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Mobile DNA

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https://www.readbyqxmd.com/read/28491150/dynamic-silencing-of-somatic-l1-retrotransposon-insertions-reflects-the-developmental-and-cellular-contexts-of-their-genomic-integration
#1
Manoj Kannan, Jingfeng Li, Sarah E Fritz, Kathryn E Husarek, Jonathan C Sanford, Teresa L Sullivan, Pawan Kumar Tiwary, Wenfeng An, Jef D Boeke, David E Symer
BACKGROUND: The ongoing mobilization of mammalian transposable elements (TEs) contributes to natural genetic variation. To survey the epigenetic control and expression of reporter genes inserted by L1 retrotransposition in diverse cellular and genomic contexts, we engineered highly sensitive, real-time L1 retrotransposon reporter constructs. RESULTS: Here we describe different patterns of expression and epigenetic controls of newly inserted sequences retrotransposed by L1 in various somatic cells and tissues including cultured human cancer cells, mouse embryonic stem cells, and tissues of pseudofounder transgenic mice and their progeny...
2017: Mobile DNA
https://www.readbyqxmd.com/read/28465726/evolutionary-history-of-ltr-retrotransposons-among-20-drosophila-species
#2
Nicolas Bargues, Emmanuelle Lerat
BACKGROUND: The presence of transposable elements (TEs) in genomes is known to explain in part the variations of genome sizes among eukaryotes. Even among closely related species, the variation of TE amount may be striking, as for example between the two sibling species, Drosophila melanogaster and D. simulans. However, not much is known concerning the TE content and dynamics among other Drosophila species. The sequencing of several Drosophila genomes, covering the two subgenus Sophophora and Drosophila, revealed a large variation of the repeat content among these species but no much information is known concerning their precise TE content...
2017: Mobile DNA
https://www.readbyqxmd.com/read/28450901/insertion-and-deletion-polymorphisms-of-the-ancient-alus-family-in-the-human-genome
#3
Maria S Kryatova, Jared P Steranka, Kathleen H Burns, Lindsay M Payer
BACKGROUND: Polymorphic Alu elements account for 17% of structural variants in the human genome. The majority of these belong to the youngest AluY subfamilies, and most structural variant discovery efforts have focused on identifying Alu polymorphisms from these currently retrotranspositionally active subfamilies. In this report we analyze polymorphisms from the evolutionarily older AluS subfamily, whose peak activity was tens of millions of years ago. We annotate the AluS polymorphisms, assess their likely mechanism of origin, and evaluate their contribution to structural variation in the human genome...
2017: Mobile DNA
https://www.readbyqxmd.com/read/28405230/lorte-detecting-transposon-induced-genomic-variants-using-low-coverage-pacbio-long-read-sequences
#4
Eric Disdero, Jonathan Filée
BACKGROUND: Population genomic analysis of transposable elements has greatly benefited from recent advances of sequencing technologies. However, the short size of the reads and the propensity of transposable elements to nest in highly repeated regions of genomes limits the efficiency of bioinformatic tools when Illumina or 454 technologies are used. Fortunately, long read sequencing technologies generating read length that may span the entire length of full transposons are now available...
2017: Mobile DNA
https://www.readbyqxmd.com/read/28293305/convergence-of-retrotransposons-in-oomycetes-and-plants
#5
Kirill Ustyantsev, Alexandr Blinov, Georgy Smyshlyaev
BACKGROUND: Retrotransposons comprise a ubiquitous and abundant class of eukaryotic transposable elements. All members of this class rely on reverse transcriptase activity to produce a DNA copy of the element from the RNA template. However, other activities of the retrotransposon-encoded polyprotein may differ between diverse retrotransposons. The polyprotein domains corresponding to each of these activities may have their own evolutionary history independent from that of the reverse transcriptase, thus underlying the modular view on the evolution of retrotransposons...
2017: Mobile DNA
https://www.readbyqxmd.com/read/28228849/considerations-and-complications-of-mapping-small-rna-high-throughput-data-to-transposable-elements
#6
Alexandros Bousios, Brandon S Gaut, Nikos Darzentas
BACKGROUND: High-throughput sequencing (HTS) has revolutionized the way in which epigenetic research is conducted. When coupled with fully-sequenced genomes, millions of small RNA (sRNA) reads are mapped to regions of interest and the results scrutinized for clues about epigenetic mechanisms. However, this approach requires careful consideration in regards to experimental design, especially when one investigates repetitive parts of genomes such as transposable elements (TEs), or when such genomes are large, as is often the case in plants...
2017: Mobile DNA
https://www.readbyqxmd.com/read/28138342/chicken-gallus-gallus-endogenous-retrovirus-generates-genomic-variations-in-the-chicken-genome
#7
Jinmin Lee, Seyoung Mun, Dong Hee Kim, Chun-Sung Cho, Dong-Yep Oh, Kyudong Han
BACKGROUND: Transposable elements (TEs) comprise ~10% of the chicken (Gallus gallus) genome. The content of TEs is much lower than that of mammalian genomes, where TEs comprise around half of the genome. Endogenous retroviruses are responsible for ~1.3% of the chicken genome. Among them is Gallus gallus endogenous retrovirus 10 (GGERV10), one of the youngest endogenous retrovirus families, which emerged in the chicken genome around 3 million years ago. RESULTS: We identified a total of 593 GGERV10 elements in the chicken reference genome using UCSC genome database and RepeatMasker...
2017: Mobile DNA
https://www.readbyqxmd.com/read/28096902/functional-characterization-of-the-active-mutator-like-transposable-element-muta1-from-the-mosquito-aedes-aegypti
#8
Kun Liu, Susan R Wessler
BACKGROUND: Mutator-like transposable elements (MULEs) are widespread with members in fungi, plants, and animals. Most of the research on the MULE superfamily has focused on plant MULEs where they were discovered and where some are extremely active and have significant impact on genome structure. The maize MuDR element has been widely used as a tool for both forward and reverse genetic studies because of its high transposition rate and preference for targeting genic regions. However, despite being widespread, only a few active MULEs have been identified, and only one, the rice Os3378, has demonstrated activity in a non-host organism...
2017: Mobile DNA
https://www.readbyqxmd.com/read/27990178/non-canonical-helitrons-in-fusarium-oxysporum
#9
Biju Vadakkemukadiyil Chellapan, Peter van Dam, Martijn Rep, Ben J C Cornelissen, Like Fokkens
BACKGROUND: Helitrons are eukaryotic rolling circle transposable elements that can have a large impact on host genomes due to their copy-number and their ability to capture and copy genes and regulatory elements. They occur widely in plants and animals, and have thus far been relatively little investigated in fungi. RESULTS: Here, we comprehensively survey Helitrons in several completely sequenced genomes representing the F. oxysporum species complex (FOSC). We thoroughly characterize 5 different Helitron subgroups and determine their impact on genome evolution and assembly in this species complex...
2016: Mobile DNA
https://www.readbyqxmd.com/read/27980690/the-intron-enriched-herv-k-hml-10-family-suppresses-apoptosis-an-indicator-of-malignant-transformation
#10
Felix Broecker, Roger Horton, Jochen Heinrich, Alexandra Franz, Michal-Ruth Schweiger, Hans Lehrach, Karin Moelling
BACKGROUND: Human endogenous retroviruses (HERVs) constitute 8% of the human genome and contribute substantially to the transcriptome. HERVs have been shown to generate RNAs that modulate host gene expression. However, experimental evidence for an impact of these regulatory transcripts on the cellular phenotype has been lacking. RESULTS: We characterized the previously little described HERV-K(HML-10) endogenous retrovirus family on a genome-wide scale. HML-10 invaded the ancestral genome of Old World monkeys about 35 Million years ago and is enriched within introns of human genes when compared to other HERV families...
2016: Mobile DNA
https://www.readbyqxmd.com/read/27980689/endogenous-retroviral-promoter-exaptation-in-human-cancer
#11
REVIEW
Artem Babaian, Dixie L Mager
Cancer arises from a series of genetic and epigenetic changes, which result in abnormal expression or mutational activation of oncogenes, as well as suppression/inactivation of tumor suppressor genes. Aberrant expression of coding genes or long non-coding RNAs (lncRNAs) with oncogenic properties can be caused by translocations, gene amplifications, point mutations or other less characterized mechanisms. One such mechanism is the inappropriate usage of normally dormant, tissue-restricted or cryptic enhancers or promoters that serve to drive oncogenic gene expression...
2016: Mobile DNA
https://www.readbyqxmd.com/read/27895722/deciphering-fact-from-artifact-when-using-reporter-assays-to-investigate-the-roles-of-host-factors-on-l1-retrotransposition
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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