Functional Genomic Analysis of the Periodic Transcriptome in the Developing Drosophila Wing

Liang, Liang (2014). Functional Genomic Analysis of the Periodic Transcriptome in the Developing Drosophila Wing. PhD thesis The Open University.

DOI: https://doi.org/10.21954/ou.ro.0000f04d

Abstract

The eukaryotic cell cycle is the central molecular oscillator underlying tissue growth. Although previous studies have analyzed global cell cycle-associated transcription using unicellular systems, precisely how cell cycle-dependent processes are integrated in multicellular development in vivo remains unclear. One multicellular context-specific cell cycle event is the Interkinetic Nuclear Migration (IKNM), a conserved process by which proliferating nuclei translocate to the apical epithelial surface of the epithelium to execute mitosis. How cell cycle progression is linked with IKNM remains poorly understood. Here, I report the global cell cycle-associated transcriptomes of Drosophila wing disc epithelial cells (multicellular system) and cultured S2 cells (unicellular system). With an integrative FACS-microarray technique, we identified over 600 genes with periodic expression profiles in each context. Intriguingly, despite the common periodic genes identified, we also identified 200 genes periodically expressed only in the wing disc cells, including many core cell cycle components. I further explored the function of those wing disc periodic genes by tissue-specific RNAi knockdown. Combining flow cytometry and confocal imaging, I defined 107 periodic genes that control wing growth, wherein 35 periodic genes control cell cycle progression in the developing wing but not in S2 cells (com-pared with results from S2 RNAi screens). In addition to several novel regulators of mitotic cell size and chromosome segregation, I also identified two novel wing disc-specific periodic genes, knockdown of which disrupt IKNM. Strikingly, in both cases, disconnecting nuclei positioning with mitosis does not disrupt cell cycle progression per se. One of the IKNM genes is a potential lincRNA, which may regulate the expression of kinesin-like protein, Klp54D, and is required for normal centriole function. Taken together, my study provided a global functional perspective on cell cycle regulation in vivo, and identified numerous novel periodic genes that control growth, cell proliferation and IKNM in the epithelial context.