Mobile DNA最新文献

{"title":"T3E: a tool for characterising the epigenetic profile of transposable elements using ChIP-seq data.","authors":"Michelle Almeida da Paz, Leila Taher","doi":"10.1186/s13100-022-00285-z","DOIUrl":"10.1186/s13100-022-00285-z","url":null,"abstract":"<p><strong>Background: </strong>Despite the advent of Chromatin Immunoprecipitation Sequencing (ChIP-seq) having revolutionised our understanding of the mammalian genome's regulatory landscape, many challenges remain. In particular, because of their repetitive nature, the sequencing reads derived from transposable elements (TEs) pose a real bioinformatics challenge, to the point that standard analysis pipelines typically ignore reads whose genomic origin cannot be unambiguously ascertained.</p><p><strong>Results: </strong>We show that discarding ambiguously mapping reads may lead to a systematic underestimation of the number of reads associated with young TE families/subfamilies. We also provide evidence suggesting that the strategy of randomly permuting the location of the read mappings (or the TEs) that is often used to compute the background for enrichment calculations at TE families/subfamilies can result in both false positive and negative enrichments. To address these problems, we present the Transposable Element Enrichment Estimator (T3E), a tool that makes use of ChIP-seq data to characterise the epigenetic profile of associated TE families/subfamilies. T3E weights the number of read mappings assigned to the individual TE copies of a family/subfamily by the overall number of genomic loci to which the corresponding reads map, and this is done at the single nucleotide level. In addition, T3E computes ChIP-seq enrichment relative to a background estimated based on the distribution of the read mappings in the input control DNA. We demonstrated the capabilities of T3E on 23 different ChIP-seq libraries. T3E identified enrichments that were consistent with previous studies. Furthermore, T3E detected context-specific enrichments that are likely to pinpoint unexplored TE families/subfamilies with individual TE copies that have been frequently exapted as cis-regulatory elements during the evolution of mammalian regulatory networks.</p><p><strong>Conclusions: </strong>T3E is a novel open-source computational tool (available for use at: https://github.com/michelleapaz/T3E ) that overcomes some of the pitfalls associated with the analysis of ChIP-seq data arising from the repetitive mammalian genome and provides a framework to shed light on the epigenetics of entire TE families/subfamilies.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"13 1","pages":"29"},"PeriodicalIF":4.9,"publicationDate":"2022-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9710123/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10333093","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}

{"title":"Recurrent co-domestication of PIF/Harbinger transposable element proteins in insects.","authors":"Dragomira N Markova,&nbsp;Fatema B Ruma,&nbsp;Claudio Casola,&nbsp;Ayda Mirsalehi,&nbsp;Esther Betrán","doi":"10.1186/s13100-022-00282-2","DOIUrl":"https://doi.org/10.1186/s13100-022-00282-2","url":null,"abstract":"<p><strong>Background: </strong>Transposable elements (TEs) are selfish DNA sequences capable of moving and amplifying at the expense of host cells. Despite this, an increasing number of studies have revealed that TE proteins are important contributors to the emergence of novel host proteins through molecular domestication. We previously described seven transposase-derived domesticated genes from the PIF/Harbinger DNA family of TEs in Drosophila and a co-domestication. All PIF TEs known in plants and animals distinguish themselves from other DNA transposons by the presence of two genes. We hypothesize that there should often be co-domestications of the two genes from the same TE because the transposase (gene 1) has been described to be translocated to the nucleus by the MADF protein (gene 2). To provide support for this model of new gene origination, we investigated available insect species genomes for additional evidence of PIF TE domestication events and explored the co-domestication of the MADF protein from the same TE insertion.</p><p><strong>Results: </strong>After the extensive insect species genomes exploration of hits to PIF transposases and analyses of their context and evolution, we present evidence of at least six independent PIF transposable elements proteins domestication events in insects: two co-domestications of both transposase and MADF proteins in Anopheles (Diptera), one transposase-only domestication event and one co-domestication in butterflies and moths (Lepidoptera), and two transposases-only domestication events in cockroaches (Blattodea). The predicted nuclear localization signals for many of those proteins and dicistronic transcription in some instances support the functional associations of co-domesticated transposase and MADF proteins.</p><p><strong>Conclusions: </strong>Our results add to a co-domestication that we previously described in fruit fly genomes and support that new gene origination through domestication of a PIF transposase is frequently accompanied by the co-domestication of a cognate MADF protein in insects, potentially for regulatory functions. We propose a detailed model that predicts that PIF TE protein co-domestication should often occur from the same PIF TE insertion.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"13 1","pages":"28"},"PeriodicalIF":4.9,"publicationDate":"2022-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9710019/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10678217","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}

{"title":"Amplification of LTRs of extrachromosomal linear DNAs (ALE-seq) identifies two active Oryco LTR retrotransposons in the rice cultivar Dongjin","authors":"Koo, Hyunjin, Kim, Soomin, Park, Hyun-Seung, Lee, Sang-Ji, Paek, Nam-Chon, Cho, Jungnam, Yang, Tae-Jin","doi":"10.1186/s13100-022-00274-2","DOIUrl":"https://doi.org/10.1186/s13100-022-00274-2","url":null,"abstract":"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.","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"29 1","pages":""},"PeriodicalIF":4.9,"publicationDate":"2022-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138518116","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}

{"title":"Correction: Characterization of transposable elements within the Bemisia tabaci species complex","authors":"Juan Paolo A. Sicat, Paul Visendi, Steven O. Sewe, S. Bouvaine, S. Seal","doi":"10.1186/s13100-022-00273-3","DOIUrl":"https://doi.org/10.1186/s13100-022-00273-3","url":null,"abstract":"","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":" ","pages":""},"PeriodicalIF":4.9,"publicationDate":"2022-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44901530","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}

{"title":"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","authors":"Ting Chen, C. Winefield","doi":"10.1186/s13100-022-00271-5","DOIUrl":"https://doi.org/10.1186/s13100-022-00271-5","url":null,"abstract":"","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"36 1","pages":""},"PeriodicalIF":4.9,"publicationDate":"2022-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65814814","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}

{"title":"On Turedo Hierarchies and Intrinsic Universality","authors":"Samuel Nalin, Guillaume Theyssier","doi":"10.48550/arXiv.2205.04103","DOIUrl":"https://doi.org/10.48550/arXiv.2205.04103","url":null,"abstract":"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.","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"26 1 1","pages":"6:1-6:18"},"PeriodicalIF":4.9,"publicationDate":"2022-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86102084","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}

{"title":"Correction: A beginner’s guide to manual curation of transposable elements","authors":"Goubert, Clement, Craig, Rory J., Bilat, Agustin F., Peona, Valentina, Vogan, Aaron A., Protasio, Anna V.","doi":"10.1186/s13100-022-00272-4","DOIUrl":"https://doi.org/10.1186/s13100-022-00272-4","url":null,"abstract":"&lt;p&gt;\u0000&lt;b&gt;Correction to: Mobile DNA 13, 7 (2022)&lt;/b&gt;\u0000&lt;/p&gt;&lt;p&gt;\u0000&lt;b&gt;https://doi.org/10.1186/s13100-021-00259-7&lt;/b&gt;\u0000&lt;/p&gt;&lt;p&gt;Following the publication of the original article [1] the author reported that Additional files 3, 4 and 5 in the published article are corrupted.&lt;/p&gt;&lt;p&gt;The original article [1] has been updated.&lt;/p&gt;&lt;ol&gt;&lt;li data-counter=\"1.\"&gt;&lt;p&gt;Goubert C, Craig RJ, Bilat AF, et al. A beginner’s guide to manual curation of transposable elements. Mobile DNA. 2022;13:7. https://doi.org/10.1186/s13100-021-00259-7.&lt;/p&gt;&lt;p&gt;Article PubMed PubMed Central Google Scholar &lt;/p&gt;&lt;/li&gt;&lt;/ol&gt;&lt;p&gt;Download references&lt;svg aria-hidden=\"true\" focusable=\"false\" height=\"16\" role=\"img\" width=\"16\"&gt;&lt;use xlink:href=\"#global-icon-download\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"&gt;&lt;/use&gt;&lt;/svg&gt;&lt;/p&gt;&lt;h3&gt;Affiliations&lt;/h3&gt;&lt;ol&gt;&lt;li&gt;&lt;p&gt;Canadian Center for Computational Genomics, McGill University, Montreal, Québec, Canada&lt;/p&gt;&lt;p&gt;Clement Goubert&lt;/p&gt;&lt;/li&gt;&lt;li&gt;&lt;p&gt;Department of Human Genetics, McGill University, Montreal, Québec, Canada&lt;/p&gt;&lt;p&gt;Clement Goubert&lt;/p&gt;&lt;/li&gt;&lt;li&gt;&lt;p&gt;Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK&lt;/p&gt;&lt;p&gt;Rory J. Craig&lt;/p&gt;&lt;/li&gt;&lt;li&gt;&lt;p&gt;Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay&lt;/p&gt;&lt;p&gt;Agustin F. Bilat&lt;/p&gt;&lt;/li&gt;&lt;li&gt;&lt;p&gt;Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden&lt;/p&gt;&lt;p&gt;Valentina Peona &amp; Aaron A. Vogan&lt;/p&gt;&lt;/li&gt;&lt;li&gt;&lt;p&gt;Department of Pathology, Tennis Court Road, Cambridge, CB1 2PQ, UK&lt;/p&gt;&lt;p&gt;Anna V. Protasio&lt;/p&gt;&lt;/li&gt;&lt;li&gt;&lt;p&gt;Christ’s College, St Andrews Street, Cambridge, CB2 3BU, UK&lt;/p&gt;&lt;p&gt;Anna V. Protasio&lt;/p&gt;&lt;/li&gt;&lt;/ol&gt;&lt;span&gt;Authors&lt;/span&gt;&lt;ol&gt;&lt;li&gt;&lt;span&gt;Clement Goubert&lt;/span&gt;View author publications&lt;p&gt;You can also search for this author in &lt;span&gt;PubMed&lt;span&gt; &lt;/span&gt;Google Scholar&lt;/span&gt;&lt;/p&gt;&lt;/li&gt;&lt;li&gt;&lt;span&gt;Rory J. Craig&lt;/span&gt;View author publications&lt;p&gt;You can also search for this author in &lt;span&gt;PubMed&lt;span&gt; &lt;/span&gt;Google Scholar&lt;/span&gt;&lt;/p&gt;&lt;/li&gt;&lt;li&gt;&lt;span&gt;Agustin F. Bilat&lt;/span&gt;View author publications&lt;p&gt;You can also search for this author in &lt;span&gt;PubMed&lt;span&gt; &lt;/span&gt;Google Scholar&lt;/span&gt;&lt;/p&gt;&lt;/li&gt;&lt;li&gt;&lt;span&gt;Valentina Peona&lt;/span&gt;View author publications&lt;p&gt;You can also search for this author in &lt;span&gt;PubMed&lt;span&gt; &lt;/span&gt;Google Scholar&lt;/span&gt;&lt;/p&gt;&lt;/li&gt;&lt;li&gt;&lt;span&gt;Aaron A. Vogan&lt;/span&gt;View author publications&lt;p&gt;You can also search for this author in &lt;span&gt;PubMed&lt;span&gt; &lt;/span&gt;Google Scholar&lt;/span&gt;&lt;/p&gt;&lt;/li&gt;&lt;li&gt;&lt;span&gt;Anna V. Protasio&lt;/span&gt;View author publications&lt;p&gt;You can also search for this author in &lt;span&gt;PubMed&lt;span&gt; &lt;/span&gt;Google Scholar&lt;/span&gt;&lt;/p&gt;&lt;/li&gt;&lt;/ol&gt;&lt;h3&gt;Corresponding author&lt;/h3&gt;&lt;p&gt;Correspondence to Anna V. Protasio.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Open Access&lt;/b&gt; This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons lic","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"124 1","pages":""},"PeriodicalIF":4.9,"publicationDate":"2022-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138518115","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}

{"title":"Software evaluation for de novo detection of transposons","authors":"Rodriguez, Matias, Makałowski, Wojciech","doi":"10.1186/s13100-022-00266-2","DOIUrl":"https://doi.org/10.1186/s13100-022-00266-2","url":null,"abstract":"Transposable elements (TEs) are major genomic components in most eukaryotic genomes and play an important role in genome evolution. However, despite their relevance the identification of TEs is not an easy task and a number of tools were developed to tackle this problem. To better understand how they perform, we tested several widely used tools for de novo TE detection and compared their performance on both simulated data and well curated genomic sequences. As expected, tools that build TE-models performed better than k-mer counting ones, with RepeatModeler beating competitors in most datasets. However, there is a tendency for most tools to identify TE-regions in a fragmented manner and it is also frequent that small TEs or fragmented TEs are not detected. Consequently, the identification of TEs is still a challenging endeavor and it requires a significant manual curation by an experienced expert. The results will be helpful for identifying common issues associated with TE-annotation and for evaluating how comparable are the results obtained with different tools.","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"177 1","pages":""},"PeriodicalIF":4.9,"publicationDate":"2022-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138518114","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}

{"title":"Subfamily-specific differential contribution of individual monomers and the tether sequence to mouse L1 promoter activity","authors":"Lingqi Kong, Karabi Saha, Yu-Chen Hu, Jada N. Tschetter, Chase E Habben, Leanne S. Whitmore, Chang-fu Yao, Xi A. Ge, Ping Ye, Simon J. Newkirk, Wenfeng An","doi":"10.1186/s13100-022-00269-z","DOIUrl":"https://doi.org/10.1186/s13100-022-00269-z","url":null,"abstract":"","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"13 1","pages":""},"PeriodicalIF":4.9,"publicationDate":"2022-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65814702","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}

{"title":"Characterization of transposable elements within the Bemisia tabaci species complex","authors":"Juan Paolo A. Sicat, Paul Visendi, Steven O. Sewe, S. Bouvaine, S. Seal","doi":"10.1186/s13100-022-00270-6","DOIUrl":"https://doi.org/10.1186/s13100-022-00270-6","url":null,"abstract":"","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"13 1","pages":""},"PeriodicalIF":4.9,"publicationDate":"2022-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65814761","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}