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Mobile DNA

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https://www.readbyqxmd.com/read/29225705/using-bioinformatic-and-phylogenetic-approaches-to-classify-transposable-elements-and-understand-their-complex-evolutionary-histories
#1
REVIEW
Irina R Arkhipova
In recent years, much attention has been paid to comparative genomic studies of transposable elements (TEs) and the ensuing problems of their identification, classification, and annotation. Different approaches and diverse automated pipelines are being used to catalogue and categorize mobile genetic elements in the ever-increasing number of prokaryotic and eukaryotic genomes, with little or no connectivity between different domains of life. Here, an overview of the current picture of TE classification and evolutionary relationships is presented, updating the diversity of TE types uncovered in sequenced genomes...
2017: Mobile DNA
https://www.readbyqxmd.com/read/29225704/transcription-coupled-repair-and-biased-insertion-of-human-retrotransposon-l1-in-transcribed-genes
#2
Geraldine Servant, Vincent A Streva, Prescott L Deininger
Background: L1 retrotransposons inserted within genes in the human genome show a strong bias against sense orientation with respect to the gene. One suggested explanation for this observation was the possibility that L1 inserted randomly, but that there was negative selection against sense-oriented insertions. However, multiple studies have now found that de novo and polymorphic L1 insertions, which have little opportunity for selection to act, also show the same bias. Results: Here we show that the transcription-coupled sub-pathway of nucleotide excision repair does not affect the overall rate of insertion of L1 elements, which is in contrast with the regulation by the global sub-pathway of nucleotide excision repair...
2017: Mobile DNA
https://www.readbyqxmd.com/read/29201157/detection-of-the-line-1-retrotransposon-rna-binding-protein-orf1p-in-different-anatomical-regions-of-the-human-brain
#3
Debpali Sur, Raj Kishor Kustwar, Savita Budania, Anita Mahadevan, Dustin C Hancks, Vijay Yadav, S K Shankar, Prabhat K Mandal
Background: Recent reports indicate that retrotransposons - a type of mobile DNA - can contribute to neuronal genetic diversity in mammals. Retrotransposons are genetic elements that mobilize via an RNA intermediate by a "copy-and-paste" mechanism termed retrotransposition. Long Interspersed Element-1 (LINE-1 or L1) is the only active autonomous retrotransposon in humans and its activity is responsible for ~ 30% of genomic mass. Historically, L1 retrotransposition was thought to be restricted to the germline; however, new data indicate L1 s are active in somatic tissue with certain regions of the brain being highly permissive...
2017: Mobile DNA
https://www.readbyqxmd.com/read/29151899/globular-domain-structure-and-function-of-restriction-like-endonuclease-lines-similarities-to-eukaryotic-splicing-factor-prp8
#4
M Murshida Mahbub, Saiful M Chowdhury, Shawn M Christensen
Background: R2 elements are a clade of early branching Long Interspersed Elements (LINEs). LINEs are retrotransposable elements whose replication can have profound effects on the genomes in which they reside. No crystal or EM structures exist for the reverse transcriptase (RT) and linker regions of LINEs. Results: Using limited proteolysis as a probe for globular domain structure, we show that the protein encoded by the Bombyx mori R2 element has two major globular domains: (1) a small globular domain consisting of the N-terminal zinc finger and Myb motifs, and (2) a large globular domain consisting of the RT, linker, and type II restriction-like endonuclease (RLE)...
2017: Mobile DNA
https://www.readbyqxmd.com/read/29118853/identification-of-a-novel-herv-k-hml10-comprehensive-characterization-and-comparative-analysis-in-non-human-primates-provide-insights-about-hml10-proviruses-structure-and-diffusion
#5
Nicole Grandi, Marta Cadeddu, Maria Paola Pisano, Francesca Esposito, Jonas Blomberg, Enzo Tramontano
Background: About half of the human genome is constituted of transposable elements, including human endogenous retroviruses (HERV). HERV sequences represent the 8% of our genetic material, deriving from exogenous infections occurred millions of years ago in the germ line cells and being inherited by the offspring in a Mendelian fashion. HERV-K elements (classified as HML1-10) are among the most studied HERV groups, especially due to their possible correlation with human diseases. In particular, the HML10 group was reported to be upregulated in persistent HIV-1 infected cells as well as in tumor cells and samples, and proposed to have a role in the control of host genes expression...
2017: Mobile DNA
https://www.readbyqxmd.com/read/29093758/tgtt-and-aaca-two-transcriptionally-active-ltr-retrotransposon-subfamilies-with-a-specific-ltr-structure-and-horizontal-transfer-in-four-rosaceae-species
#6
Hao Yin, Xiao Wu, Dongqing Shi, Yangyang Chen, Kaijie Qi, Zhengqiang Ma, Shaoling Zhang
Background: Long terminal repeat retrotransposons (LTR-RTs) are major components of plant genomes. Common LTR-RTs contain the palindromic dinucleotide 5'-'TG'-'CA'-3' motif at the ends. Thus, further analyses of non-canonical LTR-RTs with non-palindromic motifs will enhance our understanding of their structures and evolutionary history. Results: Here, we report two new LTR-RT subfamilies (TGTT and AACA) with atypical dinucleotide ends of 5'-'TG'-'TT'-3', and 5'-'AA'-'CA'-3' in pear, apple, peach and mei...
2017: Mobile DNA
https://www.readbyqxmd.com/read/29075336/diversity-of-p-element-pirna-production-among-m-and-q-strains-and-its-association-with-p-m-hybrid-dysgenesis-in-drosophila-melanogaster
#7
Keiko Tsuji Wakisaka, Kenji Ichiyanagi, Seiko Ohno, Masanobu Itoh
BACKGROUND: Transposition of P elements in the genome causes P-M hybrid dysgenesis in Drosophila melanogaster. For the P strain, the P-M phenotypes are associated with the ability to express a class of small RNAs, called piwi-interacting small RNAs (piRNAs), that suppress the P elements in female gonads. However, little is known about the extent to which piRNAs are involved in the P-M hybrid dysgenesis in M' and Q strains, which show different abilities to regulate the P elements from P strains...
2017: Mobile DNA
https://www.readbyqxmd.com/read/29026445/viral-communities-of-the-human-gut-metagenomic-analysis-of-composition-and-dynamics
#8
REVIEW
Varun Aggarwala, Guanxiang Liang, Frederic D Bushman
BACKGROUND: The numerically most abundant biological entities on Earth are viruses. Vast populations prey on the cellular microbiota in all habitats, including the human gut. MAIN BODY: Here we review approaches for studying the human virome, and some recent results on movement of viral sequences between bacterial cells and eukaryotic hosts. We first overview biochemical and bioinformatic methods, emphasizing that specific choices in the methods used can have strong effects on the results obtained...
2017: Mobile DNA
https://www.readbyqxmd.com/read/28814978/evolutionary-history-of-the-mariner-element-galluhop-in-avian-genomes
#9
Natasha Avila Bertocchi, Fabiano Pimentel Torres, Analía Del Valle Garnero, Ricardo José Gunski, Gabriel Luz Wallau
BACKGROUND: Transposable elements (TEs) are highly abundant genomic parasites in eukaryote genomes. Although several genomes have been screened for TEs, so far very limited information is available regarding avian TEs and their evolutionary histories. Taking advantage of the rich genomic data available for birds, we characterized the evolutionary history of the galluhop element, originally described in Gallus gallus, through the use of several bioinformatic analyses. RESULTS: galluhop homologous sequences were found in 6 of 72 genomes analyzed: 5 species of Galliformes (Gallus gallus, Meleagris gallopavo, Coturnix japonica, Colinus virginianus, Lyrurus tetrix) and one Buceritiformes (Buceros rhinoceros)...
2017: Mobile DNA
https://www.readbyqxmd.com/read/28770012/discovery-of-rare-diagnostic-aluyb8-9-elements-in-diverse-human-populations
#10
Julie Feusier, David J Witherspoon, W Scott Watkins, Clément Goubert, Thomas A Sasani, Lynn B Jorde
BACKGROUND: Polymorphic human Alu elements are excellent tools for assessing population structure, and new retrotransposition events can contribute to disease. Next-generation sequencing has greatly increased the potential to discover Alu elements in human populations, and various sequencing and bioinformatics methods have been designed to tackle the problem of detecting these highly repetitive elements. However, current techniques for Alu discovery may miss rare, polymorphic Alu elements...
2017: Mobile DNA
https://www.readbyqxmd.com/read/28491150/dynamic-silencing-of-somatic-l1-retrotransposon-insertions-reflects-the-developmental-and-cellular-contexts-of-their-genomic-integration
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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