Mobile element derived chromatin looping variability in human populations

人群中移动元件衍生的染色质循环变异

• 批准号: 10340478
• 负责人: Alan P Boyle
• 金额: $ 39万
• 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: 2022-09-23 至 2026-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10340478
• 关键词: 3-Dimensional; Address; Affect; Automobile Driving; Binding; CRISPR/Cas technology; Catalogs; Chromatin; Chromatin Conformation Capture and Sequencing; Chromatin Loop; Code; Computer Analysis; Computing Methodologies; DNA Insertion Elements; DNA Transposable Elements; Data; Development; Elements; Etiology; Evolution; Failure; Gene Expression; Gene Expression Regulation; Genome; Genomics; Goals; Human; Human Biology; Human Genome; Individual; Knowledge; Length; Location; Maps; Mediating; Methods; Molecular Computations; Mutagenesis; Outcome; Pattern; Phenotype; Play; Population; Process; Regulator Genes; Retinal blind spot; Role; Sampling; Site; Technology; Tissue-Specific Gene Expression; Untranslated RNA; Variant; Work; base; computational basis; cost; disorder risk; genome sequencing; genome-wide; human disease; improved; innovation; nanopore; novel; study population; three dimensional structure; transcription factor; whole genome

Project Summary Mobile element insertions (MEIs), or transposable elements, have been established to contribute to ongoing mutagenesis of the human genome, leading to widespread variability and sporadic cases of human disease. Recent work has begun to illuminate underlying roles through which MEIs affect regulatory processes through their combined effects on transcription factor binding and 3D chromatin looping. Recent work from our group has demonstrated the importance of MEIs in establishing chromatin looping variability in driving differential gene expression. These observations have precipitated development of molecular and computational approaches to study their impact on human biology, including whole-genome and target-capture strategies leveraging short- read sequencing technologies. However, these methods fail to accurately capture the entire landscape of MEIs within the human genome because of their limited ability to identify non-reference polymorphic MEIs. This failure derives in part from a blind-spot of short-read genome sequencing: because the human genome harbors over 1 million MEIs, unambiguous alignment of short reads is problematic. Given the demonstrated importance of MEIs to human biology and evolution, it is imperative that novel methods capable of comprehensively mapping their locations across many human genomes be developed. In this proposal we aim to 1) Quantify the effects of TE activity on CTCF binding in a human population sample of 51 well-studied individuals using computational meth- ods, 2) Map invariant and polymorphic LTR13 insertions in the CEU population and investigate their effects on intraspecies variability in CTCF binding, chromatin looping, and gene regulation, and 3) Directly map HARVK/LTR13-anchored chromatin loops through enrichment-capture combined with ONT-based chromatin conformation capture sequencing. We expect completion of these aims to yield the following outcomes: We will: 1) Present the first reliable estimate of the contribution of polymorphic MEIs to CTCF-mediated chromatin looping variation in a human population. 2) Improve understanding of how fixed and polymorphic MEIs contribute to population-level variability in regulatory activity, gene expression, and disease risk. 3) Demonstrate causality of ongoing MEI activity regarding population-level looping variation and differential gene expression. The new meth- ods proposed here will address the shortcomings of existing short-read sequencing technologies, allowing us to comprehensively and cost-effectively map target MEIs across a broad population sample, bridging important gaps in our knowledge of how gene regulatory processes evolve in the human genome.

项目摘要 已经建立了移动元件插入(MEI)或转座元件，以促进正在进行的 人类基因组的突变，导致广泛的变异和人类疾病的零星病例。 最近的工作已经开始阐明多边投资机构通过以下方式影响监管过程的潜在角色 它们对转录因子结合和3D染色质环路的联合作用。我们小组最近的工作是 证明了MEIS在建立驱动差异基因的染色质环变异性中的重要性 表情。这些观察结果促进了分子和计算方法的发展 研究它们对人类生物学的影响，包括利用短基因组和目标捕获策略 阅读测序技术。然而，这些方法不能准确地捕捉到MEIS的整个景观 这是因为它们识别非参考多态MEI的能力有限。这一失败 部分源于短读基因组测序的盲点：因为人类基因组包含超过1 百万Mei，明确的短读对齐是有问题的。鉴于MEIS的重要性已得到证实 对于人类生物学和进化论来说，能够全面绘制其 许多人类基因组的位置都被开发出来了。在这项建议中，我们的目标是1)量化TE的影响 用计算方法在51个经过充分研究的个体的人群样本中对CTCF结合的活性 Ods，2)在CEU群体中的不变和多态LTR13插入，并研究它们对 CTCF结合、染色质环和基因调控的种内变异，以及3)直接作图 HARVK/LTR13结合基于ONT的染色质富集捕获锚定染色质环 构象捕获测序。我们预计完成这些目标将产生以下结果：我们将： 1)首次可靠地估计了多态MEI对CTCF介导的染色质环化的贡献 人类群体中的变异。2)提高对固定和多态MEI如何贡献的理解 调节活动、基因表达和疾病风险的种群水平的变异性。3)证明因果关系 正在进行的MEI活动涉及种群水平的循环变异和差异基因表达。新的冰毒- 这里提出的ods将解决现有短读测序技术的缺点，使我们能够 在广泛的人群样本中全面、经济高效地绘制目标MEI图，为重要的 我们对基因调控过程如何在人类基因组中进化的了解存在差距。