Genomic analysis of RNA binding protein target specificity

RNA结合蛋白靶标特异性的基因组分析

基本信息

批准号：
7885582
负责人：
Jeremy Robert Sanford
金额：
$ 32.98万
依托单位：
UNIVERSITY OF CALIFORNIA SANTA CRUZ
依托单位国家：
美国
项目类别：
财政年份：
2008
资助国家：
美国
起止时间：
2008-09-01 至 2013-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7885582
关键词：
Address Affect Alternative Splicing Arginine Binding Binding Sites Biochemical Biochemistry Bioinformatics Biological Biological Assay Biological Process Biometry Cell Proliferation Cells Code Complex Computational Biology DNA Sequence Data Elements Employee Strikes Exons Family Functional RNA Gene Expression Gene Expression Profile Genes Genetic Transcription Genomics Goals Human Human Genome In Situ In Vitro Indiana Interdisciplinary Study Introns Life Location Medical center Methodology Methods Molecular Biology Molecular Weight Physiological Post-Transcriptional RNA Processing Post-Transcriptional Regulation Protein Binding Protein Family Proteins RNA RNA Splicing RNA-Binding Proteins RNA-Protein Interaction Reaction Regulation Regulatory Element Research Infrastructure Reverse Transcriptase Polymerase Chain Reaction Serine Signal Transduction Specificity Transcript Universities Validation cis acting element genome wide association study genome-wide genome-wide analysis human disease in vivo mRNA Precursor novel protein complex protein expression

项目摘要

DESCRIPTION (provided by applicant): The complexity of human transcriptome is far greater than previously anticipated. Transcript diversity can be expanded through post-transcriptional RNA processing reactions as well as extensive inter-genic transcription. The genomic organization of cisacting RNA elements regulating expression of protein coding genes and non-coding inter-genic transcripts is poorly defined. This deficiency not only hampers our understanding of how the information stored within the human genome is utilized, but also weakens the connections between post-transcriptional control of gene expression and biological processes such as cell proliferation, differentiation and even human disease. The goal of this proposal is to illuminate post-transcriptional networks coordinated by RNA binding proteins. To achieve this goal we will identify cis-acting RNA elements recognized by a complete family of phylogenetically conserved, essential RNA binding proteins on a genome-wide scale. Our application focuses on the Serine and Arginine-rich family of pre-mRNA splicing factors (SR proteins). Biochemical methods will be employed to purify SR protein-RNA complexes under conditions that preserve the physiological context of RNA-protein interactions in the intact cell. Copurifying RNA molecules will be directly identified by two independent high throughput methods, pyrosequencing and hybridization to tiled genomic microarrays. Our R01 application will address the following specific aims: (1) Comprehensively identify cis-acting RNA elements recognized by the SR protein family. (2) Determine the genomic landscape of cis-acting RNA elements recognized by SR proteins. (3) Functionally validate SR protein cis-acting RNA elements.

描述（由申请人提供）：人类转录组的复杂性远大于以前的预期。转录物多样性可以通过转录后RNA处理反应以及广泛的基因间转录来扩展。 Cisacting RNA元件的基因组组织调节蛋白质编码基因和非编码基因间转录本的表达的定义很差。这种缺乏不仅会阻碍我们对如何利用人类基因组中存储的信息的理解，而且削弱了基因表达的转录后控制与生物学过程（例如细胞增殖，分化甚至人类疾病）之间的联系。该提案的目的是阐明由RNA结合蛋白协调的转录后网络。为了实现这一目标，我们将确定由整个系统发育保守的，必需的RNA结合蛋白在全基因组范围内识别的顺式作用RNA元件。我们的应用集中在丝氨酸和精氨酸蛋白剪接因子（SR蛋白）上。在保留完整细胞中RNA-蛋白质相互作用的生理环境的条件下，将采用生化方法来纯化SR蛋白RNA复合物。共纯化的RNA分子将通过两种独立的高吞吐量方法直接识别，即焦磷酸测序和与瓷砖基因组微阵列的杂交。我们的R01应用将解决以下特定目的：（1）全面识别SR蛋白家族识别的顺式作用RNA元件。（2）确定SR蛋白识别的顺式作用RNA元件的基因组景观。（3）功能验证SR蛋白顺序作用RNA元件。