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Mobile DNA

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https://www.readbyqxmd.com/read/30455747/can-sine-dynamics-in-the-giant-panda-and-three-other-caniformia-genomes
#1
Changjun Peng, Lili Niu, Jiabo Deng, Jianqiu Yu, Xueyan Zhang, Chuang Zhou, Jinchuan Xing, Jing Li
Background: Although repeat sequences constitute about 37% of carnivore genomes, the characteristics and distribution of repeat sequences among carnivore genomes have not been fully investigated. Based on the updated Repbase library, we re-annotated transposable elements (TEs) in four Caniformia genomes (giant panda, polar bear, domestic dog, and domestic ferret) and performed a systematic, genome-wide comparison focusing on the Carnivora-specific SINE family, Can-SINEs. Results: We found the majority of young recently integrated transposable elements are LINEs and SINEs in carnivore genomes...
2018: Mobile DNA
https://www.readbyqxmd.com/read/30450130/an-advanced-enrichment-method-for-rare-somatic-retroelement-insertions-sequencing
#2
Alexander Y Komkov, Anastasia A Minervina, Gaiaz A Nugmanov, Mariia V Saliutina, Konstantin V Khodosevich, Yuri B Lebedev, Ilgar Z Mamedov
Background: There is increasing evidence that the transpositional activity of retroelements (REs) is not limited to germ line cells, but often occurs in tumor and normal somatic cells. Somatic transpositions were found in several human tissues and are especially typical for the brain. Several computational and experimental approaches for detection of somatic retroelement insertions was developed in the past few years. These approaches were successfully applied to detect somatic insertions in clonally expanded tumor cells...
2018: Mobile DNA
https://www.readbyqxmd.com/read/30237828/phylogenomic-analysis-reveals-splicing-as-a-mechanism-of-parallel-evolution-of-non-canonical-svas-in-hominine-primates
#3
Annette Damert
SVA (SINE-R-VNTR- Alu ) elements are non-autonomous non-LTR (Long Terminal Repeat) retrotransposons. They are found in all hominoid primates but did not amplify to appreciable numbers in gibbons. Recently, phylogenetic networks of hominid (orangutan, gorilla, chimpanzee, human) SVA elements based on comparison of overall sequence identity have been reported. Here I present a detailed phylogeny of SVA_D elements in gorilla, chimpanzee and humans based on sorting of co-segregating substitutions. Complementary comparative genomics analysis revealed that the majority (1763 out of 1826-97%) of SVA_D elements in gorilla represent species-specific insertions - indicating very low activity of the subfamily before the gorilla/chimpanzee-human split...
2018: Mobile DNA
https://www.readbyqxmd.com/read/30211913/meeting-report-mobile-genetic-elements-and-genome-plasticity-2018
#4
John M Abrams, Irina R Arkhipova, Marlene Belfort, Jef D Boeke, M Joan Curcio, Geoffrey J Faulkner, John L Goodier, Ruth Lehmann, Henry L Levin
The Mobile Genetic Elements and Genome Plasticity conference was hosted by Keystone Symposia in Santa Fe, NM USA, February 11-15, 2018. The organizers were Marlene Belfort, Evan Eichler, Henry Levin and Lynn Maquat. The goal of this conference was to bring together scientists from around the world to discuss the function of transposable elements and their impact on host species. Central themes of the meeting included recent innovations in genome analysis and the role of mobile DNA in disease and evolution. The conference included 200 scientists who participated in poster presentations, short talks selected from abstracts, and invited talks...
2018: Mobile DNA
https://www.readbyqxmd.com/read/30181787/insertion-sequence-elements-mediated-structural-variations-in-bacterial-genomes
#5
Etienne Nzabarushimana, Haixu Tang
Mobile genetic elements (MGEs) impact the evolution and stability of their host genomes. Insertion sequence (IS) elements are the most common MGEs in bacterial genomes and play a crucial role in mediating large-scale variations in bacterial genomes. It is understood that IS elements and MGEs in general coexist in a dynamical equilibrium with their respective hosts. Current studies indicate that the spontaneous movement of IS elements does not follow a constant rate in different bacterial genomes. However, due to the paucity and sparsity of the data, these observations are yet to be conclusive...
2018: Mobile DNA
https://www.readbyqxmd.com/read/30147753/impact-of-non-ltr-retrotransposons-in-the-differentiation-and-evolution-of-anatomically-modern-humans
#6
Etienne Guichard, Valentina Peona, Guidantonio Malagoli Tagliazucchi, Lucia Abitante, Evelyn Jagoda, Margherita Musella, Marco Ricci, Alejandro Rubio-Roldán, Stefania Sarno, Donata Luiselli, Davide Pettener, Cristian Taccioli, Luca Pagani, Jose Luis Garcia-Perez, Alessio Boattini
Background: Transposable elements are biologically important components of eukaryote genomes. In particular, non-LTR retrotransposons (N-LTRrs) played a key role in shaping the human genome throughout evolution. In this study, we compared retrotransposon insertions differentially present in the genomes of Anatomically Modern Humans, Neanderthals, Denisovans and Chimpanzees, in order to assess the possible impact of retrotransposition in the differentiation of the human lineage. Results: We first identified species-specific N-LTRrs and established their distribution in present day human populations...
2018: Mobile DNA
https://www.readbyqxmd.com/read/30123327/length-variations-within-the-merle-retrotransposon-of-canine-pmel-correlating-genotype-with-phenotype
#7
Sarah C Murphy, Jacquelyn M Evans, Kate L Tsai, Leigh Anne Clark
Background: The antisense insertion of a canine short interspersed element (SINEC_Cf) in the pigmentation gene PMEL (or SILV ) causes a coat pattern phenotype in dogs termed merle. Merle is a semi-dominant trait characterized by patches of full pigmentation on a diluted background. The oligo(dT) tract of the Merle retrotransposon is long and uninterrupted and is prone to dramatic truncation. Phenotypically wild-type individuals carrying shorter oligo(dT) lengths of the Merle allele have been previously described and termed cryptic merles...
2018: Mobile DNA
https://www.readbyqxmd.com/read/30100927/f-cphi-represents-a-new-homing-endonuclease-family-using-the-endo-vii-catalytic-motif
#8
Xiaoting Fang, YongLiang Jiang, Kim Li, Qinglu Zeng
Background: There are six known families of homing endonucleases, LAGLIDADG, GIY-YIG, HNH, His-Cys box, PD-(D/E)-XK, and EDxHD, which are characterized by their conserved residues. Previously, we discovered a novel homing endonuclease F-CphI encoded by ORF177 of cyanophage S-PM2. F-CphI does not resemble any characterized homing endonucleases. Instead, the C-terminus of F-CphI aligns well with the N-terminal catalytic domain of a Holliday junction DNA resolvase, phage T4 endonuclease VII (Endo VII)...
2018: Mobile DNA
https://www.readbyqxmd.com/read/30079119/srnapipe-a-galaxy-based-pipeline-for-bioinformatic-in-depth-exploration-of-small-rnaseq-data
#9
Romain Pogorelcnik, Chantal Vaury, Pierre Pouchin, Silke Jensen, Emilie Brasset
Background: The field of small RNA is one of the most investigated research areas since they were shown to regulate transposable elements and gene expression and play essential roles in fundamental biological processes. Small RNA deep sequencing (sRNA-seq) is now routinely used for large-scale analyses of small RNA. Such high-throughput sequencing typically produces several millions reads. Results: Here we present a computational pipeline (sRNAPipe: small RNA pipeline) based on the Galaxy framework that takes as input a fastq file of small RNA-seq reads and performs successive steps of mapping to categories of genomic sequences: transposable elements, gene transcripts, microRNAs, small nuclear RNAs, ribosomal RNAs and transfer RNAs...
2018: Mobile DNA
https://www.readbyqxmd.com/read/30026817/deletion-of-the-sex-determining-gene-sxi1%C3%AE-enhances-the-spread-of-mitochondrial-introns-in-cryptococcus-neoformans
#10
Zhun Yan, Zhimin Li, Li Yan, Yongting Yu, Yi Cheng, Jia Chen, Yunyun Liu, Chunsheng Gao, Liangbin Zeng, Xiangping Sun, Litao Guo, Jianping Xu
Background: Homing endonuclease genes (HEGs) are widely distributed genetic elements in the mitochondrial genomes of a diversity of eukaryotes. Due to their ability to self-propagate within and between genomes, these elements can spread rapidly in populations. Whether and how such elements are controlled in genomes remains largely unknown. Results: Here we report that the HEG-containing introns in the mitochondrial COX1 gene in Cryptococcus neoformans are mobile and that their spread in sexual crosses is influenced by mating type ( MAT ) α-specific homeodomain gene SXI1 α...
2018: Mobile DNA
https://www.readbyqxmd.com/read/30002736/-drosophila-parasitoid-wasps-bears-a-distinct-dna-transposon-profile
#11
Alexandre Freitas da Silva, Filipe Zimmer Dezordi, Elgion Lucio Silva Loreto, Gabriel Luz Wallau
Background: The majority of Eukaryotic genomes are composed of a small portion of stable (non-mobile) genes and a large fraction of parasitic mobile elements such as transposable elements and endogenous viruses: the Mobilome. Such important component of many genomes are normally underscored in genomic analysis and detailed characterized mobilomes only exists for model species. In this study, we used a combination of de novo and homology approaches to characterize the Mobilome of two non-model parasitoid wasp species...
2018: Mobile DNA
https://www.readbyqxmd.com/read/30002735/l1-retrotransposition-in-the-soma-a-field-jumping-ahead
#12
REVIEW
Geoffrey J Faulkner, Victor Billon
Retrotransposons are transposable elements (TEs) capable of "jumping" in germ, embryonic and tumor cells and, as is now clearly established, in the neuronal lineage. Mosaic TE insertions form part of a broader landscape of somatic genome variation and hold significant potential to generate phenotypic diversity, in the brain and elsewhere. At present, the LINE-1 (L1) retrotransposon family appears to be the most active autonomous TE in most mammals, based on experimental data obtained from disease-causing L1 mutations, engineered L1 reporter systems tested in cultured cells and transgenic rodents, and single-cell genomic analyses...
2018: Mobile DNA
https://www.readbyqxmd.com/read/29946370/extensive-exchange-of-transposable-elements-in-the-drosophila-pseudoobscura-group
#13
Tom Hill, Andrea J Betancourt
Background: As species diverge, so does their transposable element (TE) content. Within a genome, TE families may eventually become dormant due to host-silencing mechanisms, natural selection and the accumulation of inactive copies. The transmission of active copies from a TE families, both vertically and horizontally between species, can allow TEs to escape inactivation if it occurs often enough, as it may allow TEs to temporarily escape silencing in a new host. Thus, the contribution of horizontal exchange to TE persistence has been of increasing interest...
2018: Mobile DNA
https://www.readbyqxmd.com/read/29946369/unexpected-invasion-of-miniature-inverted-repeat-transposable-elements-in-viral-genomes
#14
Hua-Hao Zhang, Qiu-Zhong Zhou, Ping-Lan Wang, Xiao-Min Xiong, Andrea Luchetti, Didier Raoult, Anthony Levasseur, Sebastien Santini, Chantal Abergel, Matthieu Legendre, Jean-Michel Drezen, Catherine Béliveau, Michel Cusson, Shen-Hua Jiang, Hai-Ou Bao, Cheng Sun, Thomas E Bureau, Peng-Fei Cheng, Min-Jin Han, Ze Zhang, Xiao-Gu Zhang, Fang-Yin Dai
Background: Transposable elements (TEs) are common and often present with high copy numbers in cellular genomes. Unlike in cellular organisms, TEs were previously thought to be either rare or absent in viruses. Almost all reported TEs display only one or two copies per viral genome. In addition, the discovery of pandoraviruses with genomes up to 2.5-Mb emphasizes the need for biologists to rethink the fundamental nature of the relationship between viruses and cellular life. Results: Herein, we performed the first comprehensive analysis of miniature inverted-repeat transposable elements (MITEs) in the 5170 viral genomes for which sequences are currently available...
2018: Mobile DNA
https://www.readbyqxmd.com/read/29942366/horizontal-transfer-and-proliferation-of-tsu4-in-saccharomyces-paradoxus
#15
Casey M Bergman
Background: Recent evidence suggests that horizontal transfer plays a significant role in the evolution of of transposable elements (TEs) in eukaryotes. Many cases of horizontal TE transfer (HTT) been reported in animals and plants, however surprisingly few examples of HTT have been reported in fungi. Findings: Here I report evidence for a novel HTT event in fungi involving Tsu4 in Saccharomyces paradoxus based on (i) unexpectedly high similarity between Tsu4 elements in S...
2018: Mobile DNA
https://www.readbyqxmd.com/read/29942365/transposable-elements-and-gene-expression-during-the-evolution-of-amniotes
#16
Lu Zeng, Stephen M Pederson, R Daniel Kortschak, David L Adelson
Background: Transposable elements (TEs) are primarily responsible for the DNA losses and gains in genome sequences that occur over time within and between species. TEs themselves evolve, with clade specific LTR/ERV, LINEs and SINEs responsible for the bulk of species-specific genomic features. Because TEs can contain regulatory motifs, they can be exapted as regulators of gene expression. While TE insertions can provide evolutionary novelty for the regulation of gene expression, their overall impact on the evolution of gene expression is unclear...
2018: Mobile DNA
https://www.readbyqxmd.com/read/29745378/correction-to-the-samhd1-mediated-block-of-line-1-retroelements-is-regulated-by-phosphorylation
#17
A Herrmann, S Wittmann, D Thomas, C N Shepard, B Kim, N Ferreirós, T Gramberg
[This corrects the article DOI: 10.1186/s13100-018-0116-5.].
2018: Mobile DNA
https://www.readbyqxmd.com/read/29743957/the-case-for-not-masking-away-repetitive-dna
#18
EDITORIAL
R Keith Slotkin
In the course of analyzing whole-genome data, it is common practice to mask or filter out repetitive regions of a genome, such as transposable elements and endogenous retroviruses, in order to focus only on genes and thus simplify the results. This Commentary is a plea from one member of the Mobile DNA community to all gene-centric researchers: please do not ignore the repetitive fraction of the genome . Please stop narrowing your findings by only analyzing a minority of the genome, and instead broaden your analyses to include the rich biology of repetitive and mobile DNA...
2018: Mobile DNA
https://www.readbyqxmd.com/read/29713390/retrotransposon-targeting-to-rna-polymerase-iii-transcribed-genes
#19
REVIEW
Stephanie Cheung, Savrina Manhas, Vivien Measday
Retrotransposons are genetic elements that are similar in structure and life cycle to retroviruses by replicating via an RNA intermediate and inserting into a host genome. The Saccharomyces cerevisiae ( S. cerevisiae ) Ty1-5 elements are long terminal repeat (LTR) retrotransposons that are members of the Ty1- copia ( Pseudoviridae ) or Ty3- gypsy ( Metaviridae ) families. Four of the five S. cerevisiae Ty elements are inserted into the genome upstream of RNA Polymerase (Pol) III-transcribed genes such as transfer RNA (tRNA) genes...
2018: Mobile DNA
https://www.readbyqxmd.com/read/29632618/a-computational-reconstruction-of-papio-phylogeny-using-alu-insertion-polymorphisms
#20
Vallmer E Jordan, Jerilyn A Walker, Thomas O Beckstrom, Cody J Steely, Cullen L McDaniel, Corey P St Romain, Kim C Worley, Jane Phillips-Conroy, Clifford J Jolly, Jeffrey Rogers, Miriam K Konkel, Mark A Batzer
Background: Since the completion of the human genome project, the diversity of genome sequencing data produced for non-human primates has increased exponentially. Papio baboons are well-established biological models for studying human biology and evolution. Despite substantial interest in the evolution of Papio , the systematics of these species has been widely debated, and the evolutionary history of Papio diversity is not fully understood. Alu elements are primate-specific transposable elements with a well-documented mutation/insertion mechanism and the capacity for resolving controversial phylogenetic relationships...
2018: Mobile DNA
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