Comprehensive characterization of the Drosophila transcriptome

果蝇转录组的综合表征

• 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
• 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' 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

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.

产品说明：我们的主要目标是全面鉴定模式生物黑腹果蝇中的功能性转录序列，包括蛋白质编码和非蛋白质编码。我们将提供一个完整的基因结构与转录起始位点，多聚腺苷酸化位点，和所有可检测的替代转录本的描述。我们计划调查整个开发过程中的代表性时间点，各种组织类型和良好表征的新型细胞系。这些样本的RNA将用于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文库构建进行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罕见表达基因的转录本。将使用靶向方法筛选cDNA文库，以鉴定和分离中等至大转录物。小RNA（<100 bp）的表征需要创新策略，我们将使用高分辨率（5 bp）全基因组拼接阵列和454测序。与这些研究同时进行的是生物信息学分析，以确定新的未注释基因，这些基因首次利用合成表达、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产生蛋白质异构体的剪接变异的程度，并利用体内剪接报告基因测定、RNAi和计算分析来鉴定调节可变剪接所需的序列。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阿尔茨海默病、神经退行性疾病和癌症。此外，首次发现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，这些调控网络在动物发育过程中发挥重要作用，并已发现在人类中有助于多种人类癌症的发展。

项目成果

SmD1 Modulates the miRNA Pathway Independently of Its Pre-mRNA Splicing Function.

• DOI: 10.1371/journal.pgen.1005475
• 发表时间: 2015-08
• 期刊: PLoS genetics
• 影响因子: 4.5
• 作者: Xiong XP;Vogler G;Kurthkoti K;Samsonova A;Zhou R
• 通讯作者: Zhou R

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

• DOI: 10.1101/gr.182675.114
• 发表时间: 2015-11
• 期刊: Genome research
• 影响因子: 7
• 作者: Stoiber MH;Olson S;May GE;Duff MO;Manent J;Obar R;Guruharsha KG;Bickel PJ;Artavanis-Tsakonas S;Brown JB;Graveley BR;Celniker SE
• 通讯作者: Celniker SE

Genome-guided transcript assembly by integrative analysis of RNA sequence data.

• DOI: 10.1038/nbt.2850
• 发表时间: 2014-04
• 期刊: Nature biotechnology
• 影响因子: 46.9
• 作者: Boley N;Stoiber MH;Booth BW;Wan KH;Hoskins RA;Bickel PJ;Celniker SE;Brown JB
• 通讯作者: Brown JB

Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data.

• DOI: 10.1101/gr.170100.113
• 发表时间: 2014-07
• 期刊: Genome research
• 影响因子: 7
• 作者: Li JJ;Huang H;Bickel PJ;Brenner SE
• 通讯作者: Brenner SE

The developmental transcriptome of Drosophila melanogaster.

• DOI: 10.1038/nature09715
• 发表时间: 2011-03-24
• 期刊: Nature
• 影响因子: 64.8
• 作者: Graveley BR;Brooks AN;Carlson JW;Duff MO;Landolin JM;Yang L;Artieri CG;van Baren MJ;Boley N;Booth BW;Brown JB;Cherbas L;Davis CA;Dobin A;Li R;Lin W;Malone JH;Mattiuzzo NR;Miller D;Sturgill D;Tuch BB;Zaleski C;Zhang D;Blanchette M;Dudoit S;Eads B;Green RE;Hammonds A;Jiang L;Kapranov P;Langton L;Perrimon N;Sandler JE;Wan KH;Willingham A;Zhang Y;Zou Y;Andrews J;Bickel PJ;Brenner SE;Brent MR;Cherbas P;Gingeras TR;Hoskins RA;Kaufman TC;Oliver B;Celniker SE
• 通讯作者: Celniker SE