Mobile genetic elements最新文献_第9页

Insertion sequence distribution bias in Archaea. 古细菌的插入序列分布偏倚。

Mobile genetic elements Pub Date : 2014-01-01 Epub Date: 2014-01-13 DOI: 10.4161/mge.27829

Morgan C Florek, Daniel P Gilbert, Gordon R Plague

{"title":"Insertion sequence distribution bias in Archaea.","authors":"Morgan C Florek, Daniel P Gilbert, Gordon R Plague","doi":"10.4161/mge.27829","DOIUrl":"https://doi.org/10.4161/mge.27829","url":null,"abstract":"Insertion sequences (IS) are common transposable elements in Archaea. Intergenic IS elements are usually less harmful than intragenic ISs, simply because they are less likely to disrupt host gene function. However, because regulatory sequences are intergenic and upstream of genes, we hypothesized that not all intergenic regions are selectively equivalent for IS insertion. We tested this hypothesis by analyzing the distributions of intergenic IS elements within 155 fully sequenced archaeal genomes. Of the 22 genomes with enough IS elements for statistical analysis, five have significantly fewer ISs between divergently oriented neighboring genes than expected by chance, and seven have significantly more ISs between convergently oriented genes. Furthermore, of the 85 genomes with at least one expected IS within each of the three possible neighboring gene orientations (i.e., divergent, convergent, and tandem), 73 genomes have fewer ISs between divergently oriented genes than expected, and 60 have more ISs between convergently oriented genes than expected (both values deviate significantly from binomial probabilities of random distribution). We suspect that these non-random IS distributions are molded by natural selection resulting from differential disruption of neighboring gene regulation, and that this selective pressure has affected transposable element distributions in prokaryotes for billions of years.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"4 1","pages":"e27829"},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/mge.27829","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32146668","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: 5

Does ectopic cell death cause somatic mutations in the neighboring cells by activating transposons? 异位细胞死亡是否通过激活转座子引起邻近细胞的体细胞突变?

Mobile genetic elements Pub Date : 2014-01-01 Epub Date: 2014-01-29 DOI: 10.4161/mge.28040

James A Birchler

引用次数: 0

L1 retrotransposition: The snap-velcro model and its consequences. L1逆行移位：卡扣-魔术贴模型及其后果。

Mobile genetic elements Pub Date : 2014-01-01 Epub Date: 2014-04-23 DOI: 10.4161/mge.28907

Sébastien Viollet, Clément Monot, Gaël Cristofari

引用次数: 0

Quadruplex-forming DNA sequences spread by retrotransposons may serve as genome regulators. 由反转录转座子传播的四重体形成的DNA序列可作为基因组调控因子。

Mobile genetic elements Pub Date : 2014-01-01 Epub Date: 2014-02-04 DOI: 10.4161/mge.28084

Eduard Kejnovsky, Matej Lexa

{"title":"Quadruplex-forming DNA sequences spread by retrotransposons may serve as genome regulators.","authors":"Eduard Kejnovsky, Matej Lexa","doi":"10.4161/mge.28084","DOIUrl":"https://doi.org/10.4161/mge.28084","url":null,"abstract":"Transposable elements (TEs) are ubiquitous genome inhabitants in eukaryotes. Increasing evidence shows that TEs are involved in regulatory networks of eukaryotic cells and contribute to genome evolution. Recently, we reported that many plant long-terminal repeat (LTR) retrotransposons contain DNA quadruplex-forming sequences at precise positions inside their LTRs and that quadruplexes are better preserved in evolutionary younger elements. As quadruplexes can modulate molecular processes, quadruplexes found at specific distances upstream and downstream from the endogenous TE promoter can affect transcription of the element. Moreover, quadruplexes found in solo LTRs, as well as in 3' ends of 5'-truncated copies of LINE-1 elements, can affect expression of neighboring genes. Here, we propose that this way retrotransposons can serve as vehicles for spread of DNA quadruplexes. Quadruplexes can thus fulfill a dual regulatory role-to influence both the retrotransposons carrying them and the neighboring host genes, e.g., by direct effect on transcription or by modifying the local chromatin state. Additionally, four-stranded DNA structures may serve as hotspots for recombination-based genome rearrangements.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":" ","pages":"e28084"},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/mge.28084","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40300447","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: 21

Analysis of horizontal genetic transfer in red algae in the post-genomics age. 后基因组时代红藻水平遗传转移分析。

Mobile genetic elements Pub Date : 2013-11-01 Epub Date: 2014-01-02 DOI: 10.4161/mge.27669

Cheong Xin Chan, Debashish Bhattacharya

引用次数: 8

Chromosome mapping of retrotransposable elements Rex1 and Rex3 in Leporinus Spix, 1829 species (Characiformes: Anostomidae) and its relationships among heterochromatic segments and W sex chromosome. Leporinus Spix, 1829种(特征:Anostomidae)逆转录转座因子Rex1和Rex3的染色体定位及其异色片段与W性染色体的关系

Mobile genetic elements Pub Date : 2013-11-01 Epub Date: 2013-12-10 DOI: 10.4161/mge.27460

Rafael Splendore de Borba, Edson Lourenço da Silva, Patrícia Pasquali Parise-Maltempi

{"title":"Chromosome mapping of retrotransposable elements Rex1 and Rex3 in Leporinus Spix, 1829 species (Characiformes: Anostomidae) and its relationships among heterochromatic segments and W sex chromosome.","authors":"Rafael Splendore de Borba, Edson Lourenço da Silva, Patrícia Pasquali Parise-Maltempi","doi":"10.4161/mge.27460","DOIUrl":"https://doi.org/10.4161/mge.27460","url":null,"abstract":"The family Anostomidae is an interesting model for studies of repetitive elements, mainly because of the presence of high numbers of heterochromatic segments related to a peculiar system of female heterogamety, which is restricted to a few species of Leporinus genus. Thus, cytogenetic mapping of the retrotransposable elements Rex1, Rex3, and Rex6 was performed in six Leporinus species, to elucidate the genomic organization of this genus. The sequencing of the Rex1 and Rex3 elements detected different base pair compositions in these elements among species, whereas the Rex6 element was not identified in the genomes of these species. FISH analysis using Rex1 detected different distribution patterns, L. elongatus, L. macrocephalus, and L. obtusidens had clusters in the terminal regions, whereas the signals were dispersed throughout all of the chromosomes with some signals in the terminal position in other species. The Rex3 signals were found mainly in the terminal positions in all the chromosomes of all species. The W chromosomes of L. elongatus, L. macrocephalus, and L. obtusidens contained the Rex1 and Rex3 signal in an interstitial position. These results suggest the emergence of different activity levels for these elements during the evolution of the species analyzed. Despite the conserved karyotype macrostructure species Leporinus often discussed, our results show some variation in hybridization patterns, particularly between the species with specific patterns in their sex chromosomes and species without this differentiated system.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"3 6","pages":"e27460"},"PeriodicalIF":0.0,"publicationDate":"2013-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/mge.27460","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32013376","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: 24

Lost in translation: The biogenesis of non-LTR retrotransposon proteins. 在翻译中丢失:非ltr反转录转座子蛋白的生物发生。

Mobile genetic elements Pub Date : 2013-11-01 Epub Date: 2013-12-13 DOI: 10.4161/mge.27525

Garry A Luke, Claire Roulston, Valerie Odon, Pablo de Felipe, Andriy Sukhodub, Martin D Ryan

{"title":"Lost in translation: The biogenesis of non-LTR retrotransposon proteins.","authors":"Garry A Luke, Claire Roulston, Valerie Odon, Pablo de Felipe, Andriy Sukhodub, Martin D Ryan","doi":"10.4161/mge.27525","DOIUrl":"https://doi.org/10.4161/mge.27525","url":null,"abstract":"\"Young\" APE-type non-LTR retrotransposons (non-LTRs) typically encode two open reading frames (ORFs 1 and 2). The shorter ORF1 translation product (ORF1p) comprises an RNA binding activity, thought to bind to non-LTR transcript RNA, protect against nuclease degradation and specify nuclear import of the ribonuclear protein complex (RNP). ORF2 encodes a multifunctional protein (ORF2p) comprising apurinic/apyrimidinic endonuclease (APE) and reverse-transcriptase (RT) activities, responsible for genome replication and re-integration into chromosomal DNA. However, some clades of APE-type non-LTRs only encode a single ORF-corresponding to the multifunctional ORF2p outlined above (and for simplicity referred-to as ORF2 below). The absence of an ORF1 correlates with the acquisition of a 2A oligopeptide translational recoding element (some 18-30 amino acids) into the N-terminal region of ORF2p. In the case of non-LTRs encoding two ORFs, the presence of ORF1 would necessarily downregulate the translation of ORF2. We argue that in the absence of an ORF1, 2A could provide the corresponding translational downregulation of ORF2. While multiple molecules of ORF1p are required to decorate the non-LTR transcript RNA in the cytoplasm, conceivably only a single molecule of ORF2p is required for target-primed reverse transcription/integration in the nucleus. Why would the translation of ORF2 need to be controlled by such mechanisms? An \"excess\" of ORF2p could result in disadvantageous levels of genome instability by, for example, enhancing short, interspersed, element (SINE) retrotransposition and the generation of processed pseudogenes. If so, the acquisition of mechanisms-such as 2A-to control ORF2p biogenesis would be advantageous.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"3 6","pages":"e27525"},"PeriodicalIF":0.0,"publicationDate":"2013-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/mge.27525","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32072100","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: 6

Continuing analysis of microRNA origins: Formation from transposable element insertions and noncoding RNA mutations. microRNA起源的持续分析:转座元件插入和非编码RNA突变的形成。

Mobile genetic elements Pub Date : 2013-11-01 Epub Date: 2014-01-10 DOI: 10.4161/mge.27755

Justin T Roberts, Elvera A Cooper, Connor J Favreau, Jacob S Howell, Lee G Lane, James E Mills, Derrick C Newman, Tabitha J Perry, Meaghan E Russell, Brittany M Wallace, Glen M Borchert

{"title":"Continuing analysis of microRNA origins: Formation from transposable element insertions and noncoding RNA mutations.","authors":"Justin T Roberts, Elvera A Cooper, Connor J Favreau, Jacob S Howell, Lee G Lane, James E Mills, Derrick C Newman, Tabitha J Perry, Meaghan E Russell, Brittany M Wallace, Glen M Borchert","doi":"10.4161/mge.27755","DOIUrl":"https://doi.org/10.4161/mge.27755","url":null,"abstract":"MicroRNAs (miRs) are small noncoding RNAs that typically act as regulators of gene expression by base pairing with the 3' UTR of messenger RNAs (mRNAs) and either repressing their translation or initiating degradation. As of this writing over 24,500 distinct miRs have been identified, but the functions of the vast majority of these remain undescribed. This paper represents a summary of our in depth analysis of the genomic origins of miR loci, detailing the formation of 1,213 of the 7,321 recently identified miRs and thereby bringing the total number of miR loci with defined molecular origin to 3,605. Interestingly, our analyses also identify evidence for a second, novel mechanism of miR locus generation through describing the formation of 273 miR loci from mutations to other forms of noncoding RNAs. Importantly, several independent investigations of the genomic origins of miR loci have now supported the hypothesis that miR hairpins are formed by the adjacent genomic insertion of two complementary transposable elements (TEs) into opposing strands. While our results agree that subsequent transcription over such TE interfaces leads to the formation of the majority of functional miR loci, we now also find evidence suggesting that a subset of miR loci were actually formed by an alternative mechanism-point mutations in other structurally complex, noncoding RNAs (e.g., tRNAs and snoRNAs).","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"3 6","pages":"e27755"},"PeriodicalIF":0.0,"publicationDate":"2013-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/mge.27755","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32072103","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: 29

LINE-1 activation and epigenetic silencing of suppressor genes in cancer: Causally related events? 癌症中抑制基因的LINE-1激活和表观遗传沉默：因果关系事件？

Mobile genetic elements Pub Date : 2013-09-01 Epub Date: 2013-10-25 DOI: 10.4161/mge.26832

Cristina Tufarelli, Hazel A Cruickshanks, Richard R Meehan

{"title":"LINE-1 activation and epigenetic silencing of suppressor genes in cancer: Causally related events?","authors":"Cristina Tufarelli, Hazel A Cruickshanks, Richard R Meehan","doi":"10.4161/mge.26832","DOIUrl":"10.4161/mge.26832","url":null,"abstract":"The ability of active retrotransposon elements to move within the host genome and alter gene expression with subsequent phenotypic variation led to their initial discovery. In recent years it has become apparent that these elements can also modulate host gene expression independently of their transposition activity. Many retrotransposons maintain endogenous promoter motifs that can potentially drive expression of adjacent DNA modules. Similarly to transposition dependent dysregulation, these proto-promoters can progress disease states when active. Indeed aberrant activation of retrotransposon derived promoters in cancer can lead to transcription of oncogenic isoforms of cellular genes. Here we propose that activation of promoters of transposable elements in cancer can also drive transcription of long non-coding RNAs whose expression leads to silencing of linked tumor suppressor genes. Such transcription driven by aberrantly active transposable elements in cancer can lead to a characteristic reprogramming of epigenetic profiles, thus extending the potential molecular mechanisms whereby retrotransposons can directly contribute to cancer development and subsequent progression.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"3 5","pages":"e26832"},"PeriodicalIF":0.0,"publicationDate":"2013-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3827066/pdf/mge-3-e26832.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31881533","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

Foreign gene recruitment to the fatty acid biosynthesis pathway in diatoms. 硅藻脂肪酸生物合成途径的外源基因募集。

Mobile genetic elements Pub Date : 2013-09-01 Epub Date: 2013-12-10 DOI: 10.4161/mge.27313

Cheong Xin Chan, Francesca L Baglivi, Christina E Jenkins, Debashish Bhattacharya

{"title":"Foreign gene recruitment to the fatty acid biosynthesis pathway in diatoms.","authors":"Cheong Xin Chan, Francesca L Baglivi, Christina E Jenkins, Debashish Bhattacharya","doi":"10.4161/mge.27313","DOIUrl":"https://doi.org/10.4161/mge.27313","url":null,"abstract":"Diatoms are highly successful marine and freshwater algae that contribute up to 20% of global carbon fixation. These species are leading candidates for biofuel production owing to ease of culturing and high fatty acid content. To assist in strain improvement and downstream applications for potential use as a biofuel, it is important to understand the evolution of lipid biosynthesis in diatoms. The evolutionary history of diatoms is however complicated by likely multiple endosymbioses involving the capture of foreign cells and horizontal gene transfer into the host genome. Using a phylogenomic approach, we assessed the evolutionary history of 12 diatom genes putatively encoding functions related to lipid biosynthesis. We found evidence of gene transfer likely from a green algal source for seven of these genes, with the remaining showing either vertical inheritance or evolutionary histories too complicated to interpret given current genome data. The functions of horizontally transferred genes encompass all aspects of lipid biosynthesis (initiation, biosynthesis, and desaturation of fatty acids) as well as fatty acid elongation, and are not restricted to plastid-targeted proteins. Our findings demonstrate that the transfer, duplication, and subfunctionalization of genes were key steps in the evolution of lipid biosynthesis in diatoms and other photosynthetic eukaryotes. This target pathway for biofuel research is highly chimeric and surprisingly, our results suggest that research done on related genes in green algae may have application to diatom models.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"3 5","pages":"e27313"},"PeriodicalIF":0.0,"publicationDate":"2013-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/mge.27313","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32013375","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