Comprehensive Discovery of Functional Elements of the Drosphila Transcriptome

果蝇转录组功能元件的全面发现

基本信息

批准号：
8402420
负责人：
SUSAN E CELNIKER
金额：
$ 100万
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：
2012
资助国家：
美国
起止时间：
2012-09-21 至 2014-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8402420
关键词：
Affinity Chromatography Animal Model Binding Binding Proteins Binding Sites Bioinformatics Biological Biological Assay Cataloging Catalogs Cell Culture Techniques Cell Line Classification Code Complex DNA Data Data Analyses Data Element Degenerative Disorder Development Differentiation and Growth Disease Drosophila Proteins Drosophila genus Elements Embryo Functional RNA Gene Expression Profile Gene Expression Regulation Generations Genes Genetic Genetic Transcription Genome Goals Health Histocompatibility Testing Homologous Gene Human Indium Malignant Neoplasms Maps Measures Messenger RNA Metabolism Modeling National Human Genome Research Institute Nuclear Export Organism Poly A Poly(A)+ RNA Principal Investigator Process Protein-Protein Interaction Map Proteins Publishing RNA RNA Binding RNA Sequences RNA Splicing RNA Stability RNA analysis RNA-Binding Proteins RNA-Protein Interaction Regulation Relative (related person)Reproducibility Research Infrastructure Resolution Resources Ribosomes Role Sampling Site Societies Staging Statistical Data Interpretation Structure Surveys System Technology Time Tissues Transcript Transcription Initiation Site Transgenic Animals Transgenic Organisms Translating Translations Validation base cost crosslink human disease insight novel protein complex protein expression research study tool

项目摘要

Our primary goal is to comprehensively identify the functional elements of the Drosophila transcriptome, including the poly(A)- transcripts, all translated regions, and all RNA elements bound by proteins. In addition, we propose to elucidate the RNA sequences and binding proteins that regulate splicing, translation and stability of RNA. We plan to survey representative time points throughout development, a wide-variety of tissue types and well-characterized cell lines. We will produce a catalog of poly(A)- transcripts with single-base resolution and validate a subset of transcription start sites and termination sites using RLM-RACE. We will discover novel translated elements of mRNAs and long non-coding RNAs using ribosome profiling and validate a subset using a protein expression assay. We will comprehensively identify the RNAs bound by the complete set of RNA-binding proteins (RBPs) in Drosophila using affinity purification followed by high throughput sequencing (RIP-seq), prioritizing human homologs. RBPs recognize and bind to specific RNA sequences, and these interactions can regulate the stability, splicing, nuclear export, subcellular localizatin, and translatability of mRNAs. Concurrent with these studies, bioinformatic analyses will identify new poly(A)- transcripts, model their secondary structures, discover novel translated elements of mRNAs such as uORFs and identify long non-coding RNAs. For each RNA-binding protein (RBPs), we will identify bound transcripts using statistical measures of reproducibility, biologica replicates and relative enrichment. We also plan to identify binding-site motifs (PWMs) and develop the network of RNA-protein interactions. We will integrate the RNA-protein interaction map with the published Drosophila Protein Interaction Map. The scope of these studies is unprecedented and will provide the most comprehensive set of experimental evidence for post-transcriptional gene regulation in any organism. As a public resource, these studies are a prerequisite for understanding normal metabolism, growth and differentiation that will aid in understanding these processes in other organisms and in human health and disease.

我们的主要目标是全面确定果蝇转录组的功能元素，包括poly（a） - 转录本，所有翻译区域以及所有由蛋白质绑定的RNA元素。此外，我们建议阐明调节RNA剪接，翻译和稳定性的RNA序列和结合蛋白。我们计划在整个开发过程中调查代表性的时间点，多种组织类型和特征良好的细胞系。我们将生成具有单基碱分辨率的poly（a） - 转录本的目录，并使用RLM-race验证转录起始位点和终止位点的子集。我们将使用核糖体分析发现新颖的mRNA和长非编码RNA的翻译元素，并使用蛋白质表达测定法验证子集。我们将使用亲和力纯化，然后进行高通量测序（RIP-SEQ），全面地通过果蝇中的RNA结合蛋白（RBP）组成的RNA限制，优先考虑人类同源物。 RBP识别并结合了特定的RNA序列，这些相互作用可以调节mRNA的稳定性，剪接，核输出，亚细胞定位和转换性。与这些研究同时，生物信息学分析将识别新的poly（a） - 成绩单，建模其二级结构，发现mRNA的新型翻译元素，例如UORFS，并识别长期的非编码RNA。对于每种RNA结合蛋白（RBP），我们将使用可重复性，生物学重复和相对富集的统计度量来确定结合的转录本。我们还计划识别结合位点基序（PWM）并开发RNA - 蛋白质相互作用的网络。我们将将RNA - 蛋白质相互作用图与已发表的果蝇蛋白相互作用图整合在一起。这些研究的范围是前所未有的，将为任何生物体的转录后基因调节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代谢，生长和差异化的先决条件，有助于理解其他生物体以及人类健康和疾病中的这些过程。

项目成果

期刊论文数量（1）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Genome-wide identification of zero nucleotide recursive splicing in Drosophila.

DOI：
10.1038/nature14475
发表时间：
2015-05-21
期刊：
Nature
影响因子：
64.8
作者：
Duff MO;Olson S;Wei X;Garrett SC;Osman A;Bolisetty M;Plocik A;Celniker SE;Graveley BR
通讯作者：
Graveley BR