Patterned Gene Expression in Drosophila Development

果蝇发育中的模式基因表达

• 批准号: 7144496
• 负责人: SUSAN E CELNIKER
• 金额: $ 47.57万
• 依托单位: UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-09-01 至 2010-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7144496
• 关键词: Drosophilidae; RNA; RNA splicing; bioinformatics; computational biology; developmental genetics; embryogenesis; evolution; gene expression profiling; gene interaction; high throughput technology; image processing; immunocytochemistry; in situ hybridization; molecular biology information system; nucleic acid probes; nucleic acid sequence; protein sequence

DESCRIPTION (provided by applicant): Our long-term objective is to understand the complex network of genetic interactions that underlies the processes of normal development, disease and evolution. For this, we need to determine gene expression profiles for the full complement of genes in an organism. 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 as well as annotations of the patterns using a standardized, controlled vocabulary, based on Gene Ontology (GO). Our database currently contains 75,000 annotated images showing expression patterns generated using in-situ hybridization of staged whole-mounted embryos for approximately 45% (6,000) of the protein-coding genes in the Drosophila genome. The spatial expression data are integrated with our developmental microarray data. We propose to extend these studies to: (1) the remaining 55% of the protein-coding genes, (2) alternatively-spliced transcripts, and (3) non-coding RNA candidate genes The primary resource for generation of RNA probes is our Drosophila Gene Collection (DGC) which currently contains cDNA clones corresponding to 80% of the annotated genes. To capture expression patterns for genes that do not have a representative cDNA clone (20%), 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 13,664 genes in Drosophila and will aid in elucidating the function of the homologous genes in other eukaryotes, including humans. In addition, the integration of the gene expression data with gene, transcript and protein sequences will promote research to discover networks of regulatory interactions. Using the standardized vocabulary allows cross-species descriptions of gene expression and tissue differentiation. 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.

描述（由申请人提供）：我们的长期目标是了解作为正常发育、疾病和进化过程基础的复杂遗传相互作用网络。为此，我们需要确定生物体中完整基因的基因表达谱。在伯克利果蝇基因组计划（BDGP），我们已经建立了一个基因表达资源果蝇的发展，包含空间和时间的胚胎表达模式，以及使用标准化的模式注释，控制词汇，基于基因本体论（GO）。我们的数据库目前包含75，000个注释图像，显示了使用阶段性整体安装胚胎的原位杂交产生的表达模式，约45%（6，000）的果蝇基因组中的蛋白质编码基因。将空间表达数据与我们的发育微阵列数据整合。我们建议将这些研究扩展到：（1）剩余的55%的蛋白质编码基因，（2）选择性剪接转录本，和（3）非编码RNA候选基因。RNA探针产生的主要资源是我们的果蝇基因收集（DGC），目前包含对应于80%的注释基因的cDNA克隆。为了捕获不具有代表性cDNA克隆（20%）的基因的表达模式，我们使用基因特异性PCR产物以96孔格式产生RNA探针。我们的研究产生的基因表达数据将为阐明果蝇中13，664个基因的功能提供基础信息，并将有助于阐明其他真核生物（包括人类）中同源基因的功能。此外，基因表达数据与基因、转录本和蛋白质序列的整合将促进发现调控相互作用网络的研究。使用标准化词汇可以跨物种描述基因表达和组织分化。阐明果蝇发育中全基因组基因表达和调控的机制将有助于理解人类组织的正常生长和分化，这是理解人类疾病的先决条件。