We propose to continue our analyses of the Drosophila genome during development. In the next five year period we will focus on two technological challenges in the context of Drosophila developmental and evolutionary change. The overarching theme is to study transcript diversity and variation. First we will develop new methods for assessing transcript diversity due to splicing in Drosophila. We will then apply these methods to annotate and analyze the patterns of splicing during the Drosophila life cycle. Second we will address the problem of transcript level variation between individuals and closely related species. We will measure this variation in terms of splicing and in terms of transcriptional regulation. We will focus on the developmental process of metamorphosis that is controlled by the hormone ecdysone via transcriptional mechanisms. We will then map variation in the ecdysone response at the level of transcriptional regulation, and we will determine the contribution of transcriptional variation due to variation of the in vivo binding sites of known transcription factors such as the Ecdysone Receptor. To accomplish the goals of this proposal we will use maskless photolithography for in situ synthesis of high density long oligonucleotide (36-60 n.t.) microarrays. This work will help to develop several applications for the study of complex eukaryotic genomes that were previously difficult, expensive or unfeasible using other technologies. The genome of Drosophila is representative of a complex animal but an order of magnitude smaller than the human genome, making it ideal for the proposed studies. In addition to providing technological proof-of-principle studies, the proposed research will make a contribution to our understanding of why different individuals exhibit different responses when exposed to steroids. The methods we develop should be applicable and relevant to the human genome as well, which could be the subject of similar future studies. ? ?
| Liu, Jiang; Ghanim, Murad; Xue, Lei et al. (2009) Analysis of Drosophila segmentation network identifies a JNK pathway factor overexpressed in kidney cancer. Science 323:1218-22 |
