Revealing Principles of Subcellular RNA Localization by Proximity Labeling

通过邻近标记揭示亚细胞 RNA 定位原理

• 批准号: 10441618
• 负责人: Furqan Fazal
• 金额: $ 24.9万
• 依托单位: BAYLOR COLLEGE OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-07-01 至 2024-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10441618
• 关键词: 3-Dimensional; Active Biological Transport; Address; Advisory Committees; Animal Model; Binding; Biochemical Genetics; Biological Assay; Biology; Biophysics; Caenorhabditis elegans; Cell physiology; Cells; Chromatin; Cis-Acting Sequence; Code; Collaborations; Communities; Complement; DNA; DNA Library; Data; Data Set; Development; Developmental Biology; Disease; Dynein ATPase; Elements; Embryo; Environment; Enzymes; Fractionation; Gene Expression; Gene Expression Regulation; Genes; Genetic; Genomics; Goals; Grant; Heterochromatin; Human; Human body; Image; Institution; Kinesin; Knowledge; Label; Life; Location; Machine Learning; Malignant Neoplasms; Maps; Mentors; Messenger RNA; Mitochondria; Modeling; Modification; Molecular Motors; Monitor; Morphologic artifacts; Myosin ATPase; Neurons; Nuclear; Nuclear Envelope; Nuclear Lamina; Nuclear Pore; Organelles; Outer Mitochondrial Membrane; Pattern; Peroxidases; Pharmaceutical Preparations; Phase; Positioning Attribute; Postdoctoral Fellow; Process; Proteins; Protocols documentation; RNA; RNA Splicing; RNA Transport; RNA-Binding Proteins; Recombinants; Records; Regulation; Regulatory Element; Repetitive Sequence; Reporter; Research Personnel; Resolution; Resources; Retrotransposon; Role; Single Nucleotide Polymorphism; Small Nuclear RNA; Structure; System; Techniques; Technology; Testing; Tissues; Training; Transcript; Translating; Translations; Universities; Untranslated RNA; Variant; Work; Writing; active control; authority; base; career; cell fixation; cell type; clinically significant; deep learning; design; education resources; experience; gene function; genomic tools; improved; in vitro Assay; insertion/deletion mutation; insight; medical schools; multidisciplinary; nanometer; neuropathology; overexpression; programs; ribosome profiling; skills; statistics; success; tool; transcriptome; transcriptome sequencing; transcriptomics

PROJECT SUMMARY The human body comprises of trillion of cells, which are the building blocks of life. Each cell is highly organized, with various constituents within localizing to specific regions. Location within a cell is a cardinal organizing principle of gene control and function, especially for RNAs that code for proteins or serve regulatory roles as non-coding RNAs. Each cell type has its distinct RNA-species profile, and where these RNAs are located within the cell can dictate their folding, editing, splicing, translation, degradation, binding partners, catalytic activity, and even the fate of the proteins that they encode. Unsurprisingly, perturbations in RNA localization result in disease conditions including cancers and neuropathologies. In spite of the vital importance of subcellular RNA localization in gene expression, investigating such phenomena simultaneously for many RNA species has been challenging. To address these long-standing issues, Dr. Furqan Fazal and others have recently developed a technique called APEX-seq that can track the location of thousands of RNAs in living human cells with high-temporal and nanometer-spatial resolution. APEX-seq has the transformative potential to provide high-resolution snapshots of tens of thousands of endogenous cellular RNA species, free from artifacts of overexpression, cell fixation or recombinant tagging. This proposal outlines a five-year career program for Dr. Fazal as he investigates principles of RNA subcellular localization, and reaches milestone goals that will transition him into an independent investigator. By improving the APEX-seq technique and amalgamating it with a number of cutting-edge tools including massively-parallel reporter assays and deep-learning-based approaches, Dr. Fazal will dissect how sequences within RNAs direct them to different locations, and how cells actively control RNA subcellular localization to regulate gene function. This work will be carried out at Stanford University, where Dr. Fazal will be mentored by Dr. Howard Chang, a pioneer in developing new genomics tools, and Dr. Joanna Wysocka, a leading authority in vertebrate development and non-coding genomic regulatory elements. Both mentors have highly-successful track records of placing postdoctoral fellows into independent academic positions at leading institutions around the nation and world. Additional support will be available through collaboration with Drs. Shen, Boettiger and Kundaje who will provide training and expertise in genetics, imaging, statistics and computation. An advisory committee comprising of world-leading investigators Drs. Ting, Kool, Li, Bryant and Bassik will also monitor progress and provide expertise. Further acquisition of scientific and professional skills will be achieved by utilizing the educational resources available through the Stanford University School of Medicine and Office of Postdoctoral Affairs. Stanford provides an outstanding intellectually-stimulating environment with all facilities and resources necessary for success, and all proposed training will complement Dr. Fazal’s previous knowledge in genomics and biophysics and facilitate his transition into a multidisciplinary RNA biologist in the field of spatial transcriptomics.

项目总结