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Robust, high-throughput identification of RNA processing regulators and regulatory networks genome-wide

对全基因组 RNA 加工调节因子和调节网络进行稳健、高通量的鉴定

基本信息

批准号：
10364689
负责人：
Eric Lyman Van Nostrand
金额：
$ 24.9万
依托单位：
BAYLOR COLLEGE OF MEDICINE
依托单位国家：
美国
项目类别：
财政年份：
2020
资助国家：
美国
起止时间：
2020-05-06 至 2023-02-28
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10364689
关键词：
Address Affect Alternative Splicing Amyotrophic Lateral Sclerosis Antibodies Binding Binding Proteins Binding Sites Biological Models Biotechnology CRISPR screen Cardiac Myocytes Cell Culture Techniques Cell Differentiation process Cells Code Computational Biology Computing Methodologies Coupled DNA Binding DNA Sequence Alteration Data Data Set Development Disease Ectoderm Elements Endoderm Environment Event Faculty Genetic Transcription Genetic Variation Genomics High-Throughput Nucleotide Sequencing Human Immunoprecipitation Institutes Islets of Langerhans Location Mentors Mesoderm Methodology Methods Molecular Motor Neurons Mutation Phase Phenotype Play Positioning Attribute Proteins RNA RNA Computations RNA Processing RNA Stability RNA-Binding Proteins Regulation Research Research Institute Research Personnel Resources Role Sampling Spinal Muscular Atrophy System Techniques Tissue Sample Tissues Training Translating Translations Untranslated RNA Work biological systems cancer type cell type crosslink differential expression experimental study genome-wide human disease improved in vivo induced pluripotent stem cell interest knock-down mRNA Precursor overexpression programs protein profiling stem cells transcriptome

项目摘要

PROJECT SUMMARY RNA binding proteins (RBPs) bind to non-coding, pre-, and mature RNA within the cell to regulate each step of RNA processing, including pre-mRNA alternative splicing, RNA stability and localization, and control of translation. It has become clear that altered RNA processing plays critical roles in nearly every studied biological system, and recent work has suggest that a substantial fraction of disease-causing genetic mutations affect RNA processing, including mutations that cause familial Spinal Muscular Atrophy, Amyotrophic Lateral Sclerosis, and multiple cancer types. Mechanistic understanding of the downstream regulatory network of an RBP is essential to studying and, ultimately, ameliorating these diseases; however, there remains a need for robust, unbiased genome-wide methods to characterize RBP targets and regulators. Building upon our recent development of enhanced crosslinking and immunoprecipitation (eCLIP), I propose to extend this work in three unique directions that each contribute to our ability to gain global, high-quality views of RNA processing transcriptome-wide: 1. Develop low-sample and tag-eCLIP methods for highly parallelizable in vivo profiling of RBPs in low input samples, and for RBPs which lack high-quality native antibodies for immunoprecipitation. 2. Show that transcriptome profiling coupled with RBP target identification can identify critical regulators of a biological system, using differentiation of human induced pluripotent stem cells as a model system 3. Develop methods for unbiased identification of upstream functional regulators of non-coding RNAs and RNA processing in an RNA-centric manner. My extensive expertise in genomics, computational biology, and the study of DNA and RNA binding proteins makes me an ideal candidate to perform the research proposed above. These three aims take different approaches that will coalesce in a robust ability to begin either with an RBP of interest and identify its regulated targets, or begin with an RNA of interest and identify regulator RBPs, which will serve as the basis for my independent research program as an independent faculty candidate. The Yeo lab at UCSD is an ideal environment to perform this research and complete my training towards pursuit of an independent academic faculty position, as it has consistently been a leader in developing both experimental and computational methods to characterize RBP regulation. Additionally, the location of the Yeo lab proximal to outstanding researchers at UCSD, the Salk Institute, and other research institutes and biotechnology companies in La Jolla will provide specific hands-on experimental training in stem cell culture and differentiation, as well as ample opportunities for mentored training in performing research and developing an independent research program.

项目总结