Mobile element derived chromatin looping variability in human populations

项目摘要 移动的元件插入（MEI）或转座元件已经被建立以有助于进行中的基因表达。 人类基因组的突变，导致广泛的变异性和散发的人类疾病病例。 最近的工作已经开始阐明MEIs通过以下方式影响监管过程的潜在作用： 它们对转录因子结合和3D染色质环的组合作用。我们小组最近的工作 证明了MEI在建立驱动差异基因的染色质环可变性中的重要性。 表情这些观察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- 读取测序技术。然而，这些方法无法准确地捕捉MEIs的整个景观 因为它们鉴定非参考多态性MEI的能力有限。该失效 部分来源于短读基因组测序的盲点：因为人类基因组含有超过1 百万MEI，短读段的明确比对是有问题的。鉴于MEIs的重要性， 对于人类生物学和进化来说，必须采用能够全面绘制其 在许多人类基因组中的位置。在本提案中，我们的目标是：1）量化TE的影响 使用计算方法，在51个充分研究的个体的人群样本中对CTCF结合的活性， ods，2）在CEU群体中定位不变和多态的LTR 13插入，并研究它们对 CTCF结合、染色质成环和基因调控的种内变异性，以及3）直接作图 HARVK/LTR 13锚定的染色质环通过富集-捕获结合基于ONT的染色质 构象捕获测序。我们预期这些目标的完成将产生以下成果： 1)首次可靠估计多态性MEI对CTCF介导的染色质成环的贡献 人类群体中的变异。2)更好地理解固定和多态MEI如何有助于 调节活动、基因表达和疾病风险的群体水平变异性。3)证明因果关系 正在进行的MEI活动有关人口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 在广泛的人口样本中全面、经济有效地绘制目标MEI， 我们对人类基因组中基因调控过程如何演变的知识存在空白。

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.