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Mobile DNA

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https://www.readbyqxmd.com/read/27895722/deciphering-fact-from-artifact-when-using-reporter-assays-to-investigate-the-roles-of-host-factors-on-l1-retrotransposition
#1
Pamela R Cook, G Travis Tabor
BACKGROUND: The Long INterspersed Element-1 (L1, LINE-1) is the only autonomous mobile DNA element in humans and has generated as much as half of the genome. Due to increasing clinical interest in the roles of L1 in cancer, embryogenesis and neuronal development, it has become a priority to understand L1-host interactions and identify host factors required for its activity. Apropos to this, we recently reported that L1 retrotransposition in HeLa cells requires phosphorylation of the L1 protein ORF1p at motifs targeted by host cell proline-directed protein kinases (PDPKs), which include the family of mitogen-activated protein kinases (MAPKs)...
2016: Mobile DNA
https://www.readbyqxmd.com/read/27843500/somatic-retrotransposition-is-infrequent-in-glioblastomas
#2
Pragathi Achanta, Jared P Steranka, Zuojian Tang, Nemanja Rodić, Reema Sharma, Wan Rou Yang, Sisi Ma, Mark Grivainis, Cheng Ran Lisa Huang, Anna M Schneider, Gary L Gallia, Gregory J Riggins, Alfredo Quinones-Hinojosa, David Fenyö, Jef D Boeke, Kathleen H Burns
BACKGROUND: Gliomas are the most common primary brain tumors in adults. We sought to understand the roles of endogenous transposable elements in these malignancies by identifying evidence of somatic retrotransposition in glioblastomas (GBM). We performed transposon insertion profiling of the active subfamily of Long INterspersed Element-1 (LINE-1) elements by deep sequencing (TIPseq) on genomic DNA of low passage oncosphere cell lines derived from 7 primary GBM biopsies, 3 secondary GBM tissue samples, and matched normal intravenous blood samples from the same individuals...
2016: Mobile DNA
https://www.readbyqxmd.com/read/27843499/evidence-for-l1-associated-dna-rearrangements-and-negligible-l1-retrotransposition-in-glioblastoma-multiforme
#3
Patricia E Carreira, Adam D Ewing, Guibo Li, Stephanie N Schauer, Kyle R Upton, Allister C Fagg, Santiago Morell, Michaela Kindlova, Patricia Gerdes, Sandra R Richardson, Bo Li, Daniel J Gerhardt, Jun Wang, Paul M Brennan, Geoffrey J Faulkner
BACKGROUND: LINE-1 (L1) retrotransposons are a notable endogenous source of mutagenesis in mammals. Notably, cancer cells can support unusual L1 retrotransposition and L1-associated sequence rearrangement mechanisms following DNA damage. Recent reports suggest that L1 is mobile in epithelial tumours and neural cells but, paradoxically, not in brain cancers. RESULTS: Here, using retrotransposon capture sequencing (RC-seq), we surveyed L1 mutations in 14 tumours classified as glioblastoma multiforme (GBM) or as a lower grade glioma...
2016: Mobile DNA
https://www.readbyqxmd.com/read/27807467/a-map-of-mobile-dna-insertions-in-the-nci-60-human-cancer-cell-panel
#4
John G Zampella, Nemanja Rodić, Wan Rou Yang, Cheng Ran Lisa Huang, Jane Welch, Veena P Gnanakkan, Toby C Cornish, Jef D Boeke, Kathleen H Burns
BACKGROUND: The National Cancer Institute-60 (NCI-60) cell lines are among the most widely used models of human cancer. They provide a platform to integrate DNA sequence information, epigenetic data, RNA and protein expression, and pharmacologic susceptibilities in studies of cancer cell biology. Genome-wide studies of the complete panel have included exome sequencing, karyotyping, and copy number analyses but have not targeted repetitive sequences. Interspersed repeats derived from mobile DNAs are a significant source of heritable genetic variation, and insertions of active elements can occur somatically in malignancy...
2016: Mobile DNA
https://www.readbyqxmd.com/read/27777631/functional-opsin-retrogene-in-nocturnal-moth
#5
Pengjun Xu, Roberto Feuda, Bin Lu, Haijun Xiao, Robert I Graham, Kongming Wu
BACKGROUND: Retrotransposed genes are different to other types of genes as they originate from a processed mRNA and are then inserted back into the genome. For a long time, the contribution of this mechanism to the origin of new genes, and hence to the evolutionary process, has been questioned as retrogenes usually lose their regulatory sequences upon insertion and generally decay into pseudogenes. In recent years, there is growing evidence, notably in mammals, that retrotransposition is an important process driving the origin of new genes, but the evidence in insects remains largely restricted to a few model species...
2016: Mobile DNA
https://www.readbyqxmd.com/read/27583033/convergent-evolution-of-trna-gene-targeting-preferences-in-compact-genomes
#6
Thomas Spaller, Eva Kling, Gernot Glöckner, Falk Hillmann, Thomas Winckler
BACKGROUND: In gene-dense genomes, mobile elements are confronted with highly selective pressure to amplify without causing excessive damage to the host. The targeting of tRNA genes as potentially safe integration sites has been developed by retrotransposons in various organisms such as the social amoeba Dictyostelium discoideum and the yeast Saccharomyces cerevisiae. In D. discoideum, tRNA gene-targeting retrotransposons have expanded to approximately 3 % of the genome. Recently obtained genome sequences of species representing the evolutionary history of social amoebae enabled us to determine whether the targeting of tRNA genes is a generally successful strategy for mobile elements to colonize compact genomes...
2016: Mobile DNA
https://www.readbyqxmd.com/read/27525044/restricting-retrotransposons-a-review
#7
REVIEW
John L Goodier
Retrotransposons have generated about 40 % of the human genome. This review examines the strategies the cell has evolved to coexist with these genomic "parasites", focussing on the non-long terminal repeat retrotransposons of humans and mice. Some of the restriction factors for retrotransposition, including the APOBECs, MOV10, RNASEL, SAMHD1, TREX1, and ZAP, also limit replication of retroviruses, including HIV, and are part of the intrinsic immune system of the cell. Many of these proteins act in the cytoplasm to degrade retroelement RNA or inhibit its translation...
2016: Mobile DNA
https://www.readbyqxmd.com/read/27489570/pinpointing-the-vesper-bat-transposon-revolution-using-the-miniopterus-natalensis-genome
#8
Roy N Platt, Sarah F Mangum, David A Ray
BACKGROUND: Around 40 million years ago DNA transposons began accumulating in an ancestor of bats in the family Vespertilionidae. Since that time, Class II transposons have been continuously reinvading and accumulating in vespertilionid genomes at a rate that is unprecedented in mammals. Miniopterus (Miniopteridae), a genus of long-fingered bats that was recently elevated from Vespertilionidae, is the sister taxon to the vespertilionids and is often used as an outgroup when studying transposable elements in vesper bats...
2016: Mobile DNA
https://www.readbyqxmd.com/read/27478512/identification-of-polymorphic-sva-retrotransposons-using-a-mobile-element-scanning-method-for-sva-me-scan-sva
#9
Hongseok Ha, Jui Wan Loh, Jinchuan Xing
BACKGROUND: Mobile element insertions are a major source of human genomic variation. SVA (SINE-R/VNTR/Alu) is the youngest retrotransposon family in the human genome and a number of diseases are known to be caused by SVA insertions. However, inter-individual genomic variations generated by SVA insertions and their impacts have not been studied extensively due to the difficulty in identifying polymorphic SVA insertions. RESULTS: To systematically identify SVA insertions at the population level and assess their genomic impact, we developed a mobile element scanning (ME-Scan) protocol we called ME-Scan-SVA...
2016: Mobile DNA
https://www.readbyqxmd.com/read/27471551/virus-like-attachment-sites-as-structural-landmarks-of-plants-retrotransposons
#10
Edgar Andres Ochoa Cruz, Guilherme Marcello Queiroga Cruz, Andréia Prata Vieira, Marie-Anne Van Sluys
BACKGROUND: The genomic data available nowadays has enabled the study of repetitive sequences and their relationship to viruses. Among them, long terminal repeat retrotransposons (LTR-RTs) are the largest component of most plant genomes, the Gypsy and Copia superfamilies being the most common. Recently it has been found that Del lineage, an LTR-RT of Gypsy superfamily, has putative virus-like attachment (vl-att) sites. This signature, originally described for retroviruses, is recognized by retroviral integrase conferring specificity to the integration process...
2016: Mobile DNA
https://www.readbyqxmd.com/read/27330569/distribution-of-the-dna-transposon-family-pokey-in-the-daphnia-pulex-species-complex
#11
Shannon H C Eagle, Teresa J Crease
BACKGROUND: The Pokey family of DNA transposons consists of two putatively autonomous groups, PokeyA and PokeyB, and two groups of Miniature Inverted-repeat Transposable Elements (MITEs), mPok1 and mPok2. This TE family is unusual as it inserts into a specific site in ribosomal (r)DNA, as well as other locations in Daphnia genomes. The goals of this study were to determine the distribution of the Pokey family in lineages of the Daphnia pulex species complex, and to test the hypothesis that unusally high PokeyA number in some isolates of Daphnia pulicaria is the result of recent transposition...
2016: Mobile DNA
https://www.readbyqxmd.com/read/27158269/genomic-analysis-of-mouse-vl30-retrotransposons
#12
Georgios Markopoulos, Dimitrios Noutsopoulos, Stefania Mantziou, Demetrios Gerogiannis, Soteroula Thrasyvoulou, Georgios Vartholomatos, Evangelos Kolettas, Theodore Tzavaras
BACKGROUND: Retrotransposons are mobile elements that have a high impact on shaping the mammalian genomes. Since the availability of whole genomes, genomic analyses have provided novel insights into retrotransposon biology. However, many retrotransposon families and their possible genomic impact have not yet been analysed. RESULTS: Here, we analysed the structural features, the genomic distribution and the evolutionary history of mouse VL30 LTR-retrotransposons...
2016: Mobile DNA
https://www.readbyqxmd.com/read/27158268/roles-for-retrotransposon-insertions-in-human-disease
#13
REVIEW
Dustin C Hancks, Haig H Kazazian
Over evolutionary time, the dynamic nature of a genome is driven, in part, by the activity of transposable elements (TE) such as retrotransposons. On a shorter time scale it has been established that new TE insertions can result in single-gene disease in an individual. In humans, the non-LTR retrotransposon Long INterspersed Element-1 (LINE-1 or L1) is the only active autonomous TE. In addition to mobilizing its own RNA to new genomic locations via a "copy-and-paste" mechanism, LINE-1 is able to retrotranspose other RNAs including Alu, SVA, and occasionally cellular RNAs...
2016: Mobile DNA
https://www.readbyqxmd.com/read/27099633/the-endonuclease-domain-of-the-line-1-orf2-protein-can-tolerate-multiple-mutations
#14
Kristine J Kines, Mark Sokolowski, Dawn L deHaro, Claiborne M Christian, Melody Baddoo, Madison E Smither, Victoria P Belancio
BACKGROUND: Approximately 17 % of the human genome is comprised of the Long INterspersed Element-1 (LINE-1 or L1) retrotransposon, the only currently active autonomous family of retroelements. Though L1 elements have helped to shape mammalian genome evolution over millions of years, L1 activity can also be mutagenic and result in human disease. L1 expression has the potential to contribute to genomic instability via retrotransposition and DNA double-strand breaks (DSBs). Additionally, L1 is responsible for structural genomic variations induced by other transposable elements such as Alu and SVA, which rely on the L1 ORF2 protein for their propagation...
2016: Mobile DNA
https://www.readbyqxmd.com/read/27096009/alu-sine-analyses-of-3-000-year-old-human-skeletal-remains-a-pilot-study
#15
Maximilian Kothe, Verena Seidenberg, Susanne Hummel, Oliver Piskurek
BACKGROUND: As Short Interspersed Elements (SINEs), human-specific Alu elements can be used for population genetic studies. Very recent inserts are polymorphic within and between human populations. In a sample of 30 elements originating from three different Alu subfamilies, we investigated whether they are preserved in prehistorical skeletal human remains from the Bronze Age Lichtenstein cave in Lower Saxony, Germany. In the present study, we examined a prehistoric triad of father, mother and daughter...
2016: Mobile DNA
https://www.readbyqxmd.com/read/27042235/active-recombinant-tol2-transposase-for-gene-transfer-and-gene-discovery-applications
#16
Jun Ni, Kirk J Wangensteen, David Nelsen, Darius Balciunas, Kimberly J Skuster, Mark D Urban, Stephen C Ekker
BACKGROUND: The revolutionary concept of "jumping genes" was conceived by McClintock in the late 1940s while studying the Activator/Dissociation (Ac/Ds) system in maize. Transposable elements (TEs) represent the most abundant component of many eukaryotic genomes. Mobile elements are a driving force of eukaryotic genome evolution. McClintock's Ac, the autonomous element of the Ac/Ds system, together with hobo from Drosophila and Tam3 from snapdragon define an ancient and diverse DNA transposon superfamily named hAT...
2016: Mobile DNA
https://www.readbyqxmd.com/read/26865864/erratum-to-ribosomal-protein-and-biogenesis-factors-affect-multiple-steps-during-movement-of-the-saccharomyces-cerevisiae-ty1-retrotransposon
#17
Susmitha Suresh, Hyo Won Ahn, Kartikeya Joshi, Arun Dakshinamurthy, Arun Kannanganat, David J Garfinkel, Philip J Farabaugh
[This corrects the article DOI: 10.1186/s13100-015-0053-5.].
2016: Mobile DNA
https://www.readbyqxmd.com/read/26862351/the-contribution-of-transposable-elements-to-size-variations-between-four-teleost-genomes
#18
Bo Gao, Dan Shen, Songlei Xue, Cai Chen, Hengmi Cui, Chengyi Song
BACKGROUND: Teleosts are unique among vertebrates, with a wide range of haploid genome sizes in very close lineages, varying from less than 400 mega base pairs (Mb) for pufferfish to over 3000 Mb for salmon. The cause of the difference in genome size remains largely unexplained. RESULTS: In this study, we reveal that the differential success of transposable elements (TEs) correlates with the variation of genome size across four representative teleost species (zebrafish, medaka, stickleback, and tetraodon)...
2016: Mobile DNA
https://www.readbyqxmd.com/read/26855675/genome-artist-a-robust-high-accuracy-aligner-tool-for-mapping-transposon-insertions-and-self-insertions
#19
Alexandru Al Ecovoiu, Iulian Constantin Ghionoiu, Andrei Mihai Ciuca, Attila Cristian Ratiu
BACKGROUND: A critical topic of insertional mutagenesis experiments performed on model organisms is mapping the hits of artificial transposons (ATs) at nucleotide level accuracy. Mapping errors may occur when sequencing artifacts or mutations as single nucleotide polymorphisms (SNPs) and small indels are present very close to the junction between a genomic sequence and a transposon inverted repeat (TIR). Another particular item of insertional mutagenesis is mapping of the transposon self-insertions and, to our best knowledge, there is no publicly available mapping tool designed to analyze such molecular events...
2016: Mobile DNA
https://www.readbyqxmd.com/read/26811739/phylogenomic-analysis-reveals-genome-wide-purifying-selection-on-tbe-transposons-in-the-ciliate-oxytricha
#20
Xiao Chen, Laura F Landweber
BACKGROUND: Transposable elements are a major player contributing to genetic variation and shaping genome evolution. Multiple independent transposon domestication events have occurred in ciliates, recruiting transposases to key roles in cellular processes. In the ciliate Oxytricha trifallax, the telomere-bearing elements (TBE), a Tc1/mariner transposon, occupy a significant portion of the germline genome and are involved in programmed genome rearrangements that produce a transcriptionally active somatic nucleus from a copy of the germline nucleus during development...
2016: Mobile DNA
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