Gene-centered protein-RNA interaction mapping

以基因为中心的蛋白质-RNA相互作用作图

基本信息

批准号：
8268978
负责人：
A. J. Marian Walhout
金额：
$ 24.68万
依托单位：
UNIV OF MASSACHUSETTS MED SCH WORCESTER
依托单位国家：
美国
项目类别：
财政年份：
2011
资助国家：
美国
起止时间：
2011-05-30 至 2014-03-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8268978
关键词：
3&apos Untranslated Regions Affect Affinity Animal Model Binding Biochemical Biological Assay Caenorhabditis elegans Collection Communities Complex DNA Sequence Detection Development Disease Enterobacteria phage MS2 Gene Expression Gene Expression Regulation Gene Targeting Genes Genetic Transcription Genome Genomics Green Fluorescent Proteins Homeostasis Human Hybrids In Vitro Individual Laboratories Length MS2 coat protein Maps Messenger RNA Methodology Methods MicroRNAs Modeling Names Nematoda Noise Open Reading Frames Organism Physiology Poly(A)-Binding Proteins Post-Transcriptional Regulation Proteins RNA RNA Binding RNA Sequences RNA Stability RNA-Binding Proteins RNA-Protein Interaction Regulator Genes Reporter Research Research Personnel Resources Sensitivity and Specificity Signal Transduction Stretching System Systems Biology Technology Time Transcriptional Regulation Translations Uridine Work Yeasts base cost high throughput technology human disease hybrid protein in vivo insight interest new technology novel promoter protein protein interaction research study stem transcription factor vector

项目摘要

DESCRIPTION (provided by applicant): The regulation of gene expression is vital for healthy development and physiology, and many diseases are caused by or associated with changes in gene expression. In the past decade, a tremendous amount of information has been gathered regarding transcriptional control by transcription factors that bind directly to regulatory DNA sequences in or around their target genes. In addition, microRNAs that control gene expression post-transcriptionally have been studied extensively. However, functional and biochemical information about the vast majority of RNA binding proteins has been lacking despite clear evidence of their importance in development and disease. A major factor contributing to our limited understanding of post- transcriptional control by RNA binding proteins is a shortage of appropriate technologies that start with an important mRNA, for instance corresponding to a disease gene of interest, and identify the RNA binding proteins with which this mRNA interacts. In the proposed project, we will develop a novel, high-throughput method for the detection and identification of RNA-protein interactions. We have provisionally named this technology "RNA-associated protein interaction detection" (RAPID). RAPID is based on translation and mimics endogenous RNA binding protein activity. We will first develop and apply RAPID to RNA-protein interactions in the nematode Caenorhabditis elegans because it provides a highly suitable model for further in vivo studies, and because we have clone resources such as the ORFeome available, which contains numerous full-length RNA binding protein-encoding clones. Successful completion of this project will provide the research community with a novel and broadly applicable method to detect RNA-protein interactions in an unbiased and high-throughput manner. We envision applying RAPID to the genome-scale detection of such interactions to further our understanding of complex gene regulatory networks. The methodology and RNA binding protein resource that we will develop for C. elegans will provide an important blueprint for the creation of similar resources in other model organisms and humans.

描述（由申请人提供）：基因表达的调节对于健康发育和生理学至关重要，许多疾病是由基因表达变化引起或与之相关的。在过去的十年中，通过转录因子收集了大量信息，这些信息是通过转录因子直接结合其目标基因内或周围的调节性DNA序列的。此外，在转录后控制基因表达的microRNA已被广泛研究。但是，尽管有明确的证据表明它们在发育和疾病中的重要性，但仍缺乏有关绝大多数RNA结合蛋白的功能和生化信息。 RNA结合蛋白对我们对转录后控制有限的有限理解的主要因素是对从重要的mRNA开始的适当技术的短缺，例如与感兴趣的疾病基因相对应，并确定与该mRNA相互作用的RNA结合蛋白。在拟议的项目中，我们将开发一种新型的高通量方法，用于检测和鉴定RNA-蛋白质相互作用。我们暂时将这项技术命名为“与RNA相关的蛋白质相互作用检测”（快速）。快速基于翻译和模仿内源性RNA结合蛋白活性。我们将首先开发并迅速应用于线虫秀丽隐杆线虫中的RNA蛋白质相互作用，因为它为进一步的体内研究提供了高度适合的模型，并且因为我们提供的克隆资源（例如可用的ORFEOME），其中包含许多全长RNA结合蛋白蛋白质加码的克隆。该项目的成功完成将为研究界提供一种新颖且广泛的方法，以公正和高通量方式检测RNA - 蛋白质相互作用。我们设想将快速应用于对这种相互作用的基因组规模检测，以进一步了解复杂的基因调节网络。我们将为秀丽隐杆线虫开发的方法和RNA结合蛋白资源将为在其他模型生物和人类中创建相似资源提供重要的蓝图。