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识别模型有机体果蝇中的蛋白质编码和非蛋白质编码的功能转录序列。我们将提供具有转录起始位点，聚腺苷酸位点以及所有可检测的替代转录本的完整基因结构的描述。我们计划在整个开发过程中调查代表性的时间点，多种组织类型以及特征良好的新细胞系。这些样品的RNA将用于使用全基因组瓷砖阵列，RNA连接酶介导的cDNA末端，RT-PCR和cDNA库的构造的快速扩增的转录组的高分辨率表达分析。 RT-PCR将用于识别和隔离很少表达的中小型基因的转录本。 cDNA文库将使用靶向方法筛选，以识别和分离中等大型转录本。小RNA（<100 bp）的表征需要创新的策略，我们将使用高分辨率（5BP）全基因组瓷砖阵列和454个测序。与这些研究同时，将是一项生物信息学分析，以识别新型未注释的基因，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同工型的剪接变异程度，并确定利用体内剪接报告基因测定，RNAI和计算分析所需的调节替代剪接所需的序列。最后，使用体内组织培养测定法以表达和功能来验证NCRNA。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实验证据。作为公共资源，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体中的这些过程。果蝇模型已为阿尔茨海默氏症，神经退行性疾病和癌症开发。此外，首先确定在果蝇发育中发挥作用的基因通常是保守的监管网络的组成部分，在动物发育过程中起着重要作用，并且在人类中发现了为多种人类癌症的发展做出贡献。

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）

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

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

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

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

DOI：
10.1101/gr.192518.115
发表时间：
2015-11
期刊：
Genome research
影响因子：
7
作者：
Brooks AN;Duff MO;May G;Yang L;Bolisetty M;Landolin J;Wan K;Sandler J;Booth BW;Celniker SE;Graveley BR;Brenner SE
通讯作者：
Brenner SE