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TE Hub: A community-oriented space for sharing and connecting tools, data, resources, and methods for transposable element annotation. TE Hub:面向社区的空间,用于共享和连接可转置元素注释的工具、数据、资源和方法。
IF 4.9 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2021-06-21 DOI: 10.1186/s13100-021-00244-0
Tyler A Elliott, Tony Heitkam, Robert Hubley, Hadi Quesneville, Alexander Suh, Travis J Wheeler

Transposable elements (TEs) play powerful and varied evolutionary and functional roles, and are widespread in most eukaryotic genomes. Research into their unique biology has driven the creation of a large collection of databases, software, classification systems, and annotation guidelines. The diversity of available TE-related methods and resources raises compatibility concerns and can be overwhelming to researchers and communicators seeking straightforward guidance or materials. To address these challenges, we have initiated a new resource, TE Hub, that provides a space where members of the TE community can collaborate to document and create resources and methods. The space consists of (1) a website organized with an open wiki framework,  https://tehub.org , (2) a conversation framework via a Twitter account and a Slack channel, and (3) bi-monthly Hub Update video chats on the platform's development. In addition to serving as a centralized repository and communication platform, TE Hub lays the foundation for improved integration, standardization, and effectiveness of diverse tools and protocols. We invite the TE community, both novices and experts in TE identification and analysis, to join us in expanding our community-oriented resource.

转座因子(te)广泛存在于大多数真核生物基因组中,在进化和功能上发挥着强大而多样的作用。对它们独特生物学的研究推动了大量数据库、软件、分类系统和注释指南的创建。可用的与te相关的方法和资源的多样性引起了兼容性问题,对于寻求直接指导或材料的研究人员和传播者来说可能是压倒性的。为了应对这些挑战,我们启动了一个新的资源TE Hub,它提供了一个空间,让TE社区的成员可以协作记录和创建资源和方法。该空间包括(1)一个以开放的wiki框架(https://tehub.org)组织的网站,(2)一个通过Twitter账户和Slack频道进行的对话框架,以及(3)双月一次的Hub Update视频聊天平台的开发。除了作为集中式存储库和通信平台之外,TE Hub还为改进各种工具和协议的集成、标准化和有效性奠定了基础。我们邀请TE社区,包括TE识别和分析方面的新手和专家,加入我们,扩大我们面向社区的资源。
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引用次数: 7
ENSnano: A 3D Modeling Software for DNA Nanostructures ENSnano: DNA纳米结构的三维建模软件
IF 4.9 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2021-01-01 DOI: 10.4230/LIPIcs.DNA.27.5
N. Lévy, N. Schabanel
7 Since the 1990s, increasingly complex nanostructures have been reliably obtained out of self-assembled 8 DNA strands: from “simple” 2D shapes to 3D gears and articulated nano-objects, and even computing 9 structures. The success of the assembly of these structures relies on a fine tuning of their structure 10 to match the peculiar geometry of DNA helices. Various softwares have been developed to help 11 the designer. These softwares provide essentially four kind of tools: an abstract representation of 12 DNA helices (e.g. cadnano, scadnano, DNApen, 3DNA, Hex-tiles); a 3D view of the design (e.g., 13 vHelix, Adenita, oxDNAviewer); fully automated design (e.g., BScOR, Daedalus, Perdix, Talos, 14 Athena), generally dedicated to a specific kind of design, such as wireframe origami; and coarse grain 15 or thermodynamical physics simulations (e.g., oxDNA, MrDNA, SNUPI, Nupack, ViennaRNA,...). 16 MagicDNA combines some of these approaches to ease the design of configurable DNA origamis. 17 We present our first step in the direction of conciliating all these different approaches and 18 purposes into one single reliable GUI solution: the first fully usable version (design from scratch to 19 export) of our general purpose 3D DNA nanostructure design software ENSnano . We believe that 20 its intuitive, swift and yet powerful graphical interface, combining 2D and 3D editable views, allows 21 fast and precise editing of DNA nanostructures. It also handles editing of large 2D/3D structures 22 smoothly, and imports from the most common solutions. Our software extends the concept of 23 grids introduced in cadnano . Grids allow to abstract and articulated the different parts of a design. 24 ENSnano also provides new design tools which speeds up considerably the design of complex large 3D 25 structures, most notably: a 2D split view , which allows to edit intricate 3D structures which cannot 26 easily be mapped in a 2D view, and a copy, paste & repeat functionality, which takes advantage 27 of the grids to design swiftly large repetitive chunks of a structure. ENSnano has been validated 28 experimentally, as proven by the AFM images of a DNA origami entirely designed in ENSnano . 29 ENSnano is a light-weight ready-to-run independent single-file app, running seamlessly in most of 30 the operating systems (Windows 10, MacOS 10.13+ and Linux). Precompiled versions for Windows 31 and MacOS are ready to download on ENSnano website. As of writing this paper, our software is 32 being actively developed to extend its capacities in various directions discussed in this article. Still, 33 its 3D and 2D editing interface is already meeting our usability goals. Because of its stability and 34 ease of use, we believe that ENSnano could already be integrated in anyone’s design chain, when 35 precise editing of a larger nanostructure is needed.
自20世纪90年代以来,越来越复杂的纳米结构已经可靠地从自组装的DNA链中获得:从“简单的”2D形状到3D齿轮和铰接纳米物体,甚至计算结构。这些结构的成功组装依赖于它们的结构的微调,以匹配DNA螺旋的特殊几何形状。已经开发了各种软件来帮助设计师。这些软件基本上提供了四种工具:12个DNA螺旋的抽象表示(例如cadnano, scadnano, DNApen, 3DNA, hextiles);设计的3D视图(例如,13 vHelix, Adenita, oxDNAviewer);全自动设计(例如,BScOR,代达罗斯,珀迪克斯,塔洛斯,14雅典娜),通常致力于特定类型的设计,如线框折纸;和粗颗粒或热力学物理模拟(例如,oxDNA, MrDNA, SNUPI, Nupack, ViennaRNA,…)。MagicDNA结合了这些方法中的一些来简化可配置DNA折纸的设计。我们在将所有这些不同的方法和18种目的调和成一个可靠的GUI解决方案的方向上迈出了第一步:我们通用3D DNA纳米结构设计软件ENSnano的第一个完全可用的版本(从零开始设计到导出)。我们相信其直观,快速而强大的图形界面,结合2D和3D可编辑视图,可以快速精确地编辑DNA纳米结构。它还可以平滑地处理大型2D/3D结构的编辑,并从最常见的解决方案中导入。我们的软件扩展了cadnano中引入的23个网格的概念。网格允许抽象和连接设计的不同部分。ENSnano还提供了新的设计工具,大大加快了复杂的大型3D结构的设计,最值得注意的是:2D拆分视图,允许编辑复杂的3D结构,这些结构不能轻易地在2D视图中映射,以及复制,粘贴和重复功能,它利用网格来快速设计结构的大型重复块。ENSnano已经在实验中得到了验证,正如完全在ENSnano中设计的DNA折纸的AFM图像所证明的那样。ENSnano是一个轻量级的独立的单文件应用程序,可以在大多数操作系统(Windows 10, MacOS 10.13+和Linux)上无缝运行。Windows 31和MacOS的预编译版本已准备好在ENSnano网站上下载。在撰写本文时,我们的软件正在积极开发中,以在本文中讨论的各个方向扩展其能力。不过,它的3D和2D编辑界面已经达到了我们的可用性目标。由于其稳定性和易用性,我们相信当需要对更大的纳米结构进行精确编辑时,ENSnano已经可以集成到任何人的设计链中。
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引用次数: 3
Molecular Machines from Topological Linkages 拓扑连杆的分子机器
IF 4.9 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2021-01-01 DOI: 10.4230/LIPIcs.DNA.27.7
Keenan Breik, Austin Luchsinger, D. Soloveichik
Life is built upon amazingly sophisticated molecular machines whose behavior combines mechanical and chemical action. Engineering of similarly complex nanoscale devices from first principles remains an as yet unrealized goal of bioengineering. In this paper we formalize a simple model of mechanical motion (mechanical linkages) combined with chemical bonding. The model has a natural implementation using DNA with double-stranded rigid links, and single-stranded flexible joints and binding sites. Surprisingly, we show that much of the complex behavior is preserved in an idealized topological model which considers solely the graph connectivity of the linkages. We show a number of artifacts including Boolean logic, catalysts, a fueled motor, and chemo-mechanical coupling, all of which can be understood and reasoned about in the topological model. The variety of achieved behaviors supports the use of topological chemical linkages in understanding and engineering complex molecular behaviors. 2012 ACM Subject Classification Theory of computation → Models of computation; Theory of computation → Computational geometry
生命是建立在极其复杂的分子机器之上的,它们的行为结合了机械和化学作用。从第一性原理制造类似复杂的奈米装置,仍是生物工程尚未实现的目标。在本文中,我们形式化了一个结合化学键的机械运动(机械连杆)的简单模型。该模型使用具有双链刚性链接和单链柔性关节和结合位点的DNA进行自然实现。令人惊讶的是,我们证明了在一个理想化的拓扑模型中保留了许多复杂的行为,该模型只考虑了连杆的图连通性。我们展示了许多工件,包括布尔逻辑、催化剂、燃料马达和化学-机械耦合,所有这些都可以在拓扑模型中被理解和推理。所获得的各种行为支持了拓扑化学键在理解和工程复杂分子行为中的应用。2012 ACM学科分类:计算理论→计算模型;计算理论→计算几何
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引用次数: 1
Robust Digital Molecular Design of Binarized Neural Networks 二值化神经网络的鲁棒数字分子设计
IF 4.9 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2021-01-01 DOI: 10.4230/LIPIcs.DNA.27.1
Johannes Linder, Yuan-Jyue Chen, David Wong, Georg Seelig, L. Ceze, K. Strauss
Molecular programming – a paradigm wherein molecules are engineered to perform computation – shows great potential for applications in nanotechnology, disease diagnostics and smart therapeutics. A key challenge is to identify systematic approaches for compiling abstract models of computation to molecules. Due to their wide applicability, one of the most useful abstractions to realize is neural networks. In prior work, real-valued weights were achieved by individually controlling the concentrations of the corresponding “weight” molecules. However, large-scale preparation of reactants with precise concentrations quickly becomes intractable. Here, we propose to bypass this fundamental problem using Binarized Neural Networks (BNNs), a model that is highly scalable in a molecular setting due to the small number of distinct weight values. We devise a noise-tolerant digital molecular circuit that compactly implements a majority voting operation on binary-valued inputs to compute the neuron output. The network is also rate-independent, meaning the speed at which individual reactions occur does not affect the computation, further increasing robustness to noise. We first demonstrate our design on the MNIST classification task by simulating the system as idealized chemical reactions. Next, we map the reactions to DNA strand displacement cascades, providing simulation results that demonstrate the practical feasibility of our approach. We perform extensive noise tolerance simulations, showing that digital molecular neurons are notably more robust to noise in the concentrations of chemical reactants compared to their analog counterparts. Finally, we provide initial experimental results of a single binarized neuron. Our work suggests a solid framework for building even more complex neural network computation. 2012 ACM Subject Classification Theory of computation → Models of computation; Applied computing
分子编程——其中分子被设计来执行计算的一种范例——在纳米技术、疾病诊断和智能治疗方面显示出巨大的应用潜力。一个关键的挑战是找出系统的方法来编译分子的抽象计算模型。由于其广泛的适用性,最有用的抽象实现之一是神经网络。在以前的工作中,实值的重量是通过单独控制相应“重量”分子的浓度来实现的。然而,大规模制备具有精确浓度的反应物很快变得棘手。在这里,我们建议使用二值化神经网络(bnn)来绕过这个基本问题,由于不同权重值的数量较少,该模型在分子设置中具有高度可扩展性。我们设计了一个耐噪的数字分子电路,该电路紧凑地实现了对二值输入的多数投票操作,以计算神经元的输出。该网络也是速率无关的,这意味着单个反应发生的速度不会影响计算,从而进一步增强了对噪声的鲁棒性。我们首先通过将系统模拟为理想化学反应来在MNIST分类任务上演示我们的设计。接下来,我们将反应映射到DNA链位移级联,提供模拟结果,证明我们的方法的实际可行性。我们进行了广泛的噪声容忍模拟,表明数字分子神经元对化学反应物浓度下的噪声的鲁棒性明显高于模拟神经元。最后,我们提供了单个二值化神经元的初步实验结果。我们的工作为构建更复杂的神经网络计算提供了一个坚实的框架。2012 ACM学科分类:计算理论→计算模型;应用计算
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引用次数: 2
Reactamole: Functional Reactive Molecular Programming Reactamole:功能反应性分子程序设计
IF 4.9 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2021-01-01 DOI: 10.4230/LIPIcs.DNA.27.10
T. Klinge, James I. Lathrop, Peter-Michael Osera, Allison Rogers
Chemical reaction networks (CRNs) are an important tool for molecular programming, a field that is rapidly expanding our ability to deploy computer programs into biological systems for a variety of applications. However, CRNs are also difficult to work with due to their massively parallel nature, leading to the need for higher-level languages that allow for easier computation with CRNs. Recently, research has been conducted into a variety of higher-level languages for deterministic CRNs but modeling CRN parallelism, managing error accumulation, and finding natural CRN representations are ongoing challenges. We introduce Reactamole, a higher-level language for deterministic CRNs that utilizes the functional reactive programming (FRP) paradigm to represent CRNs as a reactive dataflow network. Reactamole equates a CRN with a functional reactive program, implementing the key primitives of the FRP paradigm directly as CRNs. The functional nature of Reactamole makes reasoning about molecular programs easier, and its strong static typing allows us to ensure that a CRN is well-formed by virtue of being well-typed. In this paper, we describe the design of Reactamole and how we use CRNs to represent the common datatypes and operations found in FRP. We also demonstrate the potential of this functional reactive approach to molecular programming by giving an extended example where a CRN is constructed using FRP to modulate and demodulate an amplitude modulated signal. 2012 ACM Subject Classification Software and its engineering → Functional languages; Software and its engineering → Data flow languages
化学反应网络(crn)是分子编程的重要工具,这一领域正在迅速扩展我们将计算机程序部署到各种应用的生物系统中的能力。然而,由于crn的大规模并行特性,crn也很难处理,导致需要更高级的语言来允许更容易地使用crn进行计算。最近,研究人员对各种用于确定性CRN的高级语言进行了研究,但对CRN并行性建模、管理错误积累和寻找自然的CRN表示是持续的挑战。我们介绍Reactamole,这是一种用于确定性crn的高级语言,它利用功能性反应性编程(FRP)范式将crn表示为反应性数据流网络。Reactamole将CRN等同于功能性反应性程序,将FRP范式的关键原语直接实现为CRN。Reactamole的功能特性使分子程序的推理变得更容易,并且它的强静态类型使我们能够确保CRN由于类型良好而结构良好。在本文中,我们描述了Reactamole的设计,以及我们如何使用crn来表示FRP中常见的数据类型和操作。我们还通过给出一个扩展的例子来证明这种功能反应性方法在分子编程中的潜力,其中使用FRP构建CRN来调制和解调振幅调制信号。2012 ACM学科分类软件及其工程→函数式语言;软件及其工程→数据流语言
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引用次数: 0
Directed Non-Cooperative Tile Assembly Is Decidable 定向非合作瓷砖组装是可决定的
IF 4.9 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2021-01-01 DOI: 10.4230/LIPIcs.DNA.27.6
Pierre-Etienne Meunier, Damien Regnault
We provide a complete characterisation of all final states of a model called directed non-cooperative tile self-assembly , also called directed temperature 1 tile assembly , which proves that this model cannot possibly perform Turing computation. This model is a deterministic version of the more general undirected model, whose computational power is still open. Our result uses recent results in the domain, and solves a conjecture formalised in 2011. We believe that this is a major step towards understanding the full model. Temperature 1 tile assembly can be seen as a two-dimensional extension of finite automata, where geometry provides a form of memory and synchronisation, yet the full power of these “geometric blockings” was still largely unknown until recently (note that nontrivial algorithms which are able to build larger structures than the naive constructions have been found).
我们提供了一个称为定向非合作瓷砖自组装模型的所有最终状态的完整表征,也称为定向温度1瓷砖组装,这证明了该模型不可能执行图灵计算。这个模型是更一般的无向模型的确定性版本,其计算能力仍然是开放的。我们的结果使用了该领域的最新结果,并解决了2011年形式化的一个猜想。我们相信这是理解完整模型的重要一步。温度1瓦片组装可以看作是有限自动机的二维扩展,其中几何结构提供了一种记忆和同步形式,然而直到最近,这些“几何块”的全部功能仍然很大程度上是未知的(注意,能够构建比原始结构更大的结构的非平凡算法已经被发现)。
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引用次数: 2
New Ther1-derived SINE Squam3 in scaled reptiles 有鳞爬行动物中新的Ther1衍生SINE Squam3
IF 4.9 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2020-12-28 DOI: 10.21203/rs.3.rs-132339/v1
N. Vassetzky, S. A. Kosushkin, V. Korchagin, A. Ryskov
Background SINEs comprise a significant part of animal genomes and are used to study the evolution of diverse taxa. Despite significant advances in SINE studies in vertebrates and higher eukaryotes in general, their own evolution is poorly understood. Results We have discovered and described in detail a new Squam3 SINE specific for scaled reptiles (Squamata). The subfamilies of this SINE demonstrate different distribution in the genomes of squamates, which together with the data on similar SINEs in the tuatara allowed us to propose a scenario of their evolution in the context of reptilian evolution. Conclusions Ancestral SINEs preserved in small numbers in most genomes can give rise to taxa-specific SINE families. Analysis of this aspect of SINEs can shed light on the history and mechanisms of SINE variation in reptilian genomes.
背景SINE是动物基因组的重要组成部分,用于研究不同类群的进化。尽管脊椎动物和高等真核生物的SINE研究取得了重大进展,但对其自身的进化却知之甚少。结果我们发现并详细描述了一种新的鳞状爬行动物特有的Squam3SINE(Squamata)。这种SINE的亚科在鳞片的基因组中表现出不同的分布,这与蜥蜴中类似SINE的数据一起,使我们能够在爬行动物进化的背景下提出它们的进化场景。结论在大多数基因组中少量保存的祖先SINE可以产生特定的SINE家族。对SINE这一方面的分析可以揭示爬行动物基因组中SINE变异的历史和机制。
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引用次数: 1
SeqURE - a new copy-capture based method for sequencing of unknown Retroposition events. 一种新的基于复制捕获的方法,用于未知逆转录事件的测序。
IF 4.9 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2020-12-14 DOI: 10.1186/s13100-020-00228-6
Alexander Y Komkov, Shamil Z Urazbakhtin, Maria V Saliutina, Ekaterina A Komech, Yuri A Shelygin, Gaiaz A Nugmanov, Vitaliy P Shubin, Anastasia O Smirnova, Mikhail Y Bobrov, Alexey S Tsukanov, Anastasia V Snezhkina, Anna V Kudryavtseva, Yuri B Lebedev, Ilgar Z Mamedov

Background: Retroelements (REs) occupy a significant part of all eukaryotic genomes including humans. The majority of retroelements in the human genome are inactive and unable to retrotranspose. Dozens of active copies are repressed in most normal tissues by various cellular mechanisms. These copies can become active in normal germline and brain tissues or in cancer, leading to new retroposition events. The consequences of such events and their role in normal cell functioning and carcinogenesis are not yet fully understood. If new insertions occur in a small portion of cells they can be found only with the use of specific methods based on RE enrichment and high-throughput sequencing. The downside of the high sensitivity of such methods is the presence of various artifacts imitating real insertions, which in many cases cannot be validated due to lack of the initial template DNA. For this reason, adequate assessment of rare (< 1%) subclonal cancer specific RE insertions is complicated.

Results: Here we describe a new copy-capture technique which we implemented in a method called SeqURE for Sequencing Unknown of Retroposition Events that allows for efficient and reliable identification of new genomic RE insertions. The method is based on the capture of copies of target molecules (copy-capture), selective amplification and sequencing of genomic regions adjacent to active RE insertions from both sides. Importantly, the template genomic DNA remains intact and can be used for validation experiments. In addition, we applied a novel system for testing method sensitivity and precisely showed the ability of the developed method to reliably detect insertions present in 1 out of 100 cells and a substantial portion of insertions present in 1 out of 1000 cells. Using advantages of the method we showed the absence of somatic Alu insertions in colorectal cancer samples bearing tumor-specific L1HS insertions.

Conclusions: This study presents the first description and implementation of the copy-capture technique and provides the first methodological basis for the quantitative assessment of RE insertions present in a small portion of cells.

背景:逆转录因子(REs)在包括人类在内的所有真核生物基因组中占有重要的一部分。人类基因组中的大多数逆转录因子是无活性的,不能反转录转座。在大多数正常组织中,数十个活性拷贝通过各种细胞机制受到抑制。这些拷贝可以在正常的种系和脑组织或癌症中变得活跃,导致新的逆转录事件。这些事件的后果及其在正常细胞功能和癌变中的作用尚不完全清楚。如果新的插入发生在一小部分细胞中,则只能使用基于RE富集和高通量测序的特定方法来发现。这种方法的高灵敏度的缺点是存在模仿真实插入的各种伪影,在许多情况下,由于缺乏初始模板DNA而无法验证。结果:在这里,我们描述了一种新的复制捕获技术,我们在一种称为逆转录事件未知测序的方法中实现了一种新的复制捕获技术,该技术允许有效和可靠地识别新的基因组RE插入。该方法基于目标分子拷贝的捕获(拷贝捕获),选择性扩增和两侧活性RE插入邻近的基因组区域测序。重要的是,模板基因组DNA保持完整,可以用于验证实验。此外,我们应用了一种新的系统来测试方法的灵敏度,并精确地显示了所开发的方法能够可靠地检测到100个细胞中有1个细胞中的插入,以及1000个细胞中有1个细胞中的大部分插入。利用该方法的优势,我们发现在携带肿瘤特异性L1HS插入的结直肠癌样本中没有体细胞Alu插入。结论:本研究首次描述和实现了复制捕获技术,并为定量评估一小部分细胞中的RE插入提供了第一个方法学基础。
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引用次数: 2
Intruder (DD38E), a recently evolved sibling family of DD34E/Tc1 transposons in animals. 闯入者(DD38E),动物中DD34E/Tc1转座子最近进化的兄弟家族。
IF 4.9 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2020-12-10 DOI: 10.1186/s13100-020-00227-7
Bo Gao, Wencheng Zong, Csaba Miskey, Numan Ullah, Mohamed Diaby, Cai Chen, Xiaoyan Wang, Zoltán Ivics, Chengyi Song

Background: A family of Tc1/mariner transposons with a characteristic DD38E triad of catalytic amino acid residues, named Intruder (IT), was previously discovered in sturgeon genomes, but their evolutionary landscapes remain largely unknown.

Results: Here, we comprehensively investigated the evolutionary profiles of ITs, and evaluated their cut-and-paste activities in cells. ITs exhibited a narrow taxonomic distribution pattern in the animal kingdom, with invasions into two invertebrate phyla (Arthropoda and Cnidaria) and three vertebrate lineages (Actinopterygii, Agnatha, and Anura): very similar to that of the DD36E/IC family. Some animal orders and species seem to be more hospitable to Tc1/mariner transposons, one order of Amphibia and seven Actinopterygian orders are the most common orders with horizontal transfer events and have been invaded by all four families (DD38E/IT, DD35E/TR, DD36E/IC and DD37E/TRT) of Tc1/mariner transposons, and eight Actinopterygii species were identified as the major hosts of these families. Intact ITs have a total length of 1.5-1.7 kb containing a transposase gene flanked by terminal inverted repeats (TIRs). The phylogenetic tree and sequence identity showed that IT transposases were most closely related to DD34E/Tc1. ITs have been involved in multiple events of horizontal transfer in vertebrates and have invaded most lineages recently (< 5 million years ago) based on insertion age analysis. Accordingly, ITs presented high average sequence identity (86-95%) across most vertebrate species, suggesting that some are putatively active. ITs can transpose in human HeLa cells, and the transposition efficiency of consensus TIRs was higher than that of the TIRs of natural isolates.

Conclusions: We conclude that DD38E/IT originated from DD34E/Tc1 and can be detected in two invertebrate phyla (Arthropoda and Cnidaria), and in three vertebrate lineages (Actinopterygii, Agnatha and Anura). IT has experienced multiple HT events in animals, dominated by recent amplifications in most species and has high identity among vertebrate taxa. Our reconstructed IT transposon vector designed according to the sequence from the "cat" genome showed high cut-and-paste activity. The data suggest that IT has been acquired recently and is active in many species. This study is meaningful for understanding the evolution of the Tc1/mariner superfamily members and their hosts.

背景:先前在鲟鱼基因组中发现了一个Tc1/mariner转座子家族,其具有DD38E催化氨基酸残基的特征,称为入侵者(IT),但其进化景观仍在很大程度上未知。结果:在这里,我们全面研究了ITs的进化概况,并评估了它们在细胞中的剪切和粘贴活性。ITs在动物界的分类学分布格局较窄,入侵2个无脊椎动物门(节肢动物门和刺胞动物门)和3个脊椎动物系(放线翼动物门、Agnatha门和无尾动物门),与DD36E/IC家族非常相似。一些动物目和物种似乎对Tc1/mariner转座子更友好,两栖目1目和放光翼目7目是发生水平转移事件最常见的目,并被Tc1/mariner转座子的4个科(DD38E/IT、DD35E/TR、DD36E/IC和DD37E/TRT)入侵,放光翼目8种是这些科的主要宿主。完整ITs的总长度为1.5-1.7 kb,包含一个转座酶基因,两侧是末端倒置重复序列(TIRs)。系统发育树和序列鉴定结果表明,IT转座酶与DD34E/Tc1的亲缘关系最为密切。结论:DD38E/IT起源于DD34E/Tc1,可在2个无脊椎动物门(节肢动物门和刺胞动物门)和3个脊椎动物门(放线肢动物门、Agnatha门和无尾动物门)中检测到。IT在动物中经历了多次HT事件,以大多数物种的近期扩增为主,并且在脊椎动物分类群中具有高度的同一性。根据“猫”基因组序列设计的IT转座子重组载体显示出较高的剪切粘贴活性。数据表明,IT是最近才获得的,并且在许多物种中都很活跃。本研究对了解Tc1/mariner超家族成员及其寄主的演化具有重要意义。
{"title":"Intruder (DD38E), a recently evolved sibling family of DD34E/Tc1 transposons in animals.","authors":"Bo Gao,&nbsp;Wencheng Zong,&nbsp;Csaba Miskey,&nbsp;Numan Ullah,&nbsp;Mohamed Diaby,&nbsp;Cai Chen,&nbsp;Xiaoyan Wang,&nbsp;Zoltán Ivics,&nbsp;Chengyi Song","doi":"10.1186/s13100-020-00227-7","DOIUrl":"https://doi.org/10.1186/s13100-020-00227-7","url":null,"abstract":"<p><strong>Background: </strong>A family of Tc1/mariner transposons with a characteristic DD38E triad of catalytic amino acid residues, named Intruder (IT), was previously discovered in sturgeon genomes, but their evolutionary landscapes remain largely unknown.</p><p><strong>Results: </strong>Here, we comprehensively investigated the evolutionary profiles of ITs, and evaluated their cut-and-paste activities in cells. ITs exhibited a narrow taxonomic distribution pattern in the animal kingdom, with invasions into two invertebrate phyla (Arthropoda and Cnidaria) and three vertebrate lineages (Actinopterygii, Agnatha, and Anura): very similar to that of the DD36E/IC family. Some animal orders and species seem to be more hospitable to Tc1/mariner transposons, one order of Amphibia and seven Actinopterygian orders are the most common orders with horizontal transfer events and have been invaded by all four families (DD38E/IT, DD35E/TR, DD36E/IC and DD37E/TRT) of Tc1/mariner transposons, and eight Actinopterygii species were identified as the major hosts of these families. Intact ITs have a total length of 1.5-1.7 kb containing a transposase gene flanked by terminal inverted repeats (TIRs). The phylogenetic tree and sequence identity showed that IT transposases were most closely related to DD34E/Tc1. ITs have been involved in multiple events of horizontal transfer in vertebrates and have invaded most lineages recently (< 5 million years ago) based on insertion age analysis. Accordingly, ITs presented high average sequence identity (86-95%) across most vertebrate species, suggesting that some are putatively active. ITs can transpose in human HeLa cells, and the transposition efficiency of consensus TIRs was higher than that of the TIRs of natural isolates.</p><p><strong>Conclusions: </strong>We conclude that DD38E/IT originated from DD34E/Tc1 and can be detected in two invertebrate phyla (Arthropoda and Cnidaria), and in three vertebrate lineages (Actinopterygii, Agnatha and Anura). IT has experienced multiple HT events in animals, dominated by recent amplifications in most species and has high identity among vertebrate taxa. Our reconstructed IT transposon vector designed according to the sequence from the \"cat\" genome showed high cut-and-paste activity. The data suggest that IT has been acquired recently and is active in many species. This study is meaningful for understanding the evolution of the Tc1/mariner superfamily members and their hosts.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"11 1","pages":"32"},"PeriodicalIF":4.9,"publicationDate":"2020-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13100-020-00227-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38359348","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 13
Correction to: Characterising a human endogenous retrovirus(HERV)-derived tumour-associated antigen: enriched RNA-Seq analysis of HERV-K(HML-2) in mantle cell lymphoma cell lines. 更正:表征人内源性逆转录病毒(HERV)衍生的肿瘤相关抗原:套细胞淋巴瘤细胞系中HERV- k (HML-2)的富集RNA-Seq分析。
IF 4.9 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2020-11-30 DOI: 10.1186/s13100-020-00226-8
Witold Tatkiewicz, James Dickie, Franchesca Bedford, Alexander Jones, Mark Atkin, Michele Kiernan, Emmanuel Atangana Maze, Bora Agit, Garry Farnham, Alexander Kanapin, Robert Belshaw

An amendment to this paper has been published and can be accessed via the original article.

本文的修订版已经发布,可以通过原文访问。
{"title":"Correction to: Characterising a human endogenous retrovirus(HERV)-derived tumour-associated antigen: enriched RNA-Seq analysis of HERV-K(HML-2) in mantle cell lymphoma cell lines.","authors":"Witold Tatkiewicz,&nbsp;James Dickie,&nbsp;Franchesca Bedford,&nbsp;Alexander Jones,&nbsp;Mark Atkin,&nbsp;Michele Kiernan,&nbsp;Emmanuel Atangana Maze,&nbsp;Bora Agit,&nbsp;Garry Farnham,&nbsp;Alexander Kanapin,&nbsp;Robert Belshaw","doi":"10.1186/s13100-020-00226-8","DOIUrl":"https://doi.org/10.1186/s13100-020-00226-8","url":null,"abstract":"<p><p>An amendment to this paper has been published and can be accessed via the original article.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"11 1","pages":"31"},"PeriodicalIF":4.9,"publicationDate":"2020-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13100-020-00226-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38349912","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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Mobile DNA
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