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Genomic Analysis of Centromere Assembly and Function

着丝粒组装和功能的基因组分析

基本信息

批准号：
10667642
负责人：
BETH A SULLIVAN
金额：
$ 34.79万
依托单位：
DUKE UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2017
资助国家：
美国
起止时间：
2017-09-01 至 2026-07-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10667642
关键词：
Address Architecture Area Artificial Chromosomes Artificial Human Chromosomes Auxins Award Biological Assay Biology Bypass CRISPR/Cas technology Centromere Chimeric Proteins Chromatin Chromosomal Stability Chromosome 17 Chromosome abnormality Chromosomes Classification Competence Congenital Abnormality Coupled DNA DNA Sequence DNA Transposable Elements Defect Dicentric chromosome Disease Elements Engineering Epigenetic Process Exhibits Genome Genome Stability Genome engineering Genomics Genotype Goals Homo sapiens Human Human Chromosomes Human Genome Infertility Kinetochores Knowledge Label Link Location Maintenance Malignant Neoplasms Maps Memory Modeling Molecular Molecular Conformation Outcome Phenotype Population Process Protein Dynamics Proteins Repetitive Sequence Research Role Satellite DNA Series Site Specific qualifier value Stretching Technology Testing Variant Work centromere protein A chromosome movement density experience flexibility functional outcomes genomic locus genomic variation improved innovation monomer nanopore negative affect recruit telomere

项目摘要

Centromeres are essential to genome inheritance. Abnormal centromere function is associated with birth defects, infertility, and cancer. Human centromeric (CEN) chromatin typically forms on alpha satellite DNA, a 171bp monomeric sequence that is organized into tandem arrays extending for several megabases. The Telomere-to- Telomere (T2T) Consortium that recently produced the first complete human genome assembly revealed that nearly all endogenous human chromosomes contain multiple alpha satellite arrays. We have shown that on some chromosomes, multiple arrays are competent for centromere assembly. Using Homo sapiens chromosome 17 (HSA17) as a model, we demonstrated that centromere location is dictated by genomic variation within alpha satellite DNA. On HSA17 that has three distinct higher order repeat (HOR) unit arrays, when the largest array contains size and sequence variation, centromere assembly shifts to a nearby array. If the centromere forms at a highly variant array, fewer centromere proteins are present and the chromosome experiences instability. We hypothesize that placement/organization of variant HORs within an alpha satellite array influences centromere location and kinetochore assembly. Since most human chromosomes must choose between two (or more) sites at which to build a stable centromere, our work addresses a fundamental gap in the knowledge of basic processes that influence centromere location, competence, and long-term stability. However, we still lack a comprehensive view of the extent of alpha satellite variation within the population and thus the range of functional centromere outcomes. In this competing renewal application, the proposed work builds on our classification of specific alpha satellite variants identified in diverse human populations to assemble stable, de novo centromeres. We will also systematically test centromere competency of long-range alpha satellite organization, coupled with variant content and proximity to mobile elements. Our project goals are to: 1) produce new genomic assemblies of functionally characterized centromeres using targeted long read sequencing approaches, 2) use human artificial chromosome assays to assess competency of different alpha satellite DNA arrangements for de novo centromere formation, 3) explore the molecular basis for variant centromere defects, and 4) use genome engineering to rehabilitate and/or rescue defective variant centromeres. Successful completion of this work will result in major advancement of our basic understanding of genomic variation within large repetitive DNA arrays in humans and its link to specific centromere outcomes and long-term chromosome maintenance and stability.

着丝粒对基因组遗传是必不可少的。异常的着丝粒功能与出生缺陷有关，不孕不育和癌症人类着丝粒染色质（CEN）通常形成在α卫星DNA上，一个171 bp的被组织成延伸数兆碱基的串联阵列的单体序列。端粒- 端粒（T2 T）财团最近产生了第一个完整的人类基因组组装揭示，几乎所有的内源性人类染色体都含有多个α随体阵列。我们已经证明，在一些染色体，多个阵列是主管着丝粒组装。利用智人17号染色体（HSA 17）作为模型，我们证明了着丝粒位置是由α内的基因组变异决定的，卫星DNA在具有三个不同的高阶重复（HOR）单元阵列的HSA 17上，当最大阵列包含大小和序列变异，着丝粒组装转移到附近的阵列。如果着丝粒形成在在高度变异的阵列中，存在较少的着丝粒蛋白，并且染色体经历不稳定性。我们假设变体HOR在α卫星阵列内放置/组织影响着丝粒位置和动粒组装。由于大多数人类染色体必须在两个（或更多）位点之间进行选择，我们的工作解决了基本过程知识中的一个根本性空白，影响着丝粒的位置、能力和长期稳定性。然而，我们仍然缺乏全面的群体内α随体变异的程度以及功能性着丝粒的范围结果。在这个竞争性的更新申请中，建议的工作建立在我们对特定α的分类基础上。在不同人群中发现的卫星变体组装稳定的从头着丝粒。我们还将系统地测试长距离α卫星组织着丝粒能力，内容和接近移动的元素。我们的项目目标是：1）生产新的基因组组装体，使用靶向长读段测序方法，2）使用人类人工染色体测定以评估不同α卫星DNA排列对从头着丝粒的能力形成，3）探索变异着丝粒缺陷的分子基础，以及4）使用基因组工程，修复和/或挽救有缺陷的变体着丝粒。这项工作的成功完成将导致重大的推进我们对人类大重复DNA阵列内基因组变异的基本理解，它与特定的着丝粒结果和长期染色体维持和稳定性的联系。