Comprehensive characterization of the Drosophila transcriptome

果蝇转录组的综合表征

基本信息

批准号：
8236006
负责人：
SUSAN E CELNIKER
金额：
$ 352.92万
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 2013-03-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8236006
关键词：
Algorithms Alternative Splicing Alzheimer&apos s Disease Animal Model Animals Base Sequence Bioinformatics Biological Biological Assay Biological Process Biological Sciences Cell Line Cells Code Complementary DNA Computer Analysis Computer Simulation Data Development Differentiation and Growth Drosophila genome Drosophila genus Drosophila melanogaster Elements Evaluation Exons Expressed Sequence Tags 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 Process Protein Isoforms Proteins RNA RNA Interference RNA Ligase (ATP)RNA Splicing RNA-Binding Proteins 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 overexpression programs 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果蝇中的功能转录序列，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的代表性时间点、各种组织类型以及特征良好的新型细胞系。这些样品中的 RNA 将用于通过全基因组平铺阵列、RNA 连接酶介导的 cDNA 末端快速扩增、RT-PCR 和 cDNA 文库构建对转录组进行高分辨率表达谱分析。 RT-PCR 将用于鉴定和分离很少表达的中小型基因的转录本。将使用有针对性的方法筛选 cDNA 文库，以识别和分离中到大的转录本。小 RNA (<100 bp) 的表征需要创新策略，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生物信息学分析，以识别新的未注释基因，该基因首次利用综合表达、比较序列和基因预测的算法。此外，我们计划表征和注释用于生成蛋白质亚型的剪接变异的程度，并利用体内剪接报告基因测定、RNAi 和计算分析来鉴定调节选择性剪接所需的序列。最后，将使用体内组织培养测定来验证 ncRNA 的表达和功能。这些研究的范围是前所未有的，将为任何生物体提供最全面的转录实验证据。作为公共资源，这些研究是了解正常生长和分化的先决条件，并将有助于了解包括人类在内的其他生物体的这些过程。果蝇模型已被开发用于治疗阿尔茨海默病、神经退行性疾病和癌症。此外，首先被确定在果蝇发育中发挥作用的基因通常是保守调控网络的组成部分，这些网络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多种人类癌症的发展。

项目成果

期刊论文数量（16）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Susan Celniker: Foundational Resources To Study a Dynamic Genome.

Susan Celniker：研究动态基因组的基础资源。

DOI：
发表时间：
2016-11
期刊：
影响因子：
3.3
作者：
Celniker; Susan
通讯作者：
Susan

Extensive cross-regulation of post-transcriptional regulatory networks in Drosophila.

果蝇转录后调控网络的广泛交叉调控。

DOI：
发表时间：
2015-11
期刊：
影响因子：
7
作者：
Stoiber, Marcus H;Olson, Sara;May, Gemma E;Duff, Michael O;Manent, Jan;Obar, Robert;Guruharsha, K G;Bickel, Peter J;Artavanis;Brown, James B;Graveley, Brenton R;Celniker, Susan E
通讯作者：
Celniker, Susan E

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments.

mRNA-Seq 实验中标准化和差异表达统计方法的评估。

DOI：
发表时间：
2010-02-18
期刊：
影响因子：
3
作者：
Bullard, James H;Purdom, Elizabeth;Hansen, Kasper D;Dudoit, Sandrine
通讯作者：
Dudoit, Sandrine

Regulation of alternative splicing in Drosophila by 56 RNA binding proteins.

56 个 RNA 结合蛋白对果蝇选择性剪接的调节。

DOI：
发表时间：
2015-11
期刊：
影响因子：
7
作者：
Brooks, Angela N;Duff, Michael O;May, Gemma;Yang, Li;Bolisetty, Mohan;Landolin, Jane;Wan, Ken;Sandler, Jeremy;Booth, Benjamin W;Celniker, Susan E;Graveley, Brenton R;Brenner, Steven E
通讯作者：
Brenner, Steven E

Genome-guided transcript assembly from integrative analysis of RNA sequence data

通过 RNA 序列数据的综合分析进行基因组引导的转录本组装