Nanopore based profiling of epigenetic state

基于纳米孔的表观遗传状态分析

基本信息

批准号：
10214994
负责人：
Winston George Timp
金额：
$ 63.4万
依托单位：
JOHNS HOPKINS UNIVERSITY
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：
2021-08-01 至 2025-05-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10214994
关键词：
Address Antibodies Area Azides Bar Codes Binding Binding Proteins Binding Sites Biology Cells ChIP-seq Chemicals Chromatin Color Complex Country Cytosine DNA DNA Modification Process DNA Sequence DNA Sequence Alteration DNA sequencing DNA-Binding Proteins DNA-Protein Interaction Data Detection Development Enhancers Enzymes Epigenetic Process Funding Gene Expression Gene Expression Regulation Generations Genome Grant Heterogeneity Human Genome Ice Individual Label Length Logistics Malignant Neoplasms Measurement Measures Methodology Methods Methylation Methyltransferase Modification Molecular Mutation Nuclear Organic Chemistry Organism Peptide Sequence Determination Phase Population Proteins RNA Repetitive Sequence Resolution Signal Transduction Site Somatic Cell Stimulus Technology Time Tissues Training Translating Variant Work analysis pipeline base cofactor combinatorial epigenetic profiling epigenetic variation epigenome epigenomics glycosylation histone modification human disease human reference genome insight nanopore novel promoter response sequencing platform single molecule stem tool

项目摘要

Project Summary: Though a reference human genome and even excellent characterization of the epigenome (ENCODE, Epigenetics Roadmap, 4D Nucleome Project) has been generated, we still lack a clear understanding of how the different facets of the epigenome collaborate to control gene expression. With the advent of affordable DNA-sequencing technologies, methods have been developed for examining nuclear organization, protein-DNA interaction, chromatin accessibility, and methylation state. But these methods generally interrogate only one aspect of the epigenome at a time and reads are typically too short to provide critical correlative information. We propose the development of a novel epigenetic characterization methodology, in this round of funding focusing on protein- DNA interaction through leveraging the long reads and modified bases detectable with a nanopore sequencing platform. We will enhance the signal from subtle modifications being used to profile protein-DNA interactions. We are developing a method to insert sequence tags (nanoTUBI) near the sites of protein-DNA binding. And we will implement these methods focusing on long read sequencing, gaining insights into long correlative measurements and heretofore unexplored repetitive areas, phasing the entire epigenome. These tools and analysis pipelines will grant new insights into mechanisms of gene regulation, as well as their implications for human disease.

项目摘要：尽管参考人类基因组，甚至是表观遗传组的出色表征（编码，表观遗传学路线图，4D核心项目）已经生成，我们仍然缺乏对不同的方式的了解表观基因组的方面合作控制基因表达。随着负担得起的DNA测序的出现已经开发了用于检查核组织，蛋白质-DNA相互作用的方法，染色质的可及性和甲基化状态。但是这些方法通常仅审问一次表观基因组和阅读通常太短，无法提供关键的相关信息。我们建议在这一一轮的资金中，开发了一种新型的表观遗传特征方法，重点是蛋白质通过利用纳米孔测序可检测到的长读取和修改的基础，DNA相互作用平台。我们将通过用于介绍蛋白-DNA相互作用的细微修饰来增强信号。我们正在开发一种插入蛋白-DNA结合部位附近的序列标签（纳米图）的方法。还有我们将实施这些方法，重点是长阅读测序，获得对长相关性的见解测量和迄今未开发的重复区域，平列整个表观基因组。这些工具和分析管道将赋予对基因调节机制的新见解，以及它们对人类疾病。