Allele-specific analysis of human epigenome, transcriptome and high-resolution chromatin organization

人类表观基因组、转录组和高分辨率染色质组织的等位基因特异性分析

• 批准号: 10576452
• 负责人: Jie Liu
• 金额: $ 28万
• 依托单位: UNIVERSITY OF MICHIGAN AT ANN ARBOR
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-20 至 2024-05-19
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10576452
• 关键词: 3-Dimensional; ATAC-seq; Address; Alleles; Area; Cells; Chromatin; Chromatin Loop; Communities; Computing Methodologies; DNA; Data; Data Analyses; Data Science; Data Set; Data Sources; Funding; Genes; Genetic; Genetic Transcription; Genomic Segment; Genotype-Tissue Expression Project; Goals; Human; Human Genome; Human Genome Project; Inherited; Internet; Joints; Knowledge; Maps; Modality; Molecular; Parents; Population; Regulatory Element; Reproducibility; Research; Research Personnel; Resolution; Specificity; Tissue-Specific Gene Expression; Tissues; United States National Institutes of Health; Work; cell type; data resource; data visualization; deep learning; epigenetic variation; epigenome; epigenomics; expectation; genetic analysis; genetic variant; genome sciences; genomic data; genomic locus; human disease; human tissue; insight; interest; novel; novel sequencing technology; open data; organizational structure; transcriptome; transcriptomics; web portal; web server

Abstract The human genome has two alleles at each genetic locus, with one allele inherited from each parent. Allele- specificity has been widely observed and investigated across human transcriptome, epigenome and 3D chromatin organization respectively, as evidenced by the data collected from the GTEx project, the ENCODE project, and the 4DN project. However, the allele-level interplay among transcriptome, epigenome and 3D chromatin organization has not been systematically explored. In the proposal, we aim to leverage shared donors between these consortia and systematically investigate these connections at allele-level in many human tissue types. With the single cell datasets available from these donors, we will narrow down from tissue level to cell type level, and further interrogate these allele-specific cross-modality connections. In essential, our analysis seamlessly integrates two NIH Common Fund datasets, namely 4DN and GTEx datasets, and ENCODE datasets. With this integrated data source, biomedical researchers can easily navigate, browse, compare and investigate the high quality, high resolution, and comprehensive datasets regarding chromatin organization, regulatory elements, epigenomic status and transcriptional activity with allele-specificity and cell-type-specificity. Not only would this accomplishment have an enormous positive impact on the utility and usage of the Common Fund datasets, it would also help to promote open science and reproducible research in the areas of computational genomics and data science.

摘要 人类基因组在每个遗传位点上都有两个等位基因，每个亲本都有一个等位基因。等位基因- 人们广泛观察和研究了人类转录组、表观基因组和3D染色质中的特异性 从GTEx项目、ENCODE项目和 4DN工程。然而，转录组、表观基因组和3D染色质组织之间的等位基因水平的相互作用 还没有得到系统的探索。在该提案中，我们的目标是利用这些国家之间的共同捐赠者 并在等位基因水平上系统地研究了许多人类组织类型中的这些联系。使用 这些捐赠者提供的单细胞数据集，我们将从组织水平缩小到细胞类型水平， 并进一步询问这些等位基因特定的跨通道连接。本质上，我们的分析是无缝的 集成了NIH共同基金的两个数据集，即4DN和GTEx数据集，以及ENCODE数据集。有了这个 集成的数据源，生物医学研究人员可以轻松地导航、浏览、比较和调查 高质量、高分辨率和全面的关于染色质组织、调节元件 表观基因组状态和转录活性具有等位基因特异性和细胞类型特异性。这不仅会使 取得的成就对共同基金数据集的效用和使用产生了巨大的积极影响 还将有助于促进计算基因组学领域的开放科学和可重复研究 数据科学。