Direct Determination of Multiple Specific Forms of DNA Chemical Modifications in Human Genome

直接测定人类基因组中多种特定形式的 DNA 化学修饰

基本信息

批准号：
10576895
负责人：
Gang Fang
金额：
$ 53.52万
依托单位：
ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI
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：
2021-05-01 至 2024-02-29
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10576895
关键词：
Address Antibodies Bacteria Biological Biological Process Categories Characteristics Chemicals Chemistry Classification Complex Cytosine DNA DNA Damage DNA Methylation DNA Modification Process DNA-Directed DNA Polymerase Data Data Set Dedications Detection Development Discrimination Ensure Enzymes Epigenetic Process Evaluation Event Face Future Genome Goals Heterogeneity Human Characteristics Human Development Human Genome Immunoprecipitation Individual Maps Mediating Methods Methylation Modeling Modification Neurons Nucleic Acids Performance Ploidies Protocols documentation Protozoa Research Personnel Resolution Role Technology Third Generation Sequencing Time Training Variant base bisulfite sequencing cancer invasiveness cancer risk cell type cost deep learning model demethylation exome experience human disease innovation insight learning strategy methylome nanopore network models new technology oxidation prototype sequencing platform single molecule whole genome

项目摘要

PROJECT SUMMARY/ABSTRACT The information content of DNA is not limited to the primary sequence (A, C, G, T), but is also conveyed by chemical modifications of individual bases. For example, DNA methylation, specifically 5-methylcytosine (5mC), has been widely studied for its important regulatory roles in human development and diseases. In addition, the discovery of active demethylation of 5mC, mediated by TET enzymes, into 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) revealed great insights into the dynamic nature of the human methylome and its close relevance to multiple human diseases. Beyond these chemical modifications to cytosine, recent studies by us and others discovered that N6-methyladenine (6mA), another form of methylation previously thought exclusively existing in bacteria and protozoa, also exists in eukaryotic genomes including the human genome. In addition to these epigenetic marks, different forms of DNA damages represent another category of DNA chemical modifications that are of important biological relevance. Although a few methods for mapping individual chemical modifications have been developed and some are widely used, it is usually hard for broad researchers to master every protocol to map each form of modification. While third- generation sequencing technologies support the direct detection of DNA modifications, they face fundamental challenges distinguishing among different forms of modifications. The objective of this project is to develop a novel technology for the direct mapping of multiple forms of DNA methylation and DNA damage events simultaneously. The core idea is that each form of nucleic acid modification has a unique signature in terms of their physical interaction with DNA polymerase, or nanopores in third-generation sequencing; and these signatures can be modeled by deep learning methods. We will develop this technology using multiple innovative strategies to address a few fundamental challenges, and then comprehensively evaluate the technology to facilitate broad applications.

项目摘要/摘要 DNA的信息含量不仅限于主要序列（a，c，g，t），但也通过单个碱基的化学修饰。例如，DNA甲基化，特别是5-甲基胞嘧啶（5MC），已广泛研究其在人类发展和疾病中的重要调节作用。另外，通过TET酶介导的5MC的活性脱甲基化，进入5-羟基甲基胞嘧啶（5HMC）， 5-甲基环胞嘧啶（5FC）和5-羧基霉素（5CAC）揭示了对该动态性质的很好的见解人甲基组及其与多种人类疾病的相关性。除了这些化学修饰之外 to cytosine, recent studies by us and others discovered that N6-methyladenine (6mA), another form of 甲基化以前认为仅存在于细菌和原生动物中，也存在于真核基因组中包括人类基因组。除了这些表观遗传标记，不同形式的DNA损伤代表另一类的DNA化学修饰具有重要的生物学相关性。虽然有几个已经开发了映射单个化学修饰的方法，有些是广泛使用的，它是通常，对于广泛的研究人员而言，很难掌握每个协议来绘制每种形式的修改。而第三生成测序技术支持直接检测DNA修饰，它们面对基本挑战在不同形式的修改之间区分。该项目的目的是开发直接映射多种形式的DNA甲基化和DNA损伤事件的新技术同时地。核心思想是，每种形式的核酸修饰都具有独特的签名它们与第三代测序中的DNA聚合酶或纳米孔的物理相互作用；和这些可以通过深度学习方法对签名进行建模。我们将使用多个创新策略以应对一些基本挑战，然后全面评估促进广泛应用的技术。