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Sequence-specific Capture for Discovering Protein-IncRNA Interactions in Prostate Cancer

用于发现前列腺癌中蛋白质-IncRNA 相互作用的序列特异性捕获

基本信息

批准号：
8857740
负责人：
DAVID F. JARRARD
金额：
$ 34.42万
依托单位：
UNIVERSITY OF WISCONSIN-MADISON
依托单位国家：
美国
项目类别：
财政年份：
2015
资助国家：
美国
起止时间：
2015-03-04 至 2018-02-28
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8857740
关键词：
Address Affect Antibodies Beds Benchmarking Binding Binding Proteins Biological Biological Markers Biology Cell Culture Techniques Cell Line Cells Chromatin Complex DNA Development Disease Disease Marker Disease Progression Elements Epithelial Cells Epithelium Evaluation Formaldehyde Gene Expression Gene Expression Regulation Genetic Transcription Genome Human Human Cell Line Immunoprecipitation Individual Indolent Investigation Knowledge LNCaP Learning Location Malignant Neoplasms Malignant neoplasm of prostate Mass Spectrum Analysis Messenger RNA Methodology Methods Molecular Normal tissue morphology Nucleic Acid Hybridization Nucleic Acids Onset of illness PRC1 Protein Patients Pattern Phenotype Play Procedures Process Prostate Prostatic Neoplasms Protein Binding Protein Databases Proteins Proteomics RNA RNA-Protein Interaction Reagent Recombinant DNA Role Sampling Scientist Set protein Technology Testing Time Tissue Sample Tissues Transcriptional Regulation Translational Regulation Tumor Tissue Untranslated RNA Validation Work Yeasts aptamer crosslink differential expression histone modification in vivo innovation insight interest new technology novel marker novel strategies promoter prostate cancer cell line protein complex protein crosslink public health relevance targeted sequencing technology validation tool transcriptome sequencing

项目摘要

DESCRIPTION (provided by applicant): Protein-nucleic acid interactions play key roles in both transcriptional and translational regulation, not only in the direct interaction of proteins with DA and mRNA to regulate these processes, but also the interactions among proteins, lncRNAs, and DNAs. Understanding these interactions requires knowledge of the molecules that are involved. lncRNAs interact with proteins to achieve several consequences in gene regulation. First, lncRNAs can act as a "molecular sink" for proteins that may interact with DNA or RNA. Their interaction with the lncRNA thus diverts the protein from binding to its primary target. lncRNAs can also act as guides for proteins, leading them to their DNA targets to either repress or activate transcription. Finally, lncRNAs can act as platforms upon which molecules can congregate to perform a function, such as histone modification, as a team at a specific location and time. Each of these functions requires the interaction of lncRNAs with a diverse set of proteins. Knowledge of the proteins bound to a specific lncRNA will allow for determination of the mechanisms by which that lncRNA affects gene expression. Unraveling this tremendous diversity of interactions demands tools capable of rapid identification and quantification of proteins. In this proposal we focus on the particular problem of identifying the proteins that are bound to specific lncRNA molecules, their relationship to the progression of prostate cancer and their potential as markers of the disease and its progression. We describe an RNA-centric approach to discovery of the lncRNA-binding proteins that is innovative compared with existing technologies in two major ways. First, crosslinking of proteins to lncRNAs is done in vivo under normal cellular conditions. Therefore, proteins and lncRNAs will be folded normally, will be present at their normal cellular concentrations, and will be in their normal cellular locations. Second, sequence-specific capture of the lncRNA is used to extract the RNA of interest along with its crosslinked proteins. This is a universal capture strategy that does not rely on the availability of any other capture reagent (e.g. antibody or aptamer). Following enrichment by sequence-specific capture, mass spectrometry will be utilized to identify and quantify the associated proteins.