Experimental and bioinformatics platform for epigenome analysis using nanopore sequencing

使用纳米孔测序进行表观基因组分析的实验和生物信息学平台

• 批准号: 10654043
• 负责人: Kin Fai Au
• 金额: --
• 依托单位: OHIO STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-27 至 2023-07-02
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10654043
• 关键词: Acceleration; Address; Affect; Alleles; Binding; Biochemical Reaction; Bioinformatics; Biological; Biological Process; Biomedical Research; Cell Proliferation; Cell Reprogramming; Cellular biology; Chromatin; Collaborations; Complex; DNA; DNA Methylation; DNA Repair; DNA Transposable Elements; DNA biosynthesis; Data; Data Analyses; Development; Embryonic Development; Enhancers; Epigenetic Process; Event; Foundations; Genes; Genome; Genomic Imprinting; Genomic Segment; Germ Cells; Human; Human Genome; Individual; Investigation; Laboratory Research; Length; Methodology; Methods; Methylation; Modification; Mus; Names; Nucleosomes; Nucleotides; Pattern; Phase; Protocols documentation; Publications; Regulation; Repetitive Sequence; Research; Resolution; Role; Sampling; Scientist; Series; Signal Transduction; Solid; Structure of primordial sex cell; Techniques; Technology; Transcription Process; Universities; Work; analysis pipeline; base; bisulfite; chromatin immunoprecipitation; crosslink; data format; demethylation; epigenetic regulation; epigenome; experience; experimental study; genome integrity; human embryonic stem cell; imprint; improved; innovation; nanopore; next generation sequencing; precision medicine; prototype; public health relevance; single molecule; stem cell biology; stem cells; technique development; tool; transcription factor; transcriptome

PROJECT SUMMARY / ABSTRACT The epigenetic status of genomes including nucleosome occupancy, chromatin accessibility and DNA methylation, is highly relevant to the regulation of DNA-template biological processes from transcription to DNA replication and repair. Most existing techniques for characterizing epigenome utilize Next Generation Sequencing (NGS) following the biochemical reactions that capture the signals (e.g., bisulfite conversion, cross-linking and chromatin immunoprecipitation/ChIP). The development of these techniques has dramatically accelerated the research of different epigenetics events and has led to many important biological findings. As the new technique nanopore sequencing has been optimized to convey robust sequencing data of single DNA molecules with long read length, it brings in new discernible information that is useful for addressing certain challenging but important epigenetics problems. We develop an experimental protocol MeSMLR-seq and a series of bioinformatics methods to define the multiple types of epigenetic events, including nucleosome occupancy, chromatin accessibility and DNA methylation, at the rarely explored genome regions and biological context by leveraging the unique information of nanopore sequencing. Utilizing these experimental and bioinformatics methods, we aim to interrogate the following problems during the epigenetic reprogramming of early embryonic development and primordial germ cell development: in Aim 1, we will study the epigenetic regulation of transposable element expression and transposition. Aim 2 will construct the allele-specific epigenome and identify the genome loci with significant epigenome difference between alleles. Aim 3 will identify significant difference of the epigenomes between DNA strands and investigate their regulatory roles and dynamics during epigenetic reprogramming. These studies are anticipated to provide the first experimental and bioinformatics platform for improve our understanding of epigenome with complex biomedical context in a comprehensive manner.

项目摘要 /摘要 基因组的表观遗传状态，包括核小体占用率，染色质访问性和DNA甲基化， 与从转录到DNA复制和 维修。表征表观基因组的大多数现有技术都使用下一代测序（NGS） 遵循捕获信号的生化反应（例如，甲硫酸氢盐转换，交联和 染色质免疫沉淀/芯片）。这些技术的开发极大地加速了 对不同表观遗传学事件的研究，导致许多重要的生物学发现。作为新的 技术纳米孔测序已被优化，以传达单个DNA的可靠测序数据 长度长的分子，它带来了新的可辨认信息，可用于解决某些信息 具有挑战性但重要的表观遗传学问题。我们开发了实验协议MESMLR-SEQ和A 定义多种表观遗传事件的一系列生物信息学方法，包括核小体 在很少探索的基因组区域和生物学 通过利用纳米孔测序的独特信息来上下文。利用这些实验和 生物信息学方法，我们旨在在表观遗传重编程过程中询问以下问题 早期胚胎发育和原始生殖细胞发育：在AIM 1中，我们将研究表观遗传学 调节转座元件表达和换位。 AIM 2将构建特定于等位基因的 表观基因组并确定等位基因之间具有显着表观基因组差异的基因组基因群。目标3意志 确定DNA链之间的表观基因组的显着差异并研究其调节作用 和表观遗传重编程过程中的动态。预计这些研究将提供第一个实验 和生物信息学平台，以在一个复杂的生物医学环境中提高我们对表观基因组的理解 全面的方式。