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Comparative and functional analysis of conservation and rearrangement of topologically associating domains across mammals.

哺乳动物拓扑关联域的保护和重排的比较和功能分析。

基本信息

批准号：
10189682
负责人：
Lucia Carbone
金额：
$ 71.4万
依托单位：
OREGON HEALTH & SCIENCE UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2018
资助国家：
美国
起止时间：
2018-09-14 至 2024-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10189682
关键词：
ATAC-seq Affect Biological Biological Assay CCCTC-binding factor CRISPR/Cas technology CSPG6 gene Cell Line ChIP-seq Chromatin Chromatin Conformation Capture and Sequencing Chromatin Structure Chromosomal Rearrangement Chromosomes Clinical Congenital Disorders DNA DNA Sequence Rearrangement Data Deltastab Disease Enhancers Epigenetic Process Event Evolution Gene Activation Gene Expression Gene Expression Regulation Genes Genetic Genetic Diseases Genetic Variation Genome Genomic DNA Genomics Hi-C Human Hylobates Genus Individual Karyotype Knowledge Lead Light Malignant Neoplasms Mammals Maps Mission Modeling Molecular Conformation Mus Mutation Outcome Pathology Phenotype Pongidae Portraits Positioning Attribute Public Health Research Resolution Resources Role Source Structure Synteny TOP2B gene Testing Tissue-Specific Gene Expression Trees United States National Institutes of Health Variant comparative comparative genomics differential expression experience functional genomics functional outcomes genome editing genome-wide human disease novel prevent promoter structural genomics transcriptome sequencing

项目摘要

PROJECT SUMMARY Chromosomal rearrangements are a great source of inter- and intra-specific genetic variation and are major contributors to human disease. Although position of rearrangement breakpoints can now be mapped at high resolution, interpreting the evolutionary or clinical implications of these events remains challenging. Depending on where they occur, rearrangements can disrupt the organization of genomic functional compartments, known as topologically associating domains (TADs). Within TADs, nearby loci (i.e. promoters and enhancers) interact frequently with each other, while interactions with loci outside TADs are prevented by TAD boundaries. Disruption of TAD boundaries can result in ectopic genes regulation, aberrant phenotypes, and genetic disorders. The functional outcomes of chromosomal rearrangements, therefore, can only be fully understood when studied in the context of genome topology. To shed light on some of the evolutionary implications of genome reorganization, we recently studied the gibbon genome, which has experienced rapid and recent karyotype evolution with respect to human and the other apes. In the gibbon genome, we observed that TADs remained genetically and epigenetically intact (genomic false-shuffle), because evolutionary breakpoints overlapped almost exclusively with TAD boundaries. Comparison with human and other mammals shows that these TAD boundaries are evolutionary conserved, indicating that TAD boundary establishment predated, and may have even contributed to, occurrence of evolutionary breakage. Motivated by our preliminary findings in gibbon, we propose to use a broad comparative and functional approach to assay multiple species with naturally highly rearranged genomes across the Boreoeutheria tree, and characterize the genetic context, epigenetic state, and evolutionary conservation of their TAD boundaries. We will determine if the false shuffle is a recurring mechanism of genome evolution and we will identify chromatin states associated with evolutionary fragility, as these regions and states could be relevant to human disease (Aim 1). Additionally, we will determine the level of conservation for TAD boundaries across different clades. Overall, the combination of these annotations will be a valuable resource to aid the interpretation of clinically and/or evolutionarily relevant rearrangements. We will then use an evolutionary-motivated approach to delete a subset of highly conserved and clade-specific TAD boundaries using CRISPR/Cas9 in cell lines and mouse, to assess the functional consequences of their deletion on DNA interaction, chromatin state, and gene expression (Aim 2). Finally, by analyzing differential gene expression and chromatin conformation between closely related species with structurally different genomes, we will evaluate the extent to which chromosomal rearrangements can alter short- and long-range functional interaction and contribute to differential gene expression (Aim 3). Overall, this study will elucidate the epigenetics changes associated with evolutionary genome reorganization and will help elucidating mechanisms by which genome rearrangement can lead to pathology.

项目摘要染色体重排是种间和种内遗传变异的重要来源，人类疾病的贡献者。尽管重排断点的位置现在可以在高水平上映射，然而，解释这些事件的进化或临床意义仍然具有挑战性。取决在它们发生的地方，重排可以破坏基因组功能区室的组织，拓扑关联域（TADs）。在TADs内，附近的基因座（即启动子和增强子）相互作用经常相互作用，而与TADs以外的基因座的相互作用则被TADs边界所阻止。细胞边界的破坏可导致异位基因调节、异常表型和遗传学异常。紊乱因此，染色体重排的功能结果只有在 when studied研究in the context背景of genome基因组topology拓扑.为了阐明一些进化的含义，基因组重组，我们最近研究了基因组，它经历了快速和最近的人类和其他猿类的核型进化。我们观察到，在大肠杆菌基因组中，保持遗传和表观遗传完整（基因组假洗牌），因为进化的断点几乎完全与边界重叠。与人类和其他哺乳动物的比较表明，这些边界是进化上保守的，表明边界的建立早于，甚至可能导致了进化断裂的发生我们的初步发现，因此，我们建议使用一种广泛的比较和功能的方法来测定多个物种，在Boreoeutheria树中自然高度重排的基因组，并描述遗传背景，表观遗传状态，以及它们的生物边界的进化保守性。我们将确定是否假洗牌是基因组进化的一种循环机制，我们将识别与进化的脆弱性，因为这些地区和国家可能与人类疾病有关（目标1）。另外我们将决定不同分支之间的生态边界的保护水平。总的来说，这些注释将是一个有价值的资源，以帮助解释临床和/或进化相关重新安排然后，我们将使用进化动机的方法删除高度保守的一个子集，以及在细胞系和小鼠中使用CRISPR/Cas9的进化枝特异性DNA边界，它们的缺失对DNA相互作用、染色质状态和基因表达的影响（目的2）。最后通过分析密切相关物种之间的差异基因表达和染色质构象，结构不同的基因组，我们将评估染色体重排可以改变的程度短距离和长距离功能相互作用，并有助于差异基因表达（目的3）。总体而言，这这项研究将阐明与进化基因组重组相关的表观遗传学变化，阐明了基因组重排导致病理学的机制。