Mobile DNA最新文献

{"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":"<p>\u0000<b>Correction to: Mobile DNA 13, 7 (2022)</b>\u0000</p><p>\u0000<b>https://doi.org/10.1186/s13100-021-00259-7</b>\u0000</p><p>Following the publication of the original article [1] the author reported that Additional files 3, 4 and 5 in the published article are corrupted.</p><p>The original article [1] has been updated.</p><ol><li data-counter=\"1.\"><p>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.</p><p>Article PubMed PubMed Central Google Scholar </p></li></ol><p>Download references<svg aria-hidden=\"true\" focusable=\"false\" height=\"16\" role=\"img\" width=\"16\"><use xlink:href=\"#global-icon-download\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"></use></svg></p><h3>Affiliations</h3><ol><li><p>Canadian Center for Computational Genomics, McGill University, Montreal, Québec, Canada</p><p>Clement Goubert</p></li><li><p>Department of Human Genetics, McGill University, Montreal, Québec, Canada</p><p>Clement Goubert</p></li><li><p>Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK</p><p>Rory J. Craig</p></li><li><p>Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay</p><p>Agustin F. Bilat</p></li><li><p>Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden</p><p>Valentina Peona & Aaron A. Vogan</p></li><li><p>Department of Pathology, Tennis Court Road, Cambridge, CB1 2PQ, UK</p><p>Anna V. Protasio</p></li><li><p>Christ’s College, St Andrews Street, Cambridge, CB2 3BU, UK</p><p>Anna V. Protasio</p></li></ol><span>Authors</span><ol><li><span>Clement Goubert</span>View author publications<p>You can also search for this author in <span>PubMed<span> </span>Google Scholar</span></p></li><li><span>Rory J. Craig</span>View author publications<p>You can also search for this author in <span>PubMed<span> </span>Google Scholar</span></p></li><li><span>Agustin F. Bilat</span>View author publications<p>You can also search for this author in <span>PubMed<span> </span>Google Scholar</span></p></li><li><span>Valentina Peona</span>View author publications<p>You can also search for this author in <span>PubMed<span> </span>Google Scholar</span></p></li><li><span>Aaron A. Vogan</span>View author publications<p>You can also search for this author in <span>PubMed<span> </span>Google Scholar</span></p></li><li><span>Anna V. Protasio</span>View author publications<p>You can also search for this author in <span>PubMed<span> </span>Google Scholar</span></p></li></ol><h3>Corresponding author</h3><p>Correspondence to Anna V. Protasio.</p><p><b>Open Access</b> 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}

{"title":"Transcriptional dynamics of transposable elements in the type I IFN response in Myotis lucifugus cells","authors":"G. M. Pasquesi, Conor J. Kelly, Andrea D. Ordonez, E. Chuong","doi":"10.1101/2022.04.18.488675","DOIUrl":"https://doi.org/10.1101/2022.04.18.488675","url":null,"abstract":"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.","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":" ","pages":""},"PeriodicalIF":4.9,"publicationDate":"2022-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47153365","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":"RNA sensor MDA5 suppresses LINE-1 retrotransposition by regulating the promoter activity of LINE-1 5′-UTR","authors":"Yan, Jiaxiu, Zhao, Yifei, Du, Juan, Wang, Yu, Wang, Shaohua, Wang, Qing, Zhao, Xu, Xu, Wei, Zhao, Ke","doi":"10.1186/s13100-022-00268-0","DOIUrl":"https://doi.org/10.1186/s13100-022-00268-0","url":null,"abstract":"Type 1 long interspersed elements, or LINE-1, are the only retroelements that replicate autonomously in human cells. The retrotransposition process of LINE-1 can trigger the activation of the innate immune system and has been proposed to play a role in the development of several autoimmune diseases, including Aicardi-Goutières syndrome (AGS). In contrast, all known AGS-associated proteins, except MDA5, have been reported to affect LINE-1 activity. Thus, MDA5 is likely to also function as a LINE-1 suppressor. MDA5 was found to potently suppress LINE-1 activity in a reporter-based LINE-1 retrotransposition assay. Although MDA5 is an endogenous RNA sensor able to activate the innate immune system, increased interferon (IFN) expression only contributed in part to MDA5-mediated LINE-1 suppression. Instead, MDA5 potently regulated the promoter activity of LINE-1 5′-UTR, as confirmed by transiently expressed myc-tagged MDA5 or knockdown of endogenous MDA5 expression. Consequently, MDA5 effectively reduced the generation of LINE-1 RNA and the subsequent expression of LINE-1 ORF1p and ORF2p. Interestingly, despite MDA5 being a multi-domain protein, the N-terminal 2CARD domain alone is sufficient to interact with LINE-1 5′-UTR and inhibit LINE-1 promoter activity. Our data reveal that MDA5 functions as a promoter regulator; it directly binds to the LINE-1 5′-UTR and suppresses its promoter activity. Consequently, MDA5 reduces LINE-1 RNA and protein levels, and ultimately inhibits LINE-1 retrotransposition. In contrast, MDA5-induced IFN expression only plays a mild role in MDA5-mediated LINE-1 suppression. In addition, the N-terminal 2CARD domain was found to be a functional region for MDA5 upon inhibition of LINE-1 replication. Thus, our data suggest that besides being an initiator of the innate immune system, MDA5 is also an effector against LINE-1 activity, potentially forming a feedback loop by suppressing LINE-1-induced innate immune activation.","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"19 1","pages":""},"PeriodicalIF":4.9,"publicationDate":"2022-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138518130","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":"TE Density: a tool to investigate the biology of transposable elements","authors":"Scott J Teresi, Michael B. Teresi, P. Edger","doi":"10.1186/s13100-022-00264-4","DOIUrl":"https://doi.org/10.1186/s13100-022-00264-4","url":null,"abstract":"","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"13 1","pages":""},"PeriodicalIF":4.9,"publicationDate":"2022-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65814689","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":"SETMAR, a case of primate co-opted genes: towards new perspectives","authors":"Lié, Oriane, Renault, Sylvaine, Augé-Gouillou, Corinne","doi":"10.1186/s13100-022-00267-1","DOIUrl":"https://doi.org/10.1186/s13100-022-00267-1","url":null,"abstract":"We carry out a review of the history and biological activities of one domesticated gene in higher primates, SETMAR, by discussing current controversies. Our purpose is to open a new outlook that will serve as a framework for future work about SETMAR, possibly in the field of cognition development. What is newly important about SETMAR can be summarized as follows: (1) the whole protein sequence is under strong purifying pressure; (2) its role is to strengthen existing biological functions rather than to provide new ones; (3) it displays a tissue-specific pattern of expression, at least for the alternative-splicing it undergoes. Studies reported here demonstrate that SETMAR protein(s) may be involved in essential networks regulating replication, transcription and translation. Moreover, during embryogenesis, SETMAR appears to contribute to brain development. Our review underlines for the first time that SETMAR directly interacts with genes involved in brain functions related to vocalization and vocal learning. These findings pave the way for future works regarding SETMAR and the development of cognitive abilities in higher primates.","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"14 1","pages":"9"},"PeriodicalIF":4.9,"publicationDate":"2022-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138518121","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":"The structural diversity of CACTA transposons in genomes of Chenopodium (Amaranthaceae, Caryophyllales) species: specific traits and comparison with the similar elements of angiosperms","authors":"Belyayev, Alexander, Josefiová, Jiřina, Jandová, Michaela, Kalendar, Ruslan, Mahelka, Václav, Mandák, Bohumil, Krak, Karol","doi":"10.1186/s13100-022-00265-3","DOIUrl":"https://doi.org/10.1186/s13100-022-00265-3","url":null,"abstract":"CACTA transposable elements (TEs) comprise one of the most abundant superfamilies of Class 2 (cut-and-paste) transposons. Over recent decades, CACTA elements were widely identified in species from the plant, fungi, and animal kingdoms, but sufficiently studied in the genomes of only a few model species although non-model genomes can bring additional and valuable information. It primarily concerned the genomes of species belonging to clades in the base of large taxonomic groups whose genomes, to a certain extent, can preserve relict and/or possesses specific traits. Thus, we sought to investigate the genomes of Chenopodium (Amaranthaceae, Caryophyllales) species to unravel the structural variability of CACTA elements. Caryophyllales is a separate branch of Angiosperms and until recently the diversity of CACTA elements in this clade was unknown. Application of the short-read genome assembly algorithm followed by analysis of detected complete CACTA elements allowed for the determination of their structural diversity in the genomes of 22 Chenopodium album aggregate species. This approach yielded knowledge regarding: (i) the coexistence of two CACTA transposons subtypes in single genome; (ii) gaining of additional protein conserved domains within the coding sequence; (iii) the presence of captured gene fragments, including key genes for flower development; and (iv)) identification of captured satDNA arrays. Wide comparative database analysis revealed that identified events are scattered through Angiosperms in different proportions. Our study demonstrated that while preserving the basic element structure a wide range of coding and non-coding additions to CACTA transposons occur in the genomes of C. album aggregate species. Ability to relocate additions inside genome in combination with the proposed novel functional features of structural-different CACTA elements can impact evolutionary trajectory of the host genome.","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"177 1","pages":""},"PeriodicalIF":4.9,"publicationDate":"2022-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138518123","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":"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/s13100-021-00259-7","DOIUrl":"https://doi.org/10.1186/s13100-021-00259-7","url":null,"abstract":"In the study of transposable elements (TEs), the generation of a high confidence set of consensus sequences that represent the diversity of TEs found in a given genome is a key step in the path to investigate these fascinating genomic elements. Many algorithms and pipelines are available to automatically identify putative TE families present in a genome. Despite the availability of these valuable resources, producing a library of high-quality full-length TE consensus sequences largely remains a process of manual curation. This know-how is often passed on from mentor-to-mentee within research groups, making it difficult for those outside the field to access this highly specialised skill. Our manuscript attempts to fill this gap by providing a set of detailed computer protocols, software recommendations and video tutorials for those aiming to manually curate TEs. Detailed step-by-step protocols, aimed at the complete beginner, are presented in the Supplementary Methods. The proposed set of programs and tools presented here will make the process of manual curation achievable and amenable to all researchers and in special to those new to the field of TEs.","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"14 1","pages":""},"PeriodicalIF":4.9,"publicationDate":"2022-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138518131","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}