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

基本信息

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
项目类别：
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

项目摘要

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.

项目概要人体由数万亿个细胞组成，它们是生命的基石，每个细胞都高度组织化。细胞内不同区域的成分定位到特定的位置是一个主要的组织。基因控制和功能的原理，尤其是编码蛋白质或发挥调节作用的RNA 每种细胞类型都有其独特的 RNA 物种特征，以及这些 RNA 的位置。细胞可以决定它们的折叠、编辑、剪接、翻译、降解、结合伙伴、催化活性和甚至它们编码的蛋白质的命运也毫不奇怪，RNA 定位的扰动会导致疾病。尽管亚细胞 RNA 定位至关重要。在基因表达领域，同时研究多种 RNA 物种的此类现象具有挑战性。为了解决这些长期存在的问题，Furqan Fazal 博士和其他人最近开发了一种称为 APEX-seq 可以追踪人类活细胞中数千个 RNA 的位置，具有高时空和 APEX-seq 具有提供高分辨率快照的变革潜力。数以万计的内源性细胞 RNA 种类，不受过度表达、细胞固定或该提案概述了 Fazal 博士研究原理的五年职业计划。 RNA亚细胞定位的研究人员，并达到了里程碑式的目标，这将使他成为一个独立的通过改进 APEX-seq 技术并将其与许多尖端工具相结合。包括大规模并行报告分析和基于深度学习的方法，Fazal 博士将剖析如何 RNA 内的序列将它们引导至不同的位置，以及细胞如何主动控制 RNA 亚细胞这项工作将在斯坦福大学进行，Fazal 博士将在那里进行。由开发新基因组学工具的先驱 Howard Chang 博士和 Joanna Wysocka 博士指导两位导师都拥有脊椎动物发育和非编码基因组调控元件方面的领先权威。将博士后研究员安排到领先的独立学术职位的非常成功的记录全国和世界各地的机构将通过与沉博士的合作提供更多支持。 Boettiger 和 Kundaje 将提供遗传学、成像、统计和计算方面的培训和专业知识。由世界领先的研究人员 Ting、Kool、Li、Bryant 和 Bassik 博士组成的咨询委员会也将成立。将进一步掌握科学和专业技能。利用斯坦福大学医学院和办公室提供的教育资源斯坦福大学提供出色的智力刺激环境，设施齐全，成功所需的资源，所有拟议的培训都将补充 Fazal 博士之前的知识基因组学和生物物理学，并促进他转变为空间领域的多学科 RNA 生物学家转录组学。