Impact and biological implication of mobile elements to canine genomic diversity - F32 Wildschutte/Kidd

移动元件对犬基因组多样性的影响和生物学意义 - F32 Wildschutte/Kidd

基本信息

批准号：
8908104
负责人：
Julia Vera Halo
金额：
$ 4万
依托单位：
UNIVERSITY OF MICHIGAN AT ANN ARBOR
依托单位国家：
美国
项目类别：
财政年份：
2015
资助国家：
美国
起止时间：
2015-05-01 至 2015-12-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8908104
关键词：
Address Alu Elements Biological Biological Assay Biological Models Biology Body Size Breeding Canis familiaris Centronuclear myopathy Cleft Palate Color Complement Computer Analysis Coupled Custom DNA DNA Insertion Elements Data Data Set Disease Elements Exons Future Genes Genetic Variation Genome Genomics Genotype Goals Health Human Indium Individual Knowledge L1 Elements Length Libraries Link Long Interspersed Elements Maps Mediator of activation protein Michigan Modeling Molecular Movement Mutagenesis Narcolepsy Orthologous Gene Phenotype Plasmids Positioning Attribute Prevalence Reading Reporter Research Resources Retroelements Retrotransposition Role Sampling Short Interspersed Nucleotide Elements Site Source System Testing Training Universities Variant Work base comparative genomics disease phenotype disorder risk experimental analysis genome analysis genome sequencing genome wide association study genome-wide genomic variation human disease improved insight interdisciplinary approach public health relevance structural genomics trait transposon/insertion element

项目摘要

DESCRIPTION (provided by applicant): Mobile DNA short and long interspersed elements (SINEs and LINEs) are distinct fragments of DNA that are capable of copied movement to other regions of the genome. As non-autonomous elements, SINEs achieve retrotransposition by exploiting enzymatic functions of LINEs. Mobile element insertions (MEIs) are profound mediators of genomic variation and are associated to human disease, particularly the Alu and L1 elements that continue to generate new insertions. The dog has emerged as an important model system for mapping of disease variants, leading to discoveries of disease-associated human orthologs. Understanding the diversity in this understudied model species, especially in context of disease, should present an exceptional resource in health-related comparative genomics. The canine SINEC_Cf subfamily, like Alu in humans, has undergone recent expansion, with thousands of bimorphic copies among individuals. In dogs, unique SINEC_Cf insertions have been directly linked to phenotypes from narcolepsy and centronuclear myopathy to coat coloring and body size. However, whole-genome analysis of SINEC biology and impact is very limited. Moreover, virtually nothing is known of the recently active canid LINE, L1-Y_Cf, in its own transposition or to SINEC, though there are ~30 intact L1_Cf copies in the CanFam3.1 boxer reference, including bimorphic sites. Our preliminary data indicate >32,109 bimorphic SINEC copies in a global set of dogs and related canids, including ~23,166 from the `Cf' subfamily alone, and thousands from otherwise `inactive' SINEC subfamilies. We also find ~15,703 bimorphic L1-Y_Cf, including ~150 putative full-length copies. Finally, we directly tested a single non-reference L1-Y_Cf cloned from a breed dog, demonstrating bona fide activity in a cellular-based retrotransposition assay. These findings suggest recent movement of canine MEIs. We hypothesize that canine MEI activities have substantially contributed to phenotypes observed in genomic variation and disease in dogs. We will address this hypothesis in an approach that combines computational and molecular genomics, utilizing a unique combination of experts in genomic variation and mobile element biology offered at the University of Michigan. We will comprehensively characterize canine MEIs in the following specific aims: 1. Identification and characterization of non-reference MEIs from a diverse panel of dogs and related canids utilizing whole genome sequence data and computational genomics. 2. Molecular characterization of canid LINE retrotransposition potential and the corresponding effects to mobilization and movement of non-autonomous SINEs in dogs. The training leverages expertise at the University of Michigan in computational and experimental analyses of genomic variation. They complement and augment my own research background and will provide training in approaches required to understand the impact of MEIs on a genome wide scale.

描述（由申请人提供）：可移动 DNA 短散布元件和长散布元件（SINE 和 LINE）是能够复制移动到基因组其他区域的不同 DNA 片段，作为非自主元件，SINE 通过利用酶功能实现逆转座。移动元件插入 (MEI) 是基因组变异的重要介质，与人类疾病相关，尤其是不断产生新插入的 Alu 和 L1 元件。狗已成为绘制疾病变异图谱的重要模型系统，导致与疾病相关的人类直系同源物的发现，了解这一正在研究的模型物种的多样性，特别是在疾病背景下，应该为健康相关的比较提供特殊的资源。犬类 SINEC_Cf 亚家族，就像人类中的 Alu 一样，最近经历了扩展，在狗中具有数千个双态拷贝，独特的 SINEC_Cf 插入与嗜睡症的表型直接相关。然而，对 SINEC 生物学及其影响的全基因组分析非常有限，而且，实际上对最近活跃的犬科动物 LINE，L1-Y_Cf 本身的转座或对 SINEC 的了解非常有限。尽管 CanFam3.1 Boxer 参考中有大约 30 个完整的 L1_Cf 副本，包括双态位点，但我们的初步数据表明，在 a 中存在超过 32,109 个双态 SIEC 副本。全球范围内的狗和相关犬科动物，包括来自“Cf”亚科的约 23,166 只，以及来自其他“不活跃”SINEC 亚科的数千只，我们还发现了约 15,703 个双态 L1-Y_Cf，其中包括约 150 个假定的全长副本。我们直接测试了从品种狗克隆的单个非参考 L1-Y_Cf，证明了基于细胞的逆转录转座的真正活性这些发现表明犬 MEI 的最新动态。我们发现，犬 MEI 活动对狗的基因组变异和疾病的表型有很大影响。我们将利用一种独特的组合，通过结合计算和分子基因组学的方法来解决这一假设。我们将在以下具体目标中全面表征犬类 MEI： 1. 利用整个犬类和相关犬科动物对非参考 MEI 进行鉴定和表征。 2. 犬科动物 LINE 逆转录转座潜力的分子特征以及对狗非自主 SINE 动员和运动的相应影响该培训利用了密歇根大学在基因组变异的计算和实验分析方面的专业知识。它们补充和增强了我自己的研究背景，并将提供了解 MEI 对全基因组影响所需方法的培训。