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Transposon-derived introns as an element shaping the structure of eukaryotic genomes 转座子衍生的内含子是塑造真核生物基因组结构的一个要素
IF 4.9 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-07-27 DOI: 10.1186/s13100-024-00325-w
Weronika Mikina, Paweł Hałakuc, Rafał Milanowski
The widely accepted hypothesis postulates that the first spliceosomal introns originated from group II self-splicing introns. However, it is evident that not all spliceosomal introns in the nuclear genes of modern eukaryotes are inherited through vertical transfer of intronic sequences. Several phenomena contribute to the formation of new introns but their most common origin seems to be the insertion of transposable elements. Recent analyses have highlighted instances of mass gains of new introns from transposable elements. These events often coincide with an increase or change in the spliceosome's tolerance to splicing signals, including the acceptance of noncanonical borders. Widespread acquisitions of transposon-derived introns occur across diverse evolutionary lineages, indicating convergent processes. These events, though independent, likely require a similar set of conditions. These conditions include the presence of transposon elements with features enabling their removal at the RNA level as introns and/or the existence of a splicing mechanism capable of excising unusual sequences that would otherwise not be recognized as introns by standard splicing machinery. Herein we summarize those mechanisms across different eukaryotic lineages.
广为接受的假说认为,第一个剪接体内含子起源于第二组自剪接内含子。然而,现代真核生物核基因中的剪接体内含子显然并非都是通过内含子序列的垂直转移而遗传的。有几种现象有助于新内含子的形成,但它们最常见的起源似乎是转座元件的插入。最近的分析强调了转座元件大量增加新内含子的情况。这些事件往往与剪接体对剪接信号耐受性的增加或改变同时发生,包括接受非规范边界。转座子衍生内含子的广泛获得发生在不同的进化系中,表明了趋同的过程。这些事件虽然各自独立,但很可能需要一套相似的条件。这些条件包括转座子元件的存在,其特征是能在 RNA 水平上将其作为内含子移除,以及/或存在一种剪接机制,能够切除标准剪接机制无法识别为内含子的不寻常序列。在此,我们总结了不同真核生物系的这些机制。
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引用次数: 0
Subcellular location of L1 retrotransposon-encoded ORF1p, reverse transcription products, and DNA sensors in lupus granulocytes. 狼疮粒细胞中 L1 逆转录酶编码的 ORF1p、逆转录产物和 DNA 传感器的亚细胞位置。
IF 4.7 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-06-27 DOI: 10.1186/s13100-024-00324-x
Fatemeh Moadab, Sepideh Sohrabi, Xiaoxing Wang, Rayan Najjar, Justina C Wolters, Hua Jiang, Wenyan Miao, Donna Romero, Dennis M Zaller, Megan Tran, Alison Bays, Martin S Taylor, Rosana Kapeller, John LaCava, Tomas Mustelin

Background: Systemic lupus erythematosus (SLE) is a chronic autoimmune disease with an unpredictable course of recurrent exacerbations alternating with more stable disease. SLE is characterized by broad immune activation and autoantibodies against double-stranded DNA and numerous proteins that exist in cells as aggregates with nucleic acids, such as Ro60, MOV10, and the L1 retrotransposon-encoded ORF1p.

Results: Here we report that these 3 proteins are co-expressed and co-localized in a subset of SLE granulocytes and are concentrated in cytosolic dots that also contain DNA: RNA heteroduplexes and the DNA sensor ZBP1, but not cGAS. The DNA: RNA heteroduplexes vanished from the neutrophils when they were treated with a selective inhibitor of the L1 reverse transcriptase. We also report that ORF1p granules escape neutrophils during the extrusion of neutrophil extracellular traps (NETs) and, to a lesser degree, from neutrophils dying by pyroptosis, but not apoptosis.

Conclusions: These results bring new insights into the composition of ORF1p granules in SLE neutrophils and may explain, in part, why proteins in these granules become targeted by autoantibodies in this disease.

背景:系统性红斑狼疮(SLE)是一种慢性自身免疫性疾病,其病程难以预测,病情反复加重与较为稳定的病情交替出现。系统性红斑狼疮的特征是广泛的免疫激活和针对双链DNA的自身抗体,以及细胞中作为核酸聚集体存在的大量蛋白质,如Ro60、MOV10和L1逆转录病毒编码的ORF1p:结果:我们在此报告,这3种蛋白质在一部分系统性红斑狼疮粒细胞中共同表达和共定位,并集中在同样含有DNA的胞浆小点中:RNA异质双链和DNA传感器ZBP1,但不包括cGAS。DNA:RNA杂合双链消失了:中性粒细胞经 L1 逆转录酶选择性抑制剂处理后,DNA:RNA 杂合双链消失。我们还报告说,ORF1p颗粒在中性粒细胞胞外捕获物(NET)的挤出过程中从中性粒细胞中逸出,在较小程度上,也从因热凋亡而死亡的中性粒细胞中逸出,但不是凋亡:这些结果为了解系统性红斑狼疮中性粒细胞中ORF1p颗粒的组成提供了新的视角,并在一定程度上解释了为什么这些颗粒中的蛋白质会成为该疾病自身抗体的靶标。
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引用次数: 0
Identification of transposable element families from pangenome polymorphisms. 从盘古基因组多态性中识别转座元件家族。
IF 4.7 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-06-26 DOI: 10.1186/s13100-024-00323-y
Pío Sierra, Richard Durbin

Background: Transposable Elements (TEs) are segments of DNA, typically a few hundred base pairs up to several tens of thousands bases long, that have the ability to generate new copies of themselves in the genome. Most existing methods used to identify TEs in a newly sequenced genome are based on their repetitive character, together with detection based on homology and structural features. As new high quality assemblies become more common, including the availability of multiple independent assemblies from the same species, an alternative strategy for identification of TE families becomes possible in which we focus on the polymorphism at insertion sites caused by TE mobility.

Results: We develop the idea of using the structural polymorphisms found in pangenomes to create a library of the TE families recently active in a species, or in a closely related group of species. We present a tool, pantera, that achieves this task, and illustrate its use both on species with well-curated libraries, and on new assemblies.

Conclusions: Our results show that pantera is sensitive and accurate, tending to correctly identify complete elements with precise boundaries, and is particularly well suited to detect larger, low copy number TEs that are often undetected with existing de novo methods.

背景:可转座元件(Transposable Elements,TEs)是 DNA 片段,通常只有几百个碱基对到几万个碱基,能够在基因组中产生新的拷贝。在新测序的基因组中,现有的大多数用于识别TE的方法都是基于其重复性,以及基于同源性和结构特征的检测。随着新的高质量集合越来越常见,包括来自同一物种的多个独立集合的可用性,另一种识别 TE 家族的策略成为可能,我们将重点放在 TE 移动性引起的插入位点的多态性上:结果:我们提出了利用庞基因组中发现的结构多态性来创建一个最近在一个物种或密切相关的物种群中活跃的TE家族库的想法。我们介绍了一个实现这一任务的工具--pantera,并说明了它在具有良好整合库的物种和新的集合上的应用:我们的研究结果表明,pantera 灵敏而准确,能正确识别具有精确边界的完整元素,尤其适合检测较大的低拷贝数 TE,而现有的从头检测方法往往检测不到这些 TE。
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引用次数: 0
Internal initiation of reverse transcription in a Penelope-like retrotransposon. 类 Penelope 逆转录酶的内部反转录起始。
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-06-11 DOI: 10.1186/s13100-024-00322-z
Chris J Frangieh, Max E Wilkinson, Daniel Strebinger, Jonathan Strecker, Michelle L Walsh, Guilhem Faure, Irina A Yushenova, Rhiannon K Macrae, Irina R Arkhipova, Feng Zhang

Eukaryotic retroelements are generally divided into two classes: long terminal repeat (LTR) retrotransposons and non-LTR retrotransposons. A third class of eukaryotic retroelement, the Penelope-like elements (PLEs), has been well-characterized bioinformatically, but relatively little is known about the transposition mechanism of these elements. PLEs share some features with the R2 retrotransposon from Bombyx mori, which uses a target-primed reverse transcription (TPRT) mechanism, but their distinct phylogeny suggests PLEs may utilize a novel mechanism of mobilization. Using protein purified from E. coli, we report unique in vitro properties of a PLE from the green anole (Anolis carolinensis), revealing mechanistic aspects not shared by other retrotransposons. We found that reverse transcription is initiated at two adjacent sites within the transposon RNA that is not homologous to the cleaved DNA, a feature that is reflected in the genomic "tail" signature shared between and unique to PLEs. Our results for the first active PLE in vitro provide a starting point for understanding PLE mobilization and biology.

真核逆转录子一般分为两类:长末端重复(LTR)逆转录子和非LTR逆转录子。第三类真核逆转录子--类Penelope元件(PLEs)已经有了很好的生物信息表征,但对这些元件的转座机制却知之甚少。PLEs与来自森双翅目昆虫的R2逆转录转座子有一些共同特征,后者使用的是目标刺激反转录(TPRT)机制,但它们不同的系统发育表明PLEs可能使用了一种新的调动机制。利用从大肠杆菌中纯化的蛋白质,我们报告了绿鼹鼠(Anolis carolinensis)的一种 PLE 的独特体外特性,揭示了其他转座子所不具备的机制方面。我们发现,反转录是在转座子 RNA 的两个相邻位点启动的,而这两个位点与被切割的 DNA 并不同源,这一特征反映在基因组 "尾部 "特征上,这是 PLEs 所共有的,也是 PLEs 所独有的。我们对首个体外活性 PLE 的研究结果为了解 PLE 的动员和生物学提供了一个起点。
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引用次数: 0
Insertion of short L1 sequences generates inter-strain histone acetylation differences in the mouse. 插入短 L1 序列会导致小鼠不同品系间组蛋白乙酰化的差异。
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-05-10 DOI: 10.1186/s13100-024-00321-0
Beverly Ann G Boyboy, Kenji Ichiyanagi

Background: Gene expression divergence between populations and between individuals can emerge from genetic variations within the genes and/or in the cis regulatory elements. Since epigenetic modifications regulate gene expression, it is conceivable that epigenetic variations in cis regulatory elements can also be a source of gene expression divergence.

Results: In this study, we compared histone acetylation (namely, H3K9ac) profiles in two mouse strains of different subspecies origin, C57BL/6 J (B6) and MSM/Ms (MSM), as well as their F1 hybrids. This identified 319 regions of strain-specific acetylation, about half of which were observed between the alleles of F1 hybrids. While the allele-specific presence of the interferon regulatory factor 3 (IRF3) binding sequence was associated with allele-specific histone acetylation, we also revealed that B6-specific insertions of a short 3' fragment of LINE-1 (L1) retrotransposon occur within or proximal to MSM-specific acetylated regions. Furthermore, even in hyperacetylated domains, flanking regions of non-polymorphic 3' L1 fragments were hypoacetylated, suggesting a general activity of the 3' L1 fragment to induce hypoacetylation. Indeed, we confirmed the binding of the 3' region of L1 by three Krüppel-associated box domain-containing zinc finger proteins (KZFPs), which interact with histone deacetylases. These results suggest that even a short insertion of L1 would be excluded from gene- and acetylation-rich regions by natural selection. Finally, mRNA-seq analysis for F1 hybrids was carried out, which disclosed a link between allele-specific promoter/enhancer acetylation and gene expression.

Conclusions: This study disclosed a number of genetic changes that have changed the histone acetylation levels during the evolution of mouse subspecies, a part of which is associated with gene expression changes. Insertions of even a very short L1 fragment can decrease the acetylation level in their neighboring regions and thereby have been counter-selected in gene-rich regions, which may explain a long-standing mystery of discrete genomic distribution of LINEs and SINEs.

背景:种群之间和个体之间的基因表达差异可能来自基因内部和/或顺式调控元件的遗传变异。由于表观遗传修饰调控基因表达,可以想象顺式调控元件中的表观遗传变异也可能是基因表达差异的一个来源:在这项研究中,我们比较了两个不同亚种来源的小鼠品系--C57BL/6 J(B6)和MSM/Ms(MSM)以及它们的F1杂交种--的组蛋白乙酰化(即H3K9ac)谱。结果发现了 319 个品系特异性乙酰化区域,其中约一半是在 F1 杂交种的等位基因之间观察到的。虽然干扰素调节因子 3(IRF3)结合序列的等位基因特异性存在与等位基因特异性组蛋白乙酰化有关,但我们还发现,LINE-1(L1)反转座子短 3' 片段的 B6 特异性插入发生在 MSM 特异性乙酰化区域内或附近。此外,即使在高乙酰化区域,非多态性 3' L1 片段的侧翼区域也是低乙酰化的,这表明 3' L1 片段具有诱导低乙酰化的一般活性。事实上,我们证实了 L1 的 3' 区域与三个含 Krüppel-associated box domain 的锌指蛋白(KZFPs)的结合,这些锌指蛋白与组蛋白去乙酰化酶相互作用。这些结果表明,在自然选择的作用下,即使是短时间插入的 L1 也会被排除在基因和乙酰化富集区之外。最后,对 F1 杂交种进行了 mRNA-seq 分析,揭示了等位基因特异性启动子/增强子乙酰化与基因表达之间的联系:这项研究揭示了小鼠亚种进化过程中改变组蛋白乙酰化水平的一系列遗传变化,其中一部分与基因表达变化有关。即使是很短的L1片段的插入也会降低其邻近区域的乙酰化水平,从而在基因丰富的区域进行反选择,这可能解释了长期以来LINE和SINE在基因组中的离散分布之谜。
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引用次数: 0
Teaching transposon classification as a means to crowd source the curation of repeat annotation - a tardigrade perspective. 将转座子分类教学作为重复注释众源化的一种手段--从沙蜥的角度看问题。
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-05-06 DOI: 10.1186/s13100-024-00319-8
Valentina Peona, Jacopo Martelossi, Dareen Almojil, Julia Bocharkina, Ioana Brännström, Max Brown, Alice Cang, Tomàs Carrasco-Valenzuela, Jon DeVries, Meredith Doellman, Daniel Elsner, Pamela Espíndola-Hernández, Guillermo Friis Montoya, Bence Gaspar, Danijela Zagorski, Paweł Hałakuc, Beti Ivanovska, Christopher Laumer, Robert Lehmann, Ljudevit Luka Boštjančić, Rahia Mashoodh, Sofia Mazzoleni, Alice Mouton, Maria Anna Nilsson, Yifan Pei, Giacomo Potente, Panagiotis Provataris, José Ramón Pardos-Blas, Ravindra Raut, Tomasa Sbaffi, Florian Schwarz, Jessica Stapley, Lewis Stevens, Nusrat Sultana, Radka Symonova, Mohadeseh S Tahami, Alice Urzì, Heidi Yang, Abdullah Yusuf, Carlo Pecoraro, Alexander Suh

Background: The advancement of sequencing technologies results in the rapid release of hundreds of new genome assemblies a year providing unprecedented resources for the study of genome evolution. Within this context, the significance of in-depth analyses of repetitive elements, transposable elements (TEs) in particular, is increasingly recognized in understanding genome evolution. Despite the plethora of available bioinformatic tools for identifying and annotating TEs, the phylogenetic distance of the target species from a curated and classified database of repetitive element sequences constrains any automated annotation effort. Moreover, manual curation of raw repeat libraries is deemed essential due to the frequent incompleteness of automatically generated consensus sequences.

Results: Here, we present an example of a crowd-sourcing effort aimed at curating and annotating TE libraries of two non-model species built around a collaborative, peer-reviewed teaching process. Manual curation and classification are time-consuming processes that offer limited short-term academic rewards and are typically confined to a few research groups where methods are taught through hands-on experience. Crowd-sourcing efforts could therefore offer a significant opportunity to bridge the gap between learning the methods of curation effectively and empowering the scientific community with high-quality, reusable repeat libraries.

Conclusions: The collaborative manual curation of TEs from two tardigrade species, for which there were no TE libraries available, resulted in the successful characterization of hundreds of new and diverse TEs in a reasonable time frame. Our crowd-sourcing setting can be used as a teaching reference guide for similar projects: A hidden treasure awaits discovery within non-model organisms.

背景:随着测序技术的进步,每年都会有数百个新的基因组集合迅速发布,为基因组进化研究提供了前所未有的资源。在此背景下,深入分析重复性元件,尤其是转座元件(TEs)对理解基因组进化的意义日益得到认可。尽管有大量可用的生物信息学工具来识别和注释转座元件,但目标物种与经过整理和分类的重复元件序列数据库之间的系统发育距离限制了任何自动注释工作。此外,由于自动生成的共识序列经常不完整,因此手工整理原始重复序列库被认为是非常必要的:在这里,我们介绍了一个众包工作的例子,该工作旨在围绕协作、同行评审的教学过程,对两个非模式物种的 TE 库进行整理和注释。人工整理和分类是耗时的过程,其短期学术回报有限,而且通常仅限于少数研究小组,其方法是通过实践经验传授的。因此,众包工作可以提供一个重要的机会,弥合有效学习整理方法与通过高质量、可重复使用的重复库增强科学界能力之间的差距:通过合作手工整理两个没有TE库的沙蜥物种的TEs,在合理的时间范围内成功鉴定了数百个新的、多样的TEs。我们的众包设置可作为类似项目的教学参考指南:非模式生物中隐藏的宝藏等待着我们去发现。
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引用次数: 0
Long-read sequencing improves the genetic diagnosis of retinitis pigmentosa by identifying an Alu retrotransposon insertion in the EYS gene 长读测序通过鉴定 EYS 基因中的阿鲁逆转录质子插入提高了视网膜色素变性的基因诊断水平
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-05-04 DOI: 10.1186/s13100-024-00320-1
Elena Fernández-Suárez, María González-del Pozo, Cristina Méndez-Vidal, Marta Martín-Sánchez, Marcela Mena, Belén de la Morena-Barrio, Javier Corral, Salud Borrego, Guillermo Antiñolo
Biallelic variants in EYS are the major cause of autosomal recessive retinitis pigmentosa (arRP) in certain populations, a clinically and genetically heterogeneous disease that may lead to legal blindness. EYS is one of the largest genes (~ 2 Mb) expressed in the retina, in which structural variants (SVs) represent a common cause of disease. However, their identification using short-read sequencing (SRS) is not always feasible. Here, we conducted targeted long-read sequencing (T-LRS) using adaptive sampling of EYS on the MinION sequencing platform (Oxford Nanopore Technologies) to definitively diagnose an arRP family, whose affected individuals (n = 3) carried the heterozygous pathogenic deletion of exons 32–33 in the EYS gene. As this was a recurrent variant identified in three additional families in our cohort, we also aimed to characterize the known deletion at the nucleotide level to assess a possible founder effect. T-LRS in family A unveiled a heterozygous AluYa5 insertion in the coding exon 43 of EYS (chr6(GRCh37):g.64430524_64430525ins352), which segregated with the disease in compound heterozygosity with the previously identified deletion. Visual inspection of previous SRS alignments using IGV revealed several reads containing soft-clipped bases, accompanied by a slight drop in coverage at the Alu insertion site. This prompted us to develop a simplified program using grep command to investigate the recurrence of this variant in our cohort from SRS data. Moreover, LRS also allowed the characterization of the CNV as a ~ 56.4kb deletion spanning exons 32–33 of EYS (chr6(GRCh37):g.64764235_64820592del). The results of further characterization by Sanger sequencing and linkage analysis in the four families were consistent with a founder variant. To our knowledge, this is the first report of a mobile element insertion into the coding sequence of EYS, as a likely cause of arRP in a family. Our study highlights the value of LRS technology in characterizing and identifying hidden pathogenic SVs, such as retrotransposon insertions, whose contribution to the etiopathogenesis of rare diseases may be underestimated.
在某些人群中,常染色体隐性色素性视网膜炎(arRP)的主要病因是 EYS 的双叶变体。EYS 是视网膜中表达量最大的基因之一(约 2 Mb),其结构变异(SV)是常见的致病原因。然而,使用短线程测序(SRS)鉴定这些变异并不总是可行的。在这里,我们在 MinION 测序平台(Oxford Nanopore Technologies)上利用 EYS 的自适应采样进行了靶向长读测序(T-LRS),以明确诊断一个 arRP 家族,该家族的患病个体(n = 3)携带 EYS 基因 32-33 外显子的杂合致病性缺失。由于这是一个在我们的队列中另外三个家系中发现的复发性变异,我们还旨在从核苷酸水平上描述已知缺失的特征,以评估可能的奠基人效应。A 家系的 T-LRS 发现了 EYS 第 43 编码外显子(chr6(GRCh37):g.64430524_64430525ins352)中的杂合子 AluYa5 插入物,该插入物与之前发现的缺失以复合杂合子的形式与疾病分离。使用 IGV 对以前的 SRS 对齐进行目测发现,有几个读数含有软剪切碱基,同时在 Alu 插入位点的覆盖率略有下降。这促使我们使用 grep 命令开发了一个简化程序,以便从 SRS 数据中调查该变异在我们队列中的复发情况。此外,LRS 还将 CNV 定性为跨越 EYS 32-33 外显子的约 56.4kb 缺失(chr6(GRCh37):g.64764235_64820592del)。通过对这四个家庭进行桑格测序和关联分析,进一步鉴定的结果与创始变异一致。据我们所知,这是第一份关于 EYS 编码序列中的移动元素插入可能导致一个家族出现 arRP 的报告。我们的研究凸显了 LRS 技术在表征和鉴定隐性致病 SV(如逆转录转座子插入)方面的价值,这些 SV 对罕见病病因发病机制的贡献可能被低估。
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引用次数: 0
Look4LTRs: a Long terminal repeat retrotransposon detection tool capable of cross species studies and discovering recently nested repeats Look4LTRs:长末端重复反转座子检测工具,能够进行跨物种研究并发现最近嵌套的重复序列
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-04-16 DOI: 10.1186/s13100-024-00317-w
Anthony B. Garza, Emmanuelle Lerat, Hani Z. Girgis
Plant genomes include large numbers of transposable elements. One particular type of these elements is flanked by two Long Terminal Repeats (LTRs) and can translocate using RNA. Such elements are known as LTR-retrotransposons; they are the most abundant type of transposons in plant genomes. They have many important functions involving gene regulation and the rise of new genes and pseudo genes in response to severe stress. Additionally, LTR-retrotransposons have several applications in biotechnology. Due to the abundance and the importance of LTR-retrotransposons, multiple computational tools have been developed for their detection. However, none of these tools take advantages of the availability of related genomes; they process one chromosome at a time. Further, recently nested LTR-retrotransposons (multiple elements of the same family are inserted into each other) cannot be annotated accurately — or cannot be annotated at all — by the currently available tools. Motivated to overcome these two limitations, we built Look4LTRs, which can annotate LTR-retrotransposons in multiple related genomes simultaneously and discover recently nested elements. The methodology of Look4LTRs depends on techniques imported from the signal-processing field, graph algorithms, and machine learning with a minimal use of alignment algorithms. Four plant genomes were used in developing Look4LTRs and eight plant genomes for evaluating it in contrast to three related tools. Look4LTRs is the fastest while maintaining better or comparable F1 scores (the harmonic average of recall and precision) to those obtained by the other tools. Our results demonstrate the added benefit of annotating LTR-retrotransposons in multiple related genomes simultaneously and the ability to discover recently nested elements. Expert human manual examination of six elements — not included in the ground truth — revealed that three elements belong to known families and two elements are likely from new families. With respect to examining recently nested LTR-retrotransposons, three out of five were confirmed to be valid elements. Look4LTRs — with its speed, accuracy, and novel features — represents a true advancement in the annotation of LTR-retrotransposons, opening the door to many studies focused on understanding their functions in plants.
植物基因组包括大量转座元件。其中一种特殊的转座元件两侧有两个长末端重复序列(LTR),可以利用 RNA 进行转座。这类元件被称为 LTR-转座子;它们是植物基因组中最丰富的转座子类型。它们具有许多重要功能,包括基因调控以及在应对严重胁迫时产生新基因和伪基因。此外,LTR-反转座子在生物技术中也有多种应用。由于 LTR 反转座子的丰富性和重要性,已经开发出多种用于检测它们的计算工具。但是,这些工具都没有利用相关基因组的优势;它们一次只处理一条染色体。此外,目前可用的工具无法准确注释或根本无法注释最近嵌套的 LTR 反转座子(同一家族的多个元素相互插入)。为了克服这两个局限性,我们建立了 Look4LTRs,它可以同时注释多个相关基因组中的 LTR 反转座子,并发现最近嵌套的元件。Look4LTRs 的方法依赖于从信号处理领域引进的技术、图算法和机器学习,只使用了极少量的比对算法。开发 Look4LTRs 时使用了四个植物基因组,评估时使用了八个植物基因组,与三个相关工具进行了对比。Look4LTRs 的速度最快,同时与其他工具获得的 F1 分数(召回率和精确率的调和平均值)相比,Look4LTRs 保持了更好或相当的 F1 分数。我们的研究结果证明了同时注释多个相关基因组中的 LTR 反转座子的额外好处,以及发现最近嵌套元素的能力。专家人工检查了六个元素(不包括在基本事实中),发现三个元素属于已知的家族,两个元素可能来自新的家族。在检查最近嵌套的 LTR 反转座子方面,五个元素中有三个被确认为有效元素。Look4LTRs 的速度、准确性和新颖性代表了 LTR 反转座子注释的真正进步,为了解其在植物中的功能的许多研究打开了大门。
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引用次数: 0
Multiple horizontal transfer events of a DNA transposon into turtles, fishes, and a frog DNA 转座子向龟、鱼和青蛙的多次水平转移事件
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-04-11 DOI: 10.1186/s13100-024-00318-9
Nozhat T. Hassan, James D. Galbraith, David L. Adelson
Horizontal transfer of transposable elements (HTT) has been reported across many species and the impact of such events on genome structure and function has been well described. However, few studies have focused on reptilian genomes, especially HTT events in Testudines (turtles). Here, as a consequence of investigating the repetitive content of Malaclemys terrapin terrapin (Diamondback turtle) we found a high similarity DNA transposon, annotated in RepBase as hAT-6_XT, shared between other turtle species, ray-finned fishes, and a frog. hAT-6_XT was notably absent in reptilian taxa closely related to turtles, such as crocodiles and birds. Successful invasion of DNA transposons into new genomes requires the conservation of specific residues in the encoded transposase, and through structural analysis, these residues were identified indicating some retention of functional transposition activity. We document six recent independent HTT events of a DNA transposon in turtles, which are known to have a low genomic evolutionary rate and ancient repeats. Malaclemys terrapin terrapin (Diamondback turtle). Malaclemys terrapin pileata (Mississippi diamondback terrapin turtle). Trachemys scripta elegans (Red-eared slider turtle). Chrysemys picta bellii (Western painted turtle). Dermatemys mawii (Hickatee turtle). Sternotherus odoratus (Common musk turtle). Mesoclemmys tuberculata (Tuberculate Toad-headed turtle). Etheostoma spectabile (Orangethroat darter fish). Thalassophryne amazonica (Prehistoric monster fish). Scophthalmus maximus (Turbot fish). Syngnathus acus (Greater pipefish). Scleropages formosus (Asian Arowana fish). Xenopus tropicalis (Western clawed frog).
转座元件(HTT)的水平转移在许多物种中都有报道,这类事件对基因组结构和功能的影响也有很好的描述。然而,很少有研究关注爬行动物基因组,尤其是龟鳖类(Testudines)的 HTT 事件。在这里,通过研究菱纹龟(Malaclemys terrapin terrapin)的重复内容,我们发现了一个高相似度的 DNA 转座子,在 RepBase 中被注释为 hAT-6_XT,该转座子是其他龟类、鳐鱼和青蛙共有的。DNA 转座子成功侵入新的基因组需要编码的转座酶中特定残基的保护,通过结构分析,这些残基被确定下来,表明功能性转座活性有所保留。我们记录了最近在龟类中发生的六次独立的DNA转座子HTT事件,众所周知,龟类的基因组进化速度较低,而且有古老的重复序列。Malaclemys terrapin terrapin(菱形龟)。Malaclemys terrapin pileata(密西西比菱背陆龟)。Trachemys scripta elegans(红耳滑龟)。Chrysemys picta bellii(西部彩龟)。Dermatemys mawii(Hickatee 海龟)。Sternotherus odoratus(普通麝香龟)。Mesoclemmys tuberculata (Tuberculate Toad-headed turtle).Etheostoma spectabile(橙喉镖鱼)。Thalassophryne amazonica(史前怪鱼)。Scophthalmus maximus(多宝鱼)。大琵琶鱼(Syngnathus acus)。Scleropages formosus(亚洲箭鱼)。热带爪蛙(西方爪蛙)。
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引用次数: 0
RepEnTools: an automated repeat enrichment analysis package for ChIP-seq data reveals hUHRF1 Tandem-Tudor domain enrichment in young repeats RepEnTools:用于 ChIP-seq 数据的自动重复富集分析软件包,揭示了 hUHRF1 Tandem-Tudor 结构域在年轻重复序列中的富集情况
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-04-03 DOI: 10.1186/s13100-024-00315-y
Michel Choudalakis, Pavel Bashtrykov, Albert Jeltsch
Repeat elements (REs) play important roles for cell function in health and disease. However, RE enrichment analysis in short-read high-throughput sequencing (HTS) data, such as ChIP-seq, is a challenging task. Here, we present RepEnTools, a software package for genome-wide RE enrichment analysis of ChIP-seq and similar chromatin pulldown experiments. Our analysis package bundles together various software with carefully chosen and validated settings to provide a complete solution for RE analysis, starting from raw input files to tabular and graphical outputs. RepEnTools implementations are easily accessible even with minimal IT skills (Galaxy/UNIX). To demonstrate the performance of RepEnTools, we analysed chromatin pulldown data by the human UHRF1 TTD protein domain and discovered enrichment of TTD binding on young primate and hominid specific polymorphic repeats (SVA, L1PA1/L1HS) overlapping known enhancers and decorated with H3K4me1-K9me2/3 modifications. We corroborated these new bioinformatic findings with experimental data by qPCR assays using newly developed primate and hominid specific qPCR assays which complement similar research tools. Finally, we analysed mouse UHRF1 ChIP-seq data with RepEnTools and showed that the endogenous mUHRF1 protein colocalizes with H3K4me1-H3K9me3 on promoters of REs which were silenced by UHRF1. These new data suggest a functional role for UHRF1 in silencing of REs that is mediated by TTD binding to the H3K4me1-K9me3 double mark and conserved in two mammalian species. RepEnTools improves the previously available programmes for RE enrichment analysis in chromatin pulldown studies by leveraging new tools, enhancing accessibility and adding some key functions. RepEnTools can analyse RE enrichment rapidly, efficiently, and accurately, providing the community with an up-to-date, reliable and accessible tool for this important type of analysis.
重复元件(REs)对健康和疾病中的细胞功能起着重要作用。然而,在短读数高通量测序(HTS)数据(如 ChIP-seq)中进行 RE 富集分析是一项具有挑战性的任务。在这里,我们介绍 RepEnTools,这是一个用于 ChIP-seq 和类似染色质下拉实验的全基因组 RE 富集分析的软件包。我们的分析软件包将各种软件与精心选择和验证的设置捆绑在一起,提供了从原始输入文件到表格和图形输出的 RE 分析完整解决方案。即使只有最低限度的 IT 技能(Galaxy/UNIX),也能轻松实现 RepEnTools。为了证明 RepEnTools 的性能,我们分析了人类 UHRF1 TTD 蛋白结构域的染色质 pulldown 数据,发现在与已知增强子重叠并有 H3K4me1-K9me2/3 修饰的幼年灵长类和类人特异多态重复序列(SVA、L1PA1/L1HS)上 TTD 结合富集。我们利用新开发的灵长类和类人猿特异性 qPCR 检测方法,通过 qPCR 检测实验数据证实了这些新的生物信息学发现,这些检测方法是对类似研究工具的补充。最后,我们利用 RepEnTools 分析了小鼠 UHRF1 ChIP-seq 数据,结果表明内源性 mUHRF1 蛋白与被 UHRF1 沉默的 RE 启动子上的 H3K4me1-H3K9me3 共同定位。这些新数据表明,UHRF1在REs沉默中的功能作用是通过TTD与H3K4me1-K3K9me3双标记的结合来介导的,并且在两个哺乳动物物种中是保守的。RepEnTools 利用新工具,提高了可访问性,并增加了一些关键功能,从而改进了染色质 pulldown 研究中先前可用的 RE 富集分析程序。RepEnTools 可以快速、高效、准确地分析 RE 富集,为这一重要类型的分析提供了最新、可靠、易用的工具。
{"title":"RepEnTools: an automated repeat enrichment analysis package for ChIP-seq data reveals hUHRF1 Tandem-Tudor domain enrichment in young repeats","authors":"Michel Choudalakis, Pavel Bashtrykov, Albert Jeltsch","doi":"10.1186/s13100-024-00315-y","DOIUrl":"https://doi.org/10.1186/s13100-024-00315-y","url":null,"abstract":"Repeat elements (REs) play important roles for cell function in health and disease. However, RE enrichment analysis in short-read high-throughput sequencing (HTS) data, such as ChIP-seq, is a challenging task. Here, we present RepEnTools, a software package for genome-wide RE enrichment analysis of ChIP-seq and similar chromatin pulldown experiments. Our analysis package bundles together various software with carefully chosen and validated settings to provide a complete solution for RE analysis, starting from raw input files to tabular and graphical outputs. RepEnTools implementations are easily accessible even with minimal IT skills (Galaxy/UNIX). To demonstrate the performance of RepEnTools, we analysed chromatin pulldown data by the human UHRF1 TTD protein domain and discovered enrichment of TTD binding on young primate and hominid specific polymorphic repeats (SVA, L1PA1/L1HS) overlapping known enhancers and decorated with H3K4me1-K9me2/3 modifications. We corroborated these new bioinformatic findings with experimental data by qPCR assays using newly developed primate and hominid specific qPCR assays which complement similar research tools. Finally, we analysed mouse UHRF1 ChIP-seq data with RepEnTools and showed that the endogenous mUHRF1 protein colocalizes with H3K4me1-H3K9me3 on promoters of REs which were silenced by UHRF1. These new data suggest a functional role for UHRF1 in silencing of REs that is mediated by TTD binding to the H3K4me1-K9me3 double mark and conserved in two mammalian species. RepEnTools improves the previously available programmes for RE enrichment analysis in chromatin pulldown studies by leveraging new tools, enhancing accessibility and adding some key functions. RepEnTools can analyse RE enrichment rapidly, efficiently, and accurately, providing the community with an up-to-date, reliable and accessible tool for this important type of analysis.","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":null,"pages":null},"PeriodicalIF":4.9,"publicationDate":"2024-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140570063","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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Mobile DNA
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