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A unique eukaryotic lineage of composite-like DNA transposons encoding a DDD/E transposase and a His-Me finger homing endonuclease. 一种独特的真核生物复合样DNA转座子谱系,编码DDD/E转座酶和His-Me指归巢酶。
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-10-22 DOI: 10.1186/s13100-022-00281-3
Kenji K Kojima, Weidong Bao

Background: DNA transposons are ubiquitous components of eukaryotic genomes. A major group of them encode a DDD/E transposase and contain terminal inverted repeats (TIRs) of varying lengths. The Kolobok superfamily of DNA transposons has been found in a wide spectrum of organisms.

Results: Here we report a new Kolobok lineage, designated KolobokP. They were identified in 7 animal phyla (Mollusca, Phoronida, Annelida, Nemertea, Bryozoa, Chordata, and Echinodermata), and are especially rich in bivalves. Unlike other Kolobok families, KolobokP adopts a composite-like architecture: an internal region (INT) flanked by two long terminal direct repeats (LTDRs), which exhibit their own short terminal inverted repeats ranging up to 18 bps. The excision of LTDRs was strongly suggested. The LTDR lengths seem to be constrained to be either around 450-bp or around 660-bp. The internal region encodes a DDD/E transposase and a small His-Me finger nuclease, which likely originated from the homing endonuclease encoded by a group I intron from a eukaryotic species. The architecture of KolobokP resembles composite DNA transposons, usually observed in bacterial genomes, and long terminal repeat (LTR) retrotransposons. In addition to this monomeric LTDR-INT-LTDR structure, plenty of solo LTDRs and multimers represented as (LTDR-INT)n-LTDR are also observed. Our structural and phylogenetic analysis supported the birth of KolobokP in the late stage of the Kolobok evolution. We propose KolobokP families propagate themselves in two ways: the canonical transposition catalyzed by their transposase and the sequence-specific cleavage by their endonuclease followed by the multimerization through the unequal crossover.

Conclusions: The presence of homing endonuclease and long terminal direct repeats of KolobokP families suggest their unique dual replication mechanisms: transposition and induced unequal crossover.

背景:DNA转座子是真核生物基因组中普遍存在的组成部分。其中一组主要编码DDD/E转座酶,并包含不同长度的末端倒置重复序列(tir)。DNA转座子的Kolobok超家族已经在广泛的生物体中被发现。结果:在这里,我们报告了一个新的Kolobok谱系,命名为KolobokP。在7个动物门(软体动物门、海绵动物门、环节动物门、奈默亚门、苔藓动物门、脊索动物门和棘皮动物门)中均有发现,在双壳类动物中尤其丰富。与其他Kolobok家族不同,KolobokP采用类似复合结构的结构:一个内部区域(INT)两侧是两个长端直接重复序列(ltdr),它们表现出自己的短端倒置重复序列,最高可达18 bps。强烈建议切除ltdr。LTDR的长度似乎被限制在450个基点或660个基点左右。内部区域编码一个DDD/E转座酶和一个小的His-Me指核酸酶,可能起源于真核生物物种中I组内含子编码的归巢内切酶。KolobokP的结构类似于通常在细菌基因组中观察到的复合DNA转座子和长末端重复(LTR)反转录转座子。除了这种单体LTDR-INT- ltdr结构外,还观察到大量的单链ltdr和多链ltdr,表示为(LTDR-INT)n-LTDR。我们的结构和系统发育分析支持KolobokP在Kolobok进化的后期诞生。我们提出KolobokP家族以两种方式繁殖:由转座酶催化的典型转座和由内切酶催化的序列特异性切割,然后通过不平等交叉进行多聚化。结论:KolobokP家族的归巢内切酶和长末端直接重复的存在表明其独特的双重复制机制:转位和诱导不平等交叉。
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引用次数: 0
Mobile group I introns at nuclear rDNA position L2066 harbor sense and antisense homing endonuclease genes intervened by spliceosomal introns. 核rDNA位置L2066上的移动I组内含子携带有义和反义归巢的内切酶基因,受到剪接体内含子的干扰。
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-10-08 DOI: 10.1186/s13100-022-00280-4
Kjersti Lian, Betty M N Furulund, Anders A Tveita, Peik Haugen, Steinar D Johansen

Background: Mobile group I introns encode homing endonucleases that confer intron mobility initiated by a double-strand break in the intron-lacking allele at the site of insertion. Nuclear ribosomal DNA of some fungi and protists contain mobile group I introns harboring His-Cys homing endonuclease genes (HEGs). An intriguing question is how protein-coding genes embedded in nuclear ribosomal DNA become expressed. To address this gap of knowledge we analyzed nuclear L2066 group I introns from myxomycetes and ascomycetes.

Results: A total of 34 introns were investigated, including two identified mobile-type introns in myxomycetes with HEGs oriented in sense or antisense directions. Intriguingly, both HEGs are interrupted by spliceosomal introns. The intron in Didymium squamulosum, which harbors an antisense oriented HEG, was investigated in more detail. The group I intron RNA self-splices in vitro, thus generating ligated exons and full-length intron circles. The intron HEG is expressed in vivo in Didymium cells, which involves removal of a 47-nt spliceosomal intron (I-47) and 3' polyadenylation of the mRNA. The D. squamulosum HEG (lacking the I-47 intron) was over-expressed in E. coli, and the corresponding protein was purified and shown to confer endonuclease activity. The homing endonuclease was shown to cleave an intron-lacking DNA and to produce a pentanucleotide 3' overhang at the intron insertion site.

Conclusions: The L2066 family of nuclear group I introns all belong to the group IE subclass. The D. squamulosum L2066 intron contains major hallmarks of a true mobile group I intron by encoding a His-Cys homing endonuclease that generates a double-strand break at the DNA insertion site. We propose a potential model to explain how an antisense HEG becomes expressed from a nuclear ribosomal DNA locus.

背景:可移动的I组内含子编码归巢内切酶,赋予内含子可移动性,由插入位点缺乏内含子的等位基因的双链断裂引发。一些真菌和原生生物的核糖体DNA含有可移动的I族内含子,内含His-Cys归巢内切酶基因(HEGs)。一个有趣的问题是嵌入在核糖体DNA中的蛋白质编码基因是如何表达的。为了解决这一知识空白,我们分析了黏菌和子囊菌的核L2066 I族内含子。结果:共检测到34个内含子,其中2个为黏菌中的移动型内含子,heg定向于正义方向或反义方向。有趣的是,这两种heg都被剪接体内含子打断。对含有反义定向HEG的squamulosum中的内含子进行了更详细的研究。I组内含子RNA在体外自剪接,从而产生结扎的外显子和全长内含子环。内含子HEG在Didymium细胞体内表达,这涉及去除47-nt剪接体内含子(I-47)和mRNA的3'聚腺苷化。squamulosum HEG(缺乏I-47内含子)在大肠杆菌中过表达,相应的蛋白被纯化并显示具有内切酶活性。结果表明,归巢内切酶可切割缺乏内含子的DNA,并在内含子插入位点产生3'悬垂的五核苷酸。结论:核I族内含子L2066家族均属于IE族亚类。squamulosum L2066内含子通过编码His-Cys归巢内切酶在DNA插入位点产生双链断裂,包含了一个真正的移动I组内含子的主要特征。我们提出了一个潜在的模型来解释反义HEG如何从核糖体DNA位点表达。
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引用次数: 0
Transcriptional dynamics of transposable elements in the type I IFN response in Myotis lucifugus cells. 转座因子在I型IFN细胞应答中的转录动力学。
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-09-06 DOI: 10.1186/s13100-022-00277-z
Giulia Irene Maria Pasquesi, Conor J Kelly, Andrea D Ordonez, Edward B Chuong

Background: Bats are a major reservoir of zoonotic viruses, and there has been growing interest in characterizing bat-specific features of innate immunity and inflammation. Recent studies have revealed bat-specific adaptations affecting interferon (IFN) signaling and IFN-stimulated genes (ISGs), but we still have a limited understanding of the genetic mechanisms that have shaped the evolution of bat immunity. Here we investigated the transcriptional and epigenetic dynamics of transposable elements (TEs) during the type I IFN response in little brown bat (Myotis lucifugus) primary embryonic fibroblast cells, using RNA-seq and CUT&RUN.

Results: We found multiple bat-specific TEs that undergo both locus-specific and family-level transcriptional induction in response to IFN. Our transcriptome reassembly identified multiple ISGs that have acquired novel exons from bat-specific TEs, including NLRC5, SLNF5 and a previously unannotated isoform of the IFITM2 gene. We also identified examples of TE-derived regulatory elements, but did not find strong evidence supporting genome-wide epigenetic activation of TEs in response to IFN.

Conclusion: Collectively, our study uncovers numerous TE-derived transcripts, proteins, and alternative isoforms that are induced by IFN in Myotis lucifugus cells, highlighting candidate loci that may contribute to bat-specific immune function.

背景:蝙蝠是人畜共患病毒的主要储存库,人们对蝙蝠先天免疫和炎症特异性特征的研究越来越感兴趣。最近的研究揭示了蝙蝠的特异性适应影响干扰素(IFN)信号传导和IFN刺激基因(ISGs),但我们对形成蝙蝠免疫进化的遗传机制的理解仍然有限。本研究利用RNA-seq和CUT&RUN技术研究了小棕蝠(Myotis lucifugus)原代胚胎成纤维细胞I型IFN应答过程中转座因子(TEs)的转录和表观遗传动力学。结果:我们发现多个蝙蝠特异性te在IFN的作用下经历了位点特异性和家族水平的转录诱导。我们的转录组重组鉴定出多个isg从蝙蝠特异性te中获得了新的外显子,包括NLRC5、SLNF5和先前未注释的IFITM2基因异构体。我们也发现了te衍生的调控元件的例子,但没有发现强有力的证据支持te在IFN响应中全基因组表观遗传激活。结论:总的来说,我们的研究揭示了许多te衍生的转录本、蛋白质和IFN诱导的Myotis lucfugus细胞的替代亚型,突出了可能有助于蝙蝠特异性免疫功能的候选位点。
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引用次数: 3
SCIFER: approach for analysis of LINE-1 mRNA expression in single cells at a single locus resolution. SCIFER:以单基因座分辨率分析单细胞中 LINE-1 mRNA 表达的方法。
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-08-26 DOI: 10.1186/s13100-022-00276-0
Emily C Stow, Melody Baddoo, Alexis J LaRosa, Dawn LaCoste, Prescott Deininger, Victoria Belancio

Background: Endogenous expression of L1 mRNA is the first step in an L1-initiated mutagenesis event. However, the contribution of individual cell types to patterns of organ-specific L1 mRNA expression remains poorly understood, especially at single-locus resolution. We introduce a method to quantify expression of mobile elements at the single-locus resolution in scRNA-Seq datasets called Single Cell Implementation to Find Expressed Retrotransposons (SCIFER). SCIFER aligns scRNA-Seq reads uniquely to the genome and extracts alignments from single cells by cell-specific barcodes. In contrast to the alignment performed using default parameters, this alignment strategy increases accuracy of L1 locus identification by retaining only reads that are uniquely mapped to individual L1 loci. L1 loci expressed in single cells are unambiguously identified using a list of L1 loci manually validated to be expressed in bulk RNA-Seq datasets generated from the same cell line or organ.

Results: Validation of SCIFER using MCF7 cells determined technical parameters needed for optimal detection of L1 expression in single cells. We show that unsupervised analysis of L1 expression in single cells exponentially inflates both the levels of L1 expression and the number of expressed L1 loci. Application of SCIFER to analysis of scRNA-Seq datasets generated from mouse and human testes identified that mouse Round Spermatids and human Spermatogonia, Spermatocytes, and Round Spermatids express the highest levels of L1 mRNA. Our analysis also determined that similar to mice, human testes from unrelated individuals share as much as 80% of expressed L1 loci. Additionally, SCIFER determined that individual mouse cells co-express different L1 sub-families and different families of transposable elements, experimentally validating their co-existence in the same cell.

Conclusions: SCIFER detects mRNA expression of individual L1 loci in single cells. It is compatible with scRNA-Seq datasets prepared using traditional sequencing methods. Validated using a human cancer cell line, SCIFER analysis of mouse and human testes identified key cell types supporting L1 expression in these species. This will further our understanding of differences and similarities in endogenous L1 mRNA expression patterns in mice and humans.

背景:L1 mRNA的内源表达是L1诱变事件的第一步。然而,人们对单个细胞类型对器官特异性 L1 mRNA 表达模式的贡献仍然知之甚少,尤其是在单病灶分辨率下。我们介绍了一种在scRNA-Seq数据集中量化单病灶分辨率移动元件表达的方法,称为 "单细胞实施寻找表达的逆转座子(SCIFER)"。SCIFER 将 scRNA-Seq 读数与基因组进行唯一比对,并通过细胞特异性条形码从单细胞中提取比对结果。与使用默认参数进行的比对相比,这种比对策略只保留唯一映射到单个 L1 基因座的读数,从而提高了 L1 基因座鉴定的准确性。在单细胞中表达的 L1 基因座可通过人工验证在同一细胞系或器官生成的批量 RNA-Seq 数据集中表达的 L1 基因座列表来明确识别:使用 MCF7 细胞对 SCIFER 进行验证,确定了最佳检测单细胞中 L1 表达所需的技术参数。我们发现,对单细胞中 L1 表达的无监督分析会使 L1 表达水平和表达的 L1 基因座数量呈指数增长。应用 SCIFER 分析小鼠和人类睾丸生成的 scRNA-Seq 数据集发现,小鼠圆精子和人类精原细胞、精母细胞和圆精子表达的 L1 mRNA 水平最高。我们的分析还确定,与小鼠类似,来自非亲缘关系个体的人类睾丸共享多达 80% 的 L1 表达位点。此外,SCIFER 还确定,单个小鼠细胞共同表达不同的 L1 亚家族和不同的转座元件家族,通过实验验证了它们在同一细胞中的共存性:结论:SCIFER 可检测单个细胞中单个 L1 基因座的 mRNA 表达。结论:SCIFER 可检测单个细胞中单个 L1 基因座的 mRNA 表达,与使用传统测序方法制备的 scRNA-Seq 数据集兼容。通过使用人类癌细胞系进行验证,SCIFER 对小鼠和人类睾丸的分析确定了这些物种中支持 L1 表达的关键细胞类型。这将进一步加深我们对小鼠和人类内源性 L1 mRNA 表达模式异同的理解。
{"title":"SCIFER: approach for analysis of LINE-1 mRNA expression in single cells at a single locus resolution.","authors":"Emily C Stow, Melody Baddoo, Alexis J LaRosa, Dawn LaCoste, Prescott Deininger, Victoria Belancio","doi":"10.1186/s13100-022-00276-0","DOIUrl":"10.1186/s13100-022-00276-0","url":null,"abstract":"<p><strong>Background: </strong>Endogenous expression of L1 mRNA is the first step in an L1-initiated mutagenesis event. However, the contribution of individual cell types to patterns of organ-specific L1 mRNA expression remains poorly understood, especially at single-locus resolution. We introduce a method to quantify expression of mobile elements at the single-locus resolution in scRNA-Seq datasets called Single Cell Implementation to Find Expressed Retrotransposons (SCIFER). SCIFER aligns scRNA-Seq reads uniquely to the genome and extracts alignments from single cells by cell-specific barcodes. In contrast to the alignment performed using default parameters, this alignment strategy increases accuracy of L1 locus identification by retaining only reads that are uniquely mapped to individual L1 loci. L1 loci expressed in single cells are unambiguously identified using a list of L1 loci manually validated to be expressed in bulk RNA-Seq datasets generated from the same cell line or organ.</p><p><strong>Results: </strong>Validation of SCIFER using MCF7 cells determined technical parameters needed for optimal detection of L1 expression in single cells. We show that unsupervised analysis of L1 expression in single cells exponentially inflates both the levels of L1 expression and the number of expressed L1 loci. Application of SCIFER to analysis of scRNA-Seq datasets generated from mouse and human testes identified that mouse Round Spermatids and human Spermatogonia, Spermatocytes, and Round Spermatids express the highest levels of L1 mRNA. Our analysis also determined that similar to mice, human testes from unrelated individuals share as much as 80% of expressed L1 loci. Additionally, SCIFER determined that individual mouse cells co-express different L1 sub-families and different families of transposable elements, experimentally validating their co-existence in the same cell.</p><p><strong>Conclusions: </strong>SCIFER detects mRNA expression of individual L1 loci in single cells. It is compatible with scRNA-Seq datasets prepared using traditional sequencing methods. Validated using a human cancer cell line, SCIFER analysis of mouse and human testes identified key cell types supporting L1 expression in these species. This will further our understanding of differences and similarities in endogenous L1 mRNA expression patterns in mice and humans.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":null,"pages":null},"PeriodicalIF":4.9,"publicationDate":"2022-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9413895/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40446645","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
Multiple horizontal transfers of a Helitron transposon associated with a parasitoid wasp. 与寄生蜂相关的Helitron转座子的多重水平转移。
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-08-19 DOI: 10.1186/s13100-022-00278-y
Pedro Heringer, Gustavo C S Kuhn

In a previous study we described a Helitron transposon that apparently became one of the segments in the symbiotic Cotesia vestalis bracovirus (CvBV) from the parasitoid wasp C. vestalis. We presented evidence that this Helitron, named Hel_c35, invaded the C. vestalis genome through a horizontal transfer (HT) event from a dipteran and was later transferred horizontally from C. vestalis to a lepidopteran species. Based on the phylogeny of Hel_c35, we suggested that both HTs occurred in East Asia. We have also anticipated that, as more sequenced genomes from new species become available, more HTs involving Hel_c35 would be detected. Although the inclusion of Hel_c35 as a CvBV segment turned out to be a methodological artifact, the fact that Hel_c35 copies are present in the genomes of C. vestalis and other arthropods still remains. Here, we investigated the evolution of Hel_c35 in arthropods using an updated data set to reassess our previous findings. Most species (95%) included in the present work had their genomes sequenced after our initial study was published, thus representing new descriptions of taxa harboring Hel_c35. Our results expand considerably the number of putative HTs involving Hel_c35, with up to dozens of previously undescribed events, and suggest that the most recent HTs associated with C. vestalis took place in Europe. Considering the phylogenetic distribution of Hel_c35, and the evidence that its DNA sequences are present in the calyx fluid of C. vestalis and tissues from its parasitized host, we argue that many HT events were favored by the behavior of this wasp.

在之前的研究中,我们描述了一个Helitron转座子,该转座子显然成为来自拟寄生蜂C. vestalis的共生vesttesia brbrovirus (CvBV)的一个片段。我们提出的证据表明,这个Helitron,命名为Hel_c35,通过双翅目动物的水平转移(HT)事件侵入了C. vestalis基因组,随后从C. vestalis水平转移到鳞翅目物种。基于Hel_c35的系统发育,我们认为这两个HTs都发生在东亚。我们还预计,随着更多来自新物种的基因组测序变得可用,将检测到更多涉及Hel_c35的ht。虽然将Hel_c35作为CvBV片段被证明是一种方法上的人工产物,但Hel_c35拷贝存在于C. vestalis和其他节肢动物的基因组中这一事实仍然存在。在这里,我们使用更新的数据集研究了节肢动物中Hel_c35的进化,以重新评估我们之前的发现。在我们最初的研究发表后,大多数(95%)纳入的物种都进行了基因组测序,从而代表了携带Hel_c35的分类群的新描述。我们的研究结果大大扩展了涉及Hel_c35的假定高温高温的数量,其中包括多达数十个先前未描述的事件,并表明最近与C. vestalis相关的高温高温发生在欧洲。考虑到Hel_c35的系统发育分布,以及其DNA序列存在于灶神蜂的花萼液和被寄生寄主的组织中的证据,我们认为该蜂的行为有利于许多高温事件。
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引用次数: 4
Genomic analysis reveals the role of integrative and conjugative elements in plant pathogenic bacteria. 基因组分析揭示了整合和接合元件在植物致病菌中的作用。
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-08-12 DOI: 10.1186/s13100-022-00275-1
Jéssica Catarine Silva de Assis, Osiel Silva Gonçalves, Alexia Suellen Fernandes, Marisa Vieira de Queiroz, Denise Mara Soares Bazzolli, Mateus Ferreira Santana

Background: ICEs are mobile genetic elements found integrated into bacterial chromosomes that can excise and be transferred to a new cell. They play an important role in horizontal gene transmission and carry accessory genes that may provide interesting phenotypes for the bacteria. Here, we seek to research the presence and the role of ICEs in 300 genomes of phytopathogenic bacteria with the greatest scientific and economic impact.

Results: Seventy-eight ICEs (45 distinct elements) were identified and characterized in chromosomes of Agrobacterium tumefaciens, Dickeya dadantii, and D. solani, Pectobacterium carotovorum and P. atrosepticum, Pseudomonas syringae, Ralstonia solanacearum Species Complex, and Xanthomonas campestris. Intriguingly, the co-occurrence of four ICEs was observed in some P. syringae strains. Moreover, we identified 31 novel elements, carrying 396 accessory genes with potential influence on virulence and fitness, such as genes coding for functions related to T3SS, cell wall degradation and resistance to heavy metals. We also present the analysis of previously reported data on the expression of cargo genes related to the virulence of P. atrosepticum ICEs, which evidences the role of these genes in the infection process of tobacco plants.

Conclusions: Altogether, this paper has highlighted the potential of ICEs to affect the pathogenicity and lifestyle of these phytopathogens and direct the spread of significant putative virulence genes in phytopathogenic bacteria.

背景:ICEs是一种可移动的遗传元件,可以整合到细菌染色体中,可以切除并转移到新细胞中。它们在水平基因传递中发挥重要作用,并携带可能为细菌提供有趣表型的辅助基因。在这里,我们试图研究ice在300种具有最大科学和经济影响的植物致病菌基因组中的存在和作用。结果:在根癌农杆菌、达氏农杆菌和茄兰杆菌、胡萝卜乳杆菌和萎蔫杆菌、丁香假单胞菌、茄兰枯菌物种复合体和油菜黄单胞菌的染色体中共鉴定出78个ICEs(45个不同的元素)。有趣的是,在一些丁香假单胞菌中发现了四种ICEs的共存。此外,我们还鉴定出31个新元件,携带396个对毒力和适应度有潜在影响的附属基因,如编码T3SS、细胞壁降解和对重金属抗性相关功能的基因。我们还对先前报道的与atrosepticum ice毒力相关的货物基因表达数据进行了分析,证明了这些基因在烟草植物感染过程中的作用。结论:总之,本文强调了ice可能影响这些植物致病菌的致病性和生活方式,并指导重要的推定毒力基因在植物致病菌中的传播。
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引用次数: 3
Amplification of LTRs of extrachromosomal linear DNAs (ALE-seq) identifies two active Oryco LTR retrotransposons in the rice cultivar Dongjin 染色体外线性dna LTRs扩增(ALE-seq)鉴定了两个活性Oryco LTR反转录转座子
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-06-13 DOI: 10.1186/s13100-022-00274-2
Koo, Hyunjin, Kim, Soomin, Park, Hyun-Seung, Lee, Sang-Ji, Paek, Nam-Chon, Cho, Jungnam, Yang, Tae-Jin
Long terminal repeat retrotransposons (LTR-RTs) make up a considerable portion of plant genomes. New insertions of these active LTR-RTs modify gene structures and functions and play an important role in genome evolution. Therefore, identifying active forms of LTR-RTs could uncover the effects of these elements in plants. Extrachromosomal linear DNA (eclDNA) forms during LTR-RT replication; therefore, amplification LTRs of eclDNAs followed by sequencing (ALE-seq) uncover the current transpositional potential of the LTR-RTs. The ALE-seq protocol was validated by identification of Tos17 in callus of Nipponbare cultivar. Here, we identified two active LTR-RTs belonging to the Oryco family on chromosomes 6 and 9 in rice cultivar Dongjin callus based on the ALE-seq technology. Each Oryco family member has paired LTRs with identical sequences and internal domain regions. Comparison of the two LTR-RTs revealed 97% sequence identity in their internal domains and 65% sequence identity in their LTRs. These two putatively active Oryco LTR-RT family members could be used to expand our knowledge of retrotransposition mechanisms and the effects of LTR-RTs on the rice genome.
长末端重复反转录转座子(LTR-RTs)在植物基因组中占相当大的比例。这些活性LTR-RTs的新插入修饰了基因结构和功能,并在基因组进化中发挥重要作用。因此,鉴定活性形式的LTR-RTs可以揭示这些元素在植物中的作用。染色体外线性DNA (eclDNA)在LTR-RT复制过程中形成;因此,扩增eclnas的ltr并进行测序(ALE-seq)可以揭示LTR-RTs当前的转位潜力。通过对日本品种愈伤组织中Tos17的鉴定,验证了ALE-seq方法的有效性。本研究利用ALE-seq技术,在水稻品种东津愈伤组织的6号和9号染色体上鉴定了两个Oryco家族的活性LTR-RTs。每个Oryco家族成员都有具有相同序列和内部结构域的配对ltr。两个LTR-RTs的比较显示,其内部结构域的序列一致性为97%,ltr的序列一致性为65%。这两个推测活跃的Oryco LTR-RT家族成员可以用来扩展我们对水稻基因组逆转录转位机制和LTR-RT影响的认识。
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引用次数: 0
Correction: Characterization of transposable elements within the Bemisia tabaci species complex 更正:烟粉虱物种复合体中转座元件的特征
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-06-08 DOI: 10.1186/s13100-022-00273-3
Juan Paolo A. Sicat, Paul Visendi, Steven O. Sewe, S. Bouvaine, S. Seal
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引用次数: 0
Comprehensive analysis of both long and short read transcriptomes of a clonal and a seed-propagated model species reveal the prerequisites for transcriptional activation of autonomous and non-autonomous transposons in plants 综合分析克隆和种子繁殖模式物种的长读和短读转录组,揭示了植物自主和非自主转座子转录激活的先决条件
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-05-12 DOI: 10.1186/s13100-022-00271-5
Ting Chen, C. Winefield
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引用次数: 0
On Turedo Hierarchies and Intrinsic Universality 论社会层次与内在普遍性
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-05-09 DOI: 10.48550/arXiv.2205.04103
Samuel Nalin, Guillaume Theyssier
This paper is about turedos, which are Turing machine whose head can move in the plane (or in a higher-dimensional space) but only in a selfavoiding way, by putting marks (letters) on visited positions and moving only to unmarked, therefore unvisited, positions. The key parameter of turedos is their lookup radius: the distance up to which the head can look around in order to make its decision of where to move to and what mark to write. In this paper we study the hierarchy of turedos according to their lookup radius and the dimension of space using notions of simulation up to spatio-temporal rescaling (a standard approach in cellular automata or self-assembly systems). We establish that there is a rich interplay between the turedo parameters and the notion of simulation considered. We show in particular, for the most liberal simulations, the existence of 3D turedos of radius 1 that are intrinsically universal for all radii, but that this is impossible in dimension 2, where some radius 2 turedo are impossible to simulate at radius 1. Using stricter notions of simulation, intrinsic universality becomes impossible, even in dimension 3, and there is a strict radius hierarchy. Finally, when restricting to radius 1, universality is again possible in dimension 3, but not in dimension 2, where we show however that a radius 3 turedo can simulate all radius 1 turedos.
这篇论文是关于图灵机的,图灵机的头部可以在平面(或更高维度的空间)中移动,但只能以一种自利的方式,通过在访问位置上标记(字母),只移动到未标记的位置,因此未访问的位置。turedos的关键参数是它们的查找半径:为了决定移动到哪里和写什么标记,头部可以查看周围的距离。在本文中,我们研究了结构的层次结构,根据他们的查找半径和空间的维度,使用模拟的概念,直到时空的重新缩放(一个标准的方法在元胞自动机或自组装系统)。我们建立了在turedo参数和所考虑的模拟概念之间存在丰富的相互作用。我们特别指出,对于最自由的模拟,存在半径为1的三维turedo本质上对所有半径都是通用的,但这在2维中是不可能的,在2维中一些半径为2的turedo不可能在1维中模拟。使用更严格的模拟概念,内在的普遍性变得不可能,即使在维度3中也是如此,并且存在严格的半径层次。最后,当限制半径为1时,通用性在维度3中是可能的,但在维度2中不是,然而,我们证明了一个半径为3的turedo可以模拟所有半径为1的turedo。
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引用次数: 2
期刊
Mobile DNA
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