DNA transposons: evolutionary history and genomic impact in vertebrates

DNA 转座子：脊椎动物的进化史和基因组影响

• 批准号: 8897381
• 负责人: Cedric Feschotte
• 金额: $ 14.86万
• 依托单位: UNIVERSITY OF UTAH
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-02-01 至 2017-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8897381
• 关键词: Accounting; Architecture; Automobile Driving; Beryllium; Bioinformatics; Biological; Biology; Biomedical Research; Cataloging; Catalogs; Chiroptera; Code; Complement; DNA Sequence; DNA Transposable Elements; DNA Transposons; Data Set; Development; Elements; Eukaryota; Event; Evolution; Exons; Family; Fostering; Frequencies; Gene Expression Profile; Genes; Genetic Materials; Genome; Genome Scan; Genome Stability; Genomics; Human; Human Genome; Incidence Study; Indium; Left; Liver; Mammals; Measures; Mediating; Mining; Mobile Genetic Elements; Modeling; Mus; Nature; Organism; Pattern; Positioning Attribute; Process; Property; Proteins; Radiation; Recording of previous events; Regulatory Element; Research; Resources; Retrotransposon; Shapes; Structure; Surveys; System; Testis; Time; Transcript; Variant; Vertebrates; brain tissue; comparative genomics; design; genome sequencing; genome-wide; human disease; innovation; mammalian genome; next generation sequencing; novel; structural genomics; transcriptome sequencing; transposon/insertion element

DESCRIPTION (provided by applicant): Mobile DNA elements are major components of mammalian genomes, accounting for about half of their genetic material. Insertion and rearrangements of mobile elements poses a serious threat to genome stability, and indeed they have been tied to over a hundred human diseases. In recent years there has been a growing appreciation of the long-term influence of mobile elements in shaping genomes and fostering the emergence of biological novelty. But we still have an incomplete and biased picture of the biology and impact of mobile elements in mammals. This is because most of the research has focused on retrotransposons, a prominent class of elements in human and mouse. In this renewal we will pursue our study of another widespread class of elements, the DNA transposons, which remains understudied in mammals. DNA transposons account for 3% of the human genome and at least 12% of the bat genome. They are distinguished from retrotransposons by many facets of their biology and evolutionary dynamics. For instance, we found that some DNA transposons were introduced in diverse mammals by means of horizontal transfer, the passage of genetic material between non-mating species. Thanks to recent technological advances in DNA sequencing and bioinformatics, we are now well positioned to study the incidence and consequences of DNA transposon invasions at a genome-wide scale. In the first aim we will employ a combination of computational and experimental approaches to obtain a quantitative assessment of the frequency and breadth of horizontal transposon transfers in vertebrates. Horizontal transfer of mobile elements is a crucial mechanism for bacterial evolution. Our studies should clarify its evolutionary significance in vertebrates. In th second and third aims we capitalize on the discovery of recent and massive DNA transposon invasions in bats to examine, for the first time in any organism, the contribution of DNA transposons to genomic structural variation (Aim 2) and transcriptome evolution (Aim 3). The development of bats as a mammalian system to study DNA transposons and genome evolution is innovative and it will contribute to a growing body of genomic resources for these emerging models in biomedical research.

描述（由申请人提供）：可移动DNA元件是哺乳动物基因组的主要组成部分，约占其遗传物质的一半。移动元件的插入和重排对基因组稳定性构成严重威胁，事实上它们与一百多种人类疾病有关。近年来，人们越来越认识到移动元件在塑造基因组和促进生物新颖性的出现方面的长期影响。但我们对哺乳动物中移动元件的生物学和影响的了解仍然不完整且有偏见。这是因为大多数研究都集中在逆转录转座子上，逆转录转座子是人类和小鼠体内的一类重要元素。在本次更新中，我们将继续研究另一类广泛存在的元素，即 DNA 转座子，该元素在哺乳动物中的研究尚未充分。 DNA转座子占人类基因组的3%，至少占蝙蝠基因组的12%。它们在生物学和进化动力学的许多方面都与反转录转座子不同。例如，我们发现一些DNA转座子通过水平转移（遗传物质在非交配物种之间的传递）被引入到不同的哺乳动物中。得益于 DNA 测序和生物信息学方面的最新技术进步，我们现在能够在全基因组范围内研究 DNA 转座子入侵的发生率和后果。在第一个目标中，我们将采用计算和实验方法相结合的方法来定量评估脊椎动物水平转座子转移的频率和宽度。移动元件的水平转移是细菌进化的重要机制。我们的研究应该阐明它在脊椎动物中的进化意义。在第二个和第三个目标中，我们利用最近在蝙蝠中发现的大规模 DNA 转座子入侵，首次在任何生物体中检查 DNA 转座子对基因组结构变异（目标 2）和转录组进化（目标 3）的贡献。将蝙蝠作为研究 DNA 转座子和基因组进化的哺乳动物系统的发展是创新的，它将有助于为生物医学研究中的这些新兴模型提供越来越多的基因组资源。

项目成果

Spy: a new group of eukaryotic DNA transposons without target site duplications.

• DOI: 10.1093/gbe/evu140
• 发表时间: 2014-06-24
• 期刊: Genome biology and evolution
• 影响因子: 3.3
• 作者: Han MJ;Xu HE;Zhang HH;Feschotte C;Zhang Z
• 通讯作者: Zhang Z

Ecological networks to unravel the routes to horizontal transposon transfers.

• DOI: 10.1371/journal.pbio.2001536
• 发表时间: 2017-02
• 期刊: PLoS biology
• 影响因子: 9.8
• 作者: Venner S;Miele V;Terzian C;Biémont C;Daubin V;Feschotte C;Pontier D
• 通讯作者: Pontier D

A Polycomb repressive complex is required for RNAi-mediated heterochromatin formation and dynamic distribution of nuclear bodies.

RNAi 介导的异染色质形成和核体的动态分布需要 Polycomb 抑制复合物。

• DOI: 10.1093/nar/gkaa1262
• 发表时间: 2021-06-04
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Xu J;Zhao X;Mao F;Basrur V;Ueberheide B;Chait BT;Allis CD;Taverna SD;Gao S;Wang W;Liu Y
• 通讯作者: Liu Y

Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution.

• DOI: 10.1016/j.tree.2010.06.001
• 发表时间: 2010-09
• 期刊: Trends in ecology & evolution
• 影响因子: 16.8
• 作者: Schaack S;Gilbert C;Feschotte C
• 通讯作者: Feschotte C

Exploration of the Drosophila buzzatii transposable element content suggests underestimation of repeats in Drosophila genomes.

• DOI: 10.1186/s12864-016-2648-8
• 发表时间: 2016-05-10
• 期刊: BMC genomics
• 影响因子: 4.4
• 作者: Rius N;Guillén Y;Delprat A;Kapusta A;Feschotte C;Ruiz A
• 通讯作者: Ruiz A