Mobile genetic elements最新文献_第5页

Silencing quorum sensing and ICE mobility through antiactivation and ribosomal frameshifting 通过抗活化和核糖体移框沉默群体感应和ICE迁移

Mobile genetic elements Pub Date : 2015-10-20 DOI: 10.1080/2159256X.2015.1107177

J. Ramsay, C. Ronson

{"title":"Silencing quorum sensing and ICE mobility through antiactivation and ribosomal frameshifting","authors":"J. Ramsay, C. Ronson","doi":"10.1080/2159256X.2015.1107177","DOIUrl":"https://doi.org/10.1080/2159256X.2015.1107177","url":null,"abstract":"Mobile genetic elements run an evolutionary gauntlet to maintain their mobility in the face of selection against their selfish dissemination but, paradoxically, they can accelerate the adaptability of bacteria through the gene-transfer events that they facilitate. These temporally conflicting evolutionary forces have shaped exquisite regulation systems that silence mobility and maximize the competitive fitness of the host bacterium, but maintain the ability of the element to deliver itself to a new host should the opportunity arise. Here we review the excision regulation system of the Mesorhizobium loti symbiosis island ICEMlSymR7A, a 502-kb integrative and conjugative element (ICE) capable of converting non-symbiotic mesorhizobia into plant symbionts. ICEMlSymR7A excision is activated by quorum sensing, however, both quorum sensing and excision are strongly repressed in the vast majority of cells by dual-target antiactivation and programmed ribosomal-frameshifting mechanisms. We examine these recently discovered regulatory features under the light of natural selection and discuss common themes that can be drawn from recent developments in ICE biology.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"5 1","pages":"103 - 108"},"PeriodicalIF":0.0,"publicationDate":"2015-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/2159256X.2015.1107177","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60153715","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 8

Selective repression of SINE transcription by RNA polymerase III RNA聚合酶III选择性抑制SINE转录

Mobile genetic elements Pub Date : 2015-09-23 DOI: 10.1080/2159256X.2015.1096997

D. Varshney, Jana Vavrova-Anderson, Andrew J. Oler, B. Cairns, Robert J White

{"title":"Selective repression of SINE transcription by RNA polymerase III","authors":"D. Varshney, Jana Vavrova-Anderson, Andrew J. Oler, B. Cairns, Robert J White","doi":"10.1080/2159256X.2015.1096997","DOIUrl":"https://doi.org/10.1080/2159256X.2015.1096997","url":null,"abstract":"A million copies of the Alu short interspersed nuclear element (SINE) are scattered throughout the human genome, providing ∼11% of our total DNA. SINEs spread by retrotransposition, using a transcript generated by RNA polymerase (pol) III from an internal promoter. Levels of these pol III-dependent Alu transcripts are far lower than might be expected from the abundance of the template. This was believed to reflect transcriptional suppression through DNA methylation, denying pol III access to most SINEs through chromatin-mediated effects. Contrary to expectations, our recent study found no evidence that methylation of SINE DNA reduces its occupancy or expression by pol III. However, histone H3 associated with SINEs is prominently methylated on lysine 9, a mark that correlates with transcriptional silencing. The SUV39 methyltransferases that deposit this mark can be found at many SINEs. Furthermore, a selective inhibitor of SUV39 stimulates pol III recruitment to these loci, as well as SINE expression. These data suggest that methylation of histone H3 rather than DNA may mediate repression of SINE transcription by pol III, at least under the conditions we studied.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"5 1","pages":"86 - 91"},"PeriodicalIF":0.0,"publicationDate":"2015-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/2159256X.2015.1096997","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60153398","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

The peculiarities of piRNA expression upon heat shock exposure in Drosophila melanogaster 黑腹果蝇热休克时piRNA表达的特点

Mobile genetic elements Pub Date : 2015-09-03 DOI: 10.1080/2159256X.2015.1086502

S. Funikov, Sergei Ryazansky, E. Zelentsova, V. Popenko, O. Leonova, D. Garbuz, M. Evgen’ev, O. Zatsepina

{"title":"The peculiarities of piRNA expression upon heat shock exposure in Drosophila melanogaster","authors":"S. Funikov, Sergei Ryazansky, E. Zelentsova, V. Popenko, O. Leonova, D. Garbuz, M. Evgen’ev, O. Zatsepina","doi":"10.1080/2159256X.2015.1086502","DOIUrl":"https://doi.org/10.1080/2159256X.2015.1086502","url":null,"abstract":"Different types of stress including heat shock may induce genomic instability, due to the derepression and amplification of mobile elements (MEs). It remains unclear, however, whether piRNA-machinery regulating ME expression functions normally under stressful conditions. The aim of this study was to explore the features of piRNA expression after heat shock (HS) exposure in Drosophila melanogaster. We also evaluated functioning of piRNA-machinery in the absence of major stress protein Hsp70 in this species. We analyzed the deep sequence data of piRNA expression after HS treatment and demonstrated that it modulates the expression of certain double-stranded germinal piRNA-clusters. Notable, we demonstrated significant changes in piRNA levels targeting a group of MEs after HS only in the strain containing normal set of hsp70 genes. Surprisingly, we failed to detect any correlation between the levels of piRNAs and the transcription of complementary MEs in the studied strains. We propose that modulation of certain piRNA-clusters expression upon HS exposure in D. melanogaster occurs due to HS-induced altering of chromatin state at certain chromosome regions.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"5 1","pages":"72 - 80"},"PeriodicalIF":0.0,"publicationDate":"2015-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/2159256X.2015.1086502","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60153611","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

Composite non-LTR retrotransposons in hominoid primates 类人猿灵长类的复合非ltr反转录转座子

Mobile genetic elements Pub Date : 2015-07-24 DOI: 10.1080/2159256X.2015.1068906

A. Damert

{"title":"Composite non-LTR retrotransposons in hominoid primates","authors":"A. Damert","doi":"10.1080/2159256X.2015.1068906","DOIUrl":"https://doi.org/10.1080/2159256X.2015.1068906","url":null,"abstract":"Composite retrotransposons are widely distributed in the plant and animal kingdoms. Some of the most complex of these are found in hominoid primates. SVA, LAVA, PVA and FVA combine simple repeats, Alu fragments, a VNTR (Variable Number of Tandem Repeats) and variable 3′ domains, which are, except for PVA, derived from other retrotransposons. Although a likely precursor of SVA–a “tailed VNTR” named SVA2–had been identified in the Rhesus genome, the exact sequence and mechanism of the assembly of this type of composite retrotransposon had been elusive. The discovery of LAVA, PVA and FVA in gibbons provided the opportunity to delineate the order of assembly of the components of VNTR-containing retrotransposons. Our recent analysis suggests that an extinct “Alu-SVA2” acquired variant 3′ ends by splicing. In this commentary I will discuss the mode of assembly of VNTR composites in the context of their capacity to engage in alternative splicing to co-mobilize host RNA sequences and to become exonized. The second part will focus on structural determinants of VNTR composite retrotransposon mobilization in the context of lineage-specific expansion of particular families/subfamilies of these elements.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"5 1","pages":"67 - 71"},"PeriodicalIF":0.0,"publicationDate":"2015-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/2159256X.2015.1068906","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60153486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Transposable elements and small RNAs: Genomic fuel for species diversity 转座因子和小rna:物种多样性的基因组燃料

Mobile genetic elements Pub Date : 2015-07-24 DOI: 10.1080/2159256X.2015.1066919

F. Hoffmann, L. McGuire, B. Counterman, D. Ray

引用次数: 8

Comparison of methods for the determination of the transposition rate of mobile elements. 可移动元素转位率测定方法的比较。

Mobile genetic elements Pub Date : 2015-05-29 eCollection Date: 2015-07-01 DOI: 10.1080/2159256X.2015.1052895

Lyudmila P Zakharenko

引用次数: 0

Get the jump - Do 3'UTRs protect transposable elements from silencing? Get the jump - 3' utr是否保护转座因子免于沉默?

Mobile genetic elements Pub Date : 2015-05-27 eCollection Date: 2015-07-01 DOI: 10.1080/2159256X.2015.1052179

Tina Kabelitz, Isabel Bäurle

引用次数: 3

The coelacanth: Can a "living fossil" have active transposable elements in its genome? 腔棘鱼:“活化石”的基因组中有活性转座因子吗?

Mobile genetic elements Pub Date : 2015-05-27 eCollection Date: 2015-07-01 DOI: 10.1080/2159256X.2015.1052184

Magali Naville, Domitille Chalopin, Didier Casane, Patrick Laurenti, Jean-Nicolas Volff

{"title":"The coelacanth: Can a \"living fossil\" have active transposable elements in its genome?","authors":"Magali Naville, Domitille Chalopin, Didier Casane, Patrick Laurenti, Jean-Nicolas Volff","doi":"10.1080/2159256X.2015.1052184","DOIUrl":"https://doi.org/10.1080/2159256X.2015.1052184","url":null,"abstract":"The coelacanth has long been regarded as a \"living fossil,\" with extant specimens looking very similar to fossils dating back to the Cretaceous period. The hypothesis of a slowly or even not evolving genome has been proposed to account for this apparent morphological stasis. While this assumption seems to be sustained by different evolutionary analyses on protein-coding genes, recent studies on transposable elements have provided more conflicting results. Indeed, the coelacanth genome contains many transposable elements and has been shaped by several major bursts of transposition during evolution. In addition, comparison of orthologous genomic regions from the genomes of the 2 extant coelacanth species L. chalumnae and L. menadoensis revealed multiple species-specific insertions, indicating transposable element recent activity and contribution to post-speciation genome divergence. These observations, which do not support the genome stasis hypothesis, challenge either the impact of transposable elements on organismal evolution or the status of the coelacanth as a \"living fossil.\" Closer inspection of fossil and molecular data indicate that, even if coelacanths might evolve more slowly than some other lineages due to demographic and/or ecological factors, this variation is still in the range of a \"non-fossil\" vertebrate species.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"5 4","pages":"55-59"},"PeriodicalIF":0.0,"publicationDate":"2015-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/2159256X.2015.1052184","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34066287","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: 8

Evaluating the effect of horizontal transmission on the stability of plasmids under different selection regimes. 评价不同选择制度下水平传播对质粒稳定性的影响。

Mobile genetic elements Pub Date : 2015-05-21 eCollection Date: 2015-05-01 DOI: 10.1080/2159256X.2015.1045115

Rafael Peña-Miller, Rogelio Rodríguez-González, R Craig MacLean, Alvaro San Millan

{"title":"Evaluating the effect of horizontal transmission on the stability of plasmids under different selection regimes.","authors":"Rafael Peña-Miller, Rogelio Rodríguez-González, R Craig MacLean, Alvaro San Millan","doi":"10.1080/2159256X.2015.1045115","DOIUrl":"https://doi.org/10.1080/2159256X.2015.1045115","url":null,"abstract":"In theory, plasmids can only be maintained in a population when the rate of horizontal gene transfer is larger than the combined effect of segregational loss and the decrease of fitness associated with plasmid carriage. Recent advances in genome sequencing have shown, however, that a large fraction of plasmids do not carry the genes necessary for conjugation or mobilization. So, how are so-called non-transmissible plasmids able to persist? In order to address this question, we examined a previously published evolutionary model based on the interaction between P. aeruginosa and the non-transmissible plasmid pNUK73. Both our in silico and in vitro results demonstrated that, although compensatory adaptation can decrease the rate of plasmid decay, the conditions for the maintenance of a non-transmissible plasmid are very stringent if the genes it carries are not beneficial to the bacterial host. This result suggests that apparently non-transmissible plasmids may still experience episodes of horizontal gene transfer occurring at very low frequencies, and that these scattered transmission events are sufficient to stabilize these plasmids. We conclude by discussing different genomic and microbiological approaches that could allow for the detection of these rare transmission events and thus to obtain a reliable estimate of the rate of horizontal gene transfer.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"5 3","pages":"1-5"},"PeriodicalIF":0.0,"publicationDate":"2015-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/2159256X.2015.1045115","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34134149","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: 19

Repetitive elements regulate circular RNA biogenesis. 重复元件调节环状RNA的生物发生。

Mobile genetic elements Pub Date : 2015-05-21 eCollection Date: 2015-05-01 DOI: 10.1080/2159256X.2015.1045682

Jeremy E Wilusz

{"title":"Repetitive elements regulate circular RNA biogenesis.","authors":"Jeremy E Wilusz","doi":"10.1080/2159256X.2015.1045682","DOIUrl":"https://doi.org/10.1080/2159256X.2015.1045682","url":null,"abstract":"It was long assumed that eukaryotic precursor mRNAs (pre-mRNAs) are almost always spliced to generate a linear mRNA that is subsequently translated to produce a protein. However, it is now clear that thousands of protein-coding genes can be non-canonically spliced to produce circular noncoding RNAs, some of which are expressed at much higher levels than their associated linear mRNAs. How then does the splicing machinery decide whether to generate a linear mRNA or a circular RNA? Recent work has revealed that intronic repetitive elements, including sequences derived from transposons, are critical regulators of this decision. In most cases, circular RNA biogenesis appears to be initiated when complementary sequences from 2 different introns base pair to one another. This brings the splice sites from the intervening exon(s) into close proximity and facilitates the backsplicing event that generates the circular RNA. As many pre-mRNAs contain multiple intronic repeats, distinct circular transcripts can be produced depending on which repeats base pair to one another. Intronic repeats are thus critical regulatory sequences that control the functional output of their host genes, and potentially cause the functions of protein-coding genes to be highly divergent across species.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"5 3","pages":"1-7"},"PeriodicalIF":0.0,"publicationDate":"2015-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/2159256X.2015.1045682","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34134150","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: 61