LacZ. For autophagy-deficient conditions, we analyzed DIOM cells with RNAi-mediated knockdown of Atg18, FIP200, and Stx17. To conduct a time-course analysis, DIOM cells were isolated at distinct developmental time points, including the late third instar larva (3 IL) and four pupal stages; 1 day after puparium formation (1 d APF), 2 d APF, 3 d APF, and 4 d APF. The resulting datasets provide valuable insights into the transcriptional dynamics of muscle remodeling and the role of autophagy in this process. Overall design: We performed a comparative time-course RNA-seq of DIOM remodeling in Control (UAS-LacZ), Atg18a RNAi, FIP200 RNAi, and Stx17 RNAi DIOMs. Each sample was collected from a single animal. To prepare total RNA, six DIOM cells were isolated at five time points: 3IL  and 1 to 4 days APF.  Each conditon was analyzed with four biological replicates.