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Comprehensive characterization of the Drosophila transcriptome

果蝇转录组的综合表征

基本信息

批准号：
7268432
负责人：
SUSAN E CELNIKER
金额：
$ 363.39万
依托单位：
UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB
依托单位国家：
美国
项目类别：
财政年份：
2007
资助国家：
美国
起止时间：
2007-05-04 至 2011-03-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7268432
关键词：
Algorithms All Sites Alternative Splicing Animal Model Animals Base Sequence Bioinformatics Biological Biological Assay Biological Process Biological Sciences Cell Line Cells Classification Code Complementary DNA Computer Analysis Computer Simulation Data Development Differentiation and Growth Drosophila genome Drosophila genus Drosophila melanogaster Elements Evaluation Exons Expressed Sequence Tags Figs - dietary Foundations Functional RNA Gene Expression Profile Gene Pool Gene Structure Genes Genetic Transcription Genome Goals Histocompatibility Testing Human Human Resources Informatics Introns Malignant Neoplasms Maps Mediating Modeling Molecular Profiling Neurodegenerative Disorders Organism Play Poly A Polyadenylation Polymerase Chain Reaction Process Protein Isoforms Protein Overexpression Proteins RNA RNA Interference RNA Ligase (ATP)RNA Splicing RNA-Binding Proteins Race Reporter Research Infrastructure Research Personnel Resolution Resources Reverse Transcriptase Polymerase Chain Reaction Role Sampling Site Small RNA Staging Structure Surveys Time Tissues Transcript Transcription Initiation Site Validation Variant base cDNA Library cDNA Library Construction cell type comparative data integration density experience fly improved in vivo innovation knock-down novel programs size tissue culture

项目摘要

DESCRIPTION: Our primary goal is to comprehensively identify the functional transcribed sequences, both protein coding and non-protein coding in the model organism Drosophila melanogaster. We will provide a description of the complete gene structures with transcription start sites, polyadenylation sites, and all detectable alternative transcripts. We plan to survey representative time points throughout development, a wide-variety of tissue types and well-characterized and novel cell lines. RNAs from these samples will be used for high-resolution expression profiling of the transcriptome using whole-genome tiling arrays, RNA ligase mediated Rapid Amplification of cDNA ends, RT-PCR and cDNA library construction. RT-PCR will be used to identify and isolate transcripts for rarely expressed genes of small to medium size. The cDNA libraries will be screened using a targeted approach to identify and isolate medium to large transcripts. Characterization of small RNAs (<100 bp) requires innovative strategies and we will use high-resolution (5bp) whole-genome tiling arrays and 454 sequencing. Concurrent with these studies will be a bioinformatic analysis to identify novel unannotated genes that for the first time utilizes algorithms that synthesize expression, comparative sequence and gene prediction. Further, we plan to characterize and annotate the extent of splice variation used to generate protein isoforms and identify the sequences necessary for regulated alternative splicing utilizing in vivo splicing reporter assays, RNAi and computational analysis. Finally, ncRNAs will be validated using in vivo tissue culture assays for expression and function. The scope of these studies is unprecedented and will provide the most comprehensive set of experimental evidence of transcription for any organism. As a public resource, these studies are a prerequisite for understanding normal growth and differentiation and that will aid in understanding these processes in other organisms, including humans. Drosophila models have been developed for Alzheimers, neurodegenerative diseases and cancer. In addition, genes first identified to play a role in Drosophila development are often components of conserved regulatory networks that play important roles during animal development and have been found, in humans, to contribute to the development of a variety of human cancers.

描述：我们的主要目标是全面鉴定模式生物黑腹果蝇的功能转录序列，包括蛋白质编码和非蛋白质编码。我们将提供完整基因结构的描述，包括转录起始位点、聚腺苷酸化位点和所有可检测的替代转录物。我们计划调查整个发育过程中具有代表性的时间点，各种各样的组织类型和具有良好特征的新型细胞系。来自这些样本的RNA将使用全基因组平铺阵列、RNA连接酶介导的cDNA末端快速扩增、RT-PCR和cDNA文库构建，用于转录组的高分辨率表达谱分析。RT-PCR将用于鉴定和分离小到中等大小的很少表达的基因的转录本。cDNA文库将使用有针对性的方法进行筛选，以鉴定和分离中到大的转录本。小rna （<100 bp）的表征需要创新的策略，我们将使用高分辨率（5bp）全基因组平铺阵列和454测序。与这些研究同时进行的将是一项生物信息学分析，以鉴定新的未注释基因，该分析首次利用综合表达、比较序列和基因预测的算法。此外，我们计划描述和注释用于产生蛋白质同种异构体的剪接变异的程度，并利用体内剪接报告者测定、RNAi和计算分析鉴定受调节的选择性剪接所需的序列。最后，将使用体内组织培养试验验证ncrna的表达和功能。这些研究的范围是前所未有的，将为任何生物体的转录提供最全面的实验证据。作为一种公共资源，这些研究是理解正常生长和分化的先决条件，这将有助于理解包括人类在内的其他生物的这些过程。果蝇模型已经被开发用于阿尔茨海默病、神经退行性疾病和癌症。此外，首次确定在果蝇发育中起作用的基因通常是保守调控网络的组成部分，在动物发育过程中发挥重要作用，并且在人类中被发现有助于各种人类癌症的发展。