Patterned Gene Expression in Drosophila Development

描述（由申请人提供）：我们的长期目标是了解控制正常发育、疾病和进化过程中基因表达的复杂基因相互作用网络。在伯克利果蝇基因组计划（BDGP）中，我们建立了果蝇发育的基因表达资源，其中包含空间和时间胚胎表达模式，使用标准化，受控词汇对模式进行注释，基于解剖本体和模式的标准化虚拟表示。我们创建了工具来识别相似的、部分重叠的或反相关的表达。我们的数据库目前包含超过100,000张带注释的图像，这些图像显示了果蝇基因组中大约60%（8500）的蛋白质编码基因的原位杂交产生的表达模式。我们建议：(1)尽可能多地获取剩余40%蛋白质编码基因的表达模式；(2)利用电动显微镜和分析管道开发全自动图像采集，以加速数据收集，为高通量研究做准备；(3)继续改进和完善我们的虚拟图像表示，并为研究社区创建网络工具和界面，以便对我们的数据集和上传的图像进行分析；(4)表征和分析转录因子保守调控模块的表达模式。生成RNA探针的主要资源是我们的果蝇基因收集（DGC），目前包含88%的注释基因对应的cDNA克隆。为了捕获不具有代表性cDNA克隆（12%）的基因的表达模式，我们使用基因特异性PCR产物生成96孔格式的RNA探针。本研究获得的基因表达数据将为阐明果蝇13831个蛋白编码基因的功能提供基础信息，并将有助于阐明包括人类在内的其他真核生物中同源基因的功能。全基因组关联研究显示调控区域和基因表达在人类疾病中的重要作用。调控区域的功能分析将为转录因子的发育作用提供新的见解。此外，基因表达数据与调控和基因序列的整合将促进发现调控相互作用网络的研究。

DESCRIPTION (provided by applicant): Our long-term objective is to understand the complex network of genetic interactions that control gene expression underlying the processes of normal development, disease and evolution. At the Berkeley Drosophila Genome Project (BDGP), we have established a gene expression resource for Drosophila development that contains spatial and temporal embryonic expression patterns, annotations of the patterns using a standardized, controlled vocabulary, based on an anatomical ontology and a standardized virtual representation of the patterns. We created tools to identify similar, partially overlapping or anti-correlated expression. Our database currently contains over 100,000 annotated images showing expression patterns generated using in-situ hybridization of staged whole-mounted embryos for approximately 60% (8500) of the protein-coding genes in the Drosophila genome. We propose to: (1) obtain expression patterns for as many of the remaining 40% of the protein-coding genes as possible, (2) develop fully automatic image acquisition with a motorized microscope and analysis pipeline to accelerate data collection and in preparation for high-throughput studies, (3) continue advancements and refinements to our virtual image representation and create web-tools and interfaces for the research community to conduct analysis with our dataset and uploaded images and (4) characterize and analyze expression patterns of conserved regulatory modules from transcription factors. The primary resource for generation of RNA probes is our Drosophila Gene Collection (DGC), which currently contains cDNA clones corresponding to 88% of the annotated genes. To capture expression patterns for genes that do not have a representative cDNA clone (12%), we used gene-specific PCR products to generate RNA probes in 96- well format. The gene expression data produced by our study will provide fundamental information for elaborating the function of the 13,831 protein-coding genes in Drosophila and will aid in elucidating the function of the homologous genes in other eukaryotes, including humans. Genome wide association studies have shown fundamental roles for regulatory regions and gene expression in human diseases. The functional analysis of regulatory regions will provide novel insights into the developmental roles of transcription factors. In addition, the integration of the gene expression data with regulatory and gene sequences will promote research to discover networks of regulatory interactions. PUBLIC HEALTH RELEVANCE: Elucidating the mechanisms responsible for genome-wide gene expression and regulation in Drosophila development will aid in understanding normal growth and differentiation of tissues in humans, prerequisites for understanding human disease.