Mobile genetic elements最新文献_第7页

Integration of erm(B)-containing elements through large chromosome fragment exchange in Clostridium difficile. 艰难梭菌通过大染色体片段交换整合含erm(B)的元件。

Mobile genetic elements Pub Date : 2015-02-03 eCollection Date: 2015-01-01 DOI: 10.1080/2159256X.2015.1006111

François Wasels, Patrizia Spigaglia, Fabrizio Barbanti, Marc Monot, Laura Villa, Bruno Dupuy, Alessandra Carattoli, Paola Mastrantonio

引用次数: 6

Assembly and characterization of novel Alu inserts detected from next-generation sequencing data. 从下一代测序数据中检测到的新型Alu插入物的组装和表征。

Mobile genetic elements Pub Date : 2014-12-12 eCollection Date: 2014-10-01 DOI: 10.4161/21592543.2014.969584

Harun Mustafa, Matei David, Michael Brudno

引用次数: 2

Mining hidden polymorphic sequence motifs from divergent plant helitrons. 从不同的植物螺旋子中挖掘隐藏的多态序列基序。

Mobile genetic elements Pub Date : 2014-10-30 eCollection Date: 2014-10-01 DOI: 10.4161/21592543.2014.971635

Wenwei Xiong, Chunguang Du

{"title":"Mining hidden polymorphic sequence motifs from divergent plant helitrons.","authors":"Wenwei Xiong, Chunguang Du","doi":"10.4161/21592543.2014.971635","DOIUrl":"https://doi.org/10.4161/21592543.2014.971635","url":null,"abstract":"As a major driving force of genome evolution, transposons have been deviating from their original connotation as \"junk\" DNA ever since their important roles were revealed. The recently discovered Helitron transposons have been investigated in diverse eukaryotic genomes because of their remarkable gene-capture ability and other features that are crucial to our current understanding of genome dynamics. Helitrons are not canonical transposons in that they do not end in inverted repeats or create target site duplications, which makes them difficult to identify. Previous methods mainly rely on sequence alignment of conserved Helitron termini or manual curation. The abundance of Helitrons in genomes is still underestimated. We developed an automated and generalized tool, HelitronScanner, that identified a plethora of divergent Helitrons in many plant genomes. A local combinational variable approach as the key component of HelitronScanner offers a more granular representation of conserved nucleotide combinations and therefore is more sensitive in finding divergent Helitrons. This commentary provides an in-depth view of the local combinational variable approach and its association with Helitron sequence patterns. Analysis of Helitron terminal sequences shows that the local combinational variable approach is an efficacious representation of nucleotide patterns imperceptible at a full-sequence level.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"4 5","pages":"1-5"},"PeriodicalIF":0.0,"publicationDate":"2014-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/21592543.2014.971635","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34236996","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

An assay to monitor the activity of DNA transposition complexes yields a general quality control measure for transpositional recombination reactions. 一种监测 DNA 转座复合物活性的检测方法为转座重组反应提供了一种通用的质量控制措施。

Mobile genetic elements Pub Date : 2014-10-30 eCollection Date: 2014-10-01 DOI: 10.4161/21592543.2014.969576

Elsi Pulkkinen, Saija Haapa-Paananen, Harri Savilahti

{"title":"An assay to monitor the activity of DNA transposition complexes yields a general quality control measure for transpositional recombination reactions.","authors":"Elsi Pulkkinen, Saija Haapa-Paananen, Harri Savilahti","doi":"10.4161/21592543.2014.969576","DOIUrl":"10.4161/21592543.2014.969576","url":null,"abstract":"Transposon-based technologies have many applications in molecular biology and can be used for gene delivery into prokaryotic and eukaryotic cells. Common transpositional activity measurement assays suitable for many types of transposons would be beneficial, as diverse transposon systems could be compared for their performance attributes. Therefore, we developed a general-purpose assay to enable and standardize the activity measurement for DNA transposition complexes (transpososomes), using phage Mu transposition as a test platform. This assay quantifies transpositional recombination efficiency and is based on an in vitro transposition reaction with a target plasmid carrying a lethal ccdB gene. If transposition targets ccdB, this gene becomes inactivated, enabling plasmid-receiving Escherichia coli cells to survive and to be scored as colonies on selection plates. The assay was validated with 3 mini-Mu transposons varying in size and differing in their marker gene constitution. Tests with different amounts of transposon DNA provided a linear response and yielded a 10-fold operational range for the assay. The colony formation capacity was linearly correlated with the competence status of the E.coli cells, enabling normalization of experimental data obtained with different batches of recipient cells. The developed assay can now be used to directly compare transpososome activities with all types of mini-Mu transposons, regardless of their aimed use. Furthermore, the assay should be directly applicable to other transposition-based systems with a functional in vitro reaction, and it provides a dependable quality control measure that previously has been lacking but is highly important for the evaluation of current and emerging transposon-based applications.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"4 5","pages":"1-8"},"PeriodicalIF":0.0,"publicationDate":"2014-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/ef/88/kmge-04-05-969576.PMC4590003.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34236998","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Interspecific hybridization as a genomic stressor inducing mobilization of transposable elements in Drosophila. 种间杂交作为诱导果蝇转座因子动员的基因组应激源。

Mobile genetic elements Pub Date : 2014-08-08 eCollection Date: 2014-01-01 DOI: 10.4161/mge.34394

Maria Pilar García Guerreiro

{"title":"Interspecific hybridization as a genomic stressor inducing mobilization of transposable elements in Drosophila.","authors":"Maria Pilar García Guerreiro","doi":"10.4161/mge.34394","DOIUrl":"https://doi.org/10.4161/mge.34394","url":null,"abstract":"Transposable elements (TEs) are DNA sequences able to be mobilized in host genomes. They are currently recognized as the major mutation inducers because of their insertion in the target, their effect on neighboring regions, or their ectopic recombination. A large number of factors including chemical and physical factors as well as intraspecific crosses have traditionally been identified as inducers of transposition. Besides environmental factors, interspecific crosses have also been proposed as promoters of transposition of particular TEs in plants and different animals. Our previous published work includes a genome-wide survey with the set of genomic TEs and shows that interspecific hybridization between the species Drosophila buzzatii and Drosophila koepferae induces genomic instability by transposition bursts. A high percentage of this instability corresponds to TEs belonging to classes I and II. The detailed study of three TEs (Osvaldo, Helena, and Galileo), representative of the different TE families, shows an increase of transposition in hybrids compared with parental species, that varies depending on the element. This study suggests ample variation in TE regulation mechanisms and the question is why this variation occurs. Interspecific hybridization is a genomic stressor that disrupts the stability of TEs probably contributing to a relaxation of the mechanisms controlling TEs in the Drosophila genome. In this commentary paper we will discuss these results and the molecular mechanisms that could explain these increases of transposition rates observed in interspecific Drosophila hybrids.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"4 ","pages":"e34394"},"PeriodicalIF":0.0,"publicationDate":"2014-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/mge.34394","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32596530","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 20

SVA retrotransposons as modulators of gene expression. SVA反转录转座子作为基因表达的调节剂。

Mobile genetic elements Pub Date : 2014-07-24 eCollection Date: 2014-01-01 DOI: 10.4161/mge.32102

John P Quinn, Vivien J Bubb

{"title":"SVA retrotransposons as modulators of gene expression.","authors":"John P Quinn, Vivien J Bubb","doi":"10.4161/mge.32102","DOIUrl":"https://doi.org/10.4161/mge.32102","url":null,"abstract":"Endogenous mobile genetic elements can give rise to de novo germline or somatic mutations that can have dramatic consequences for genome regulation both local and possibly more globally based on the site of integration. However if we consider them as \"normal genetic\" components of the reference genome then they are likely to modify local chromatin structure which would have an effect on gene regulation irrelevant of their ability to further transpose. As such they can be treated as any other domain involved in a gene × environment interaction. Similarly their evolutionary appearance in the reference genome would supply a driver for species specific responses/traits. Our recent data would suggest the hominid specific subset of retrotransposons, SINE-VNTR-Alu (SVA), can function as transcriptional regulatory domains both in vivo and in vitro when analyzed in reporter gene constructs. Of particular interest in the SVA element, were the variable number tandem repeat (VNTR) domains which as their name suggests can be polymorphic. We and others have previously shown that VNTRs can be both differential regulators and biomarkers of disease based on the genotype of the repeat. Here, we provide an overview of why polymorphism in the SVA elements, in particular the VNTRs, could alter gene expression patterns that could be mechanistically associated with different traits in evolution or disease progression in humans.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"4 ","pages":"e32102"},"PeriodicalIF":0.0,"publicationDate":"2014-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/mge.32102","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32547112","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 25

Differential expression of a retrotransposable element, Rex6, in Colossoma macropomum fish from different Amazonian environments. 反转录转座子Rex6在不同亚马逊环境的大孔巨藻中的差异表达。

Mobile genetic elements Pub Date : 2014-07-21 eCollection Date: 2014-01-01 DOI: 10.4161/mge.30003

Cassiane Martins Barbosa, Edson Assunção Mareco, Maeli Dal Pai Silva, Cesar Martins, Fernanda Antunes Alves-Costa

{"title":"Differential expression of a retrotransposable element, Rex6, in Colossoma macropomum fish from different Amazonian environments.","authors":"Cassiane Martins Barbosa, Edson Assunção Mareco, Maeli Dal Pai Silva, Cesar Martins, Fernanda Antunes Alves-Costa","doi":"10.4161/mge.30003","DOIUrl":"10.4161/mge.30003","url":null,"abstract":"Transposable elements (TEs) are DNA sequences that have the ability to move and replicate within the genomes. TEs can be classified according to their intermediates of transposition, RNA (retrotransposons) or DNA. In some aquatic organisms, it has been observed that environmental factors such as pH, temperature and pollution may stimulate differential transcription and mobilization of retrotransposons. In light of this information, the present study sought to evaluate the expression of Rex6 TE transcripts in Colossoma macropomum, which is a very commercially exploited fish in Brazil. In order to establish a comparative analysis using real-time PCR, the samples were collected from Amazonian rivers with different physical and chemical characteristics (distinguished by clear water and black water). Quantitative RT-PCR analyses revealed a differential pattern of expression between tissues collected from different types of water (clear and black waters). When it came to the hepatic and muscle tissues sampled, the levels of Rex6 transcripts were significantly different between the two Amazonian water types. These results suggest that environmental conditions operate differently in the regulation of Rex6 transcription in C. macropomum, results which have implications in the reshaping of the genome against environmental variations.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"4 ","pages":"e30003"},"PeriodicalIF":0.0,"publicationDate":"2014-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/mge.30003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32556834","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 11

The Ellis Island Effect: A novel mobile element in a multi-drug resistant Bacteroides fragilis clinical isolate includes a mosaic of resistance genes from Gram-positive bacteria. 埃利斯岛效应:多重耐药脆弱拟杆菌临床分离物中的一种新的可移动元件包括来自革兰氏阳性细菌的耐药基因马赛克。

Mobile genetic elements Pub Date : 2014-07-14 eCollection Date: 2014-01-01 DOI: 10.4161/mge.29801

Fasahath Husain, Yaligara Veeranagouda, Renata Boente, Kevin Tang, Gabriela Mulato, Hannah M Wexler

{"title":"The Ellis Island Effect: A novel mobile element in a multi-drug resistant Bacteroides fragilis clinical isolate includes a mosaic of resistance genes from Gram-positive bacteria.","authors":"Fasahath Husain, Yaligara Veeranagouda, Renata Boente, Kevin Tang, Gabriela Mulato, Hannah M Wexler","doi":"10.4161/mge.29801","DOIUrl":"https://doi.org/10.4161/mge.29801","url":null,"abstract":"Objectives: Bacteroides fragilis, a Gram-negative anaerobic bacterium, is alternately a gut commensal or virulent pathogen and is an important reservoir for horizontal gene transfer (HGT) of bacterial resistance and virulence genes in the human gastrointestinal tract. We identified a unique conjugative transposon (CTn) in a multidrug resistant clinical isolate of B. fragilis (BF-HMW615); we named this element CTnHyb because it included a hybrid mosaic of foreign elements. This study reports the characterization of CTnHyb and discusses the potential impact on horizontal spread of resistance genes. Results: CTnHyb contains several efflux pump genes and several genes that confer or may confer antibiotic resistance to tetracycline, kanamycin, metronidazole and spectinomycin (truncated gene). CTnHyb also contains a mosaic of mobile elements from Gram-positive organisms. CTnHyb is easily transferred from BF-HMW615 (the original isolate) to BF638R (lab strain) and integrated into the BF638R chromosome. The \"foreign\" (from Gram-positive bacteria) nucleotide sequences within CTnHyb were > 99% preserved indicating that the gene acquisition from the Gram-positive bacteria was very recent. Conclusion: CTnHyb is a novel CTn residing in a multidrug resistant strain of B. fragilis. The global nature and wide phylogenetic reach of HGT means that any gene in any bacterium can potentially be mobilized. Understanding the mechanisms that drive the formation and transfer of these elements and, potentially, ways to limit the transfer are necessary to prevent a devastating spread of resistance elements.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"4 ","pages":"e29801"},"PeriodicalIF":0.0,"publicationDate":"2014-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/mge.29801","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32620112","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 11

Something new to explore: Plant viruses infecting and inducing gene silencing in filamentous fungi. 一些新的探索:植物病毒感染和诱导丝状真菌基因沉默。

Mobile genetic elements Pub Date : 2014-07-07 eCollection Date: 2014-01-01 DOI: 10.4161/mge.29782

Tiziana Mascia, Donato Gallitelli, Peter Palukaitis

{"title":"Something new to explore: Plant viruses infecting and inducing gene silencing in filamentous fungi.","authors":"Tiziana Mascia, Donato Gallitelli, Peter Palukaitis","doi":"10.4161/mge.29782","DOIUrl":"https://doi.org/10.4161/mge.29782","url":null,"abstract":"Functional genomics in plants has been facilitated greatly by the use of plant viruses to carry segments of host genes that can then promote the silencing of the RNAs expressed from the corresponding host genes; a process called virus-induced gene silencing (VIGS). The silencing of genes in filamentous fungi is either technically more problematic or labor-intensive, especially if transgenic plants need to be generated first. However, a recent paper from our team demonstrated that a plant virus could infect three related fungal species, as well as express a reporter gene ectopically, and also silence the correspondingly expressed reporter transgene. The gene expression and RNA silencing of the reporter gene was maintained for six passages in culture and also persisted in plants infected by the virus-infected fungus. Here, we consider how the virus can enter and migrate within the fungus, whether the virus can move back and forth between the fungus and the plant and the ramifications of this, the prospects for VIGS being used to silence fungal endogenes and possible biotechnological or therapeutic applications of using plant viruses for expressing foreign proteins in fungi or silencing fungal endogenes.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"4 ","pages":"e29782"},"PeriodicalIF":0.0,"publicationDate":"2014-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/mge.29782","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32530564","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Harnessing mobile genetic elements to explore gene regulation. 利用移动遗传元件探索基因调控。

Mobile genetic elements Pub Date : 2014-07-07 eCollection Date: 2014-01-01 DOI: 10.4161/mge.29759

Leighcraft A Shakes, Hope M Wolf, Derek C Norford, Delores J Grant, Pradeep K Chatterjee

{"title":"Harnessing mobile genetic elements to explore gene regulation.","authors":"Leighcraft A Shakes, Hope M Wolf, Derek C Norford, Delores J Grant, Pradeep K Chatterjee","doi":"10.4161/mge.29759","DOIUrl":"https://doi.org/10.4161/mge.29759","url":null,"abstract":"Sequences that regulate expression of a gene in cis but are located at large distances along the DNA from the gene, as found with most developmentally regulated genes in higher vertebrates, are difficult to identify if those sequences are not conserved across species. Mutating suspected gene-regulatory sequences to alter expression then becomes a hit-or-miss affair. The relaxed specificity of transposon insertions offers an opportunity to develop alternate strategies, to scan in an unbiased manner, pieces of chromosomal DNA cloned in BACs for transcription enhancing elements. This article illustrates how insertions of Tn10 with enhancer-traps into BAC DNA containing the gene, and its germ-line expression in zebrafish, have identified distal regulatory elements functionally. Transposition of Tn10 first introduces the enhancer-trap with a loxP site randomly into BAC DNA. Cre-recombination between the inserted loxP and the loxP endogenous to a BAC-end positions the enhancer-trap to the newly created truncated end of BAC DNA. The procedure generates a library of integration-ready enhancer-trap BACs with progressive truncations from an end in a single experiment. Individual enhancer-trap BACs from the library can be evaluated functionally in zebrafish or mice. Furthermore, the ability to readily alter sequences in a small transposon plasmid containing a regulatory domain of the gene allows re-introduction of altered parts of a BAC back into itself. It serves as a useful strategy to functionally dissect multiple discontinuous regulatory domains of a gene quickly. These methodologies have been successfully used in identifying novel regulatory domains of the Amyloid Precursor Protein (appb) gene in zebrafish, and provided important clues for regulation of the gene in humans.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"4 ","pages":"e29759"},"PeriodicalIF":0.0,"publicationDate":"2014-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/mge.29759","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32527924","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2