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Retrotransposon

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https://www.readbyqxmd.com/read/28429755/opossum-apobec1-is-a-dna-mutator-with-retrovirus-and-retroelement-restriction-activity
#1
Terumasa Ikeda, Mayuko Shimoda, Diako Ebrahimi, John L VandeBerg, Reuben S Harris, Atsushi Koito, Kazuhiko Maeda
APOBEC3s (A3s) are single-stranded DNA cytosine deaminases that provide innate immune defences against retroviruses and mobile elements. A3s are specific to eutherian mammals because no direct homologs exist at the syntenic genomic locus in metatherian (marsupial) or prototherian (monotreme) mammals. However, the A3s in these species have the likely evolutionary precursors, the antibody gene deaminase AID and the RNA/DNA editing enzyme APOBEC1 (A1). Here, we used cell culture-based assays to determine whether opossum A1 restricts the infectivity of retroviruses including human immunodeficiency virus type 1 (HIV-1) and the mobility of LTR/non-LTR retrotransposons...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28425429/evidence-of-horizontal-transmission-of-the-cancer-associated-steamer-retrotransposon-among-ecological-cohort-bivalve-species
#2
Ashley N Paynter, Michael J Metzger, Jocelyn A Sessa, Mark E Siddall
Bivalve specimens from legacy frozen tissue collections, and others freshly obtained, were surveyed for the presence of the Steamer long terminal repeat (LTR)-retrotransposon associated with disseminated hemic neoplasia of the soft-shelled clam Mya areneria. Of 22 species investigated using primers for the pol region, only Atlantic M. arenaria, Atlantic and North Sea razor clams Ensis directus, and Baltic clams Macoma balthica from the North Sea were found to possess copies of Steamer in their genomes. Notably, close relatives like Mya truncata and Siliqua patula did not exhibit evidence of Steamer...
April 20, 2017: Diseases of Aquatic Organisms
https://www.readbyqxmd.com/read/28421705/cover-image-volume-173a-number-5-may-2017
#3
Toshiki Takenouchi, Tomu Kuchikata, Hiroshi Yoshihashi, Mineko Fujiwara, Tomoko Uehara, Sahoko Miyama, Shiro Yamada, Kenjiro Kosaki
The cover image, by Toshiki Takenouchi et al., is based on the Clinical Report Diagnostic use of computational retrotransposon detection: Successful definition of pathogenetic mechanism in a ciliopathy phenotype, DOI: 10.1002/ajmg.a.38167.
May 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28421083/ltrtype-an-efficient-tool-to-characterize-structurally-complex-ltr-retrotransposons-and-nested-insertions-on-genomes
#4
Fan-Chun Zeng, You-Jie Zhao, Que-Jie Zhang, Li-Zhi Gao
The amplification and recombination of long terminal repeat (LTR) retrotransposons have proven to determine the size, organization, function, and evolution of most host genomes, especially very large plant genomes. However, the limitation of tools for an efficient discovery of structural complexity of LTR retrotransposons and the nested insertions is a great challenge to confront ever-growing amount of genomic sequences for many organisms. Here we developed a novel software, called as LTRtype, to characterize different types of structurally complex LTR retrotransposon elements as well as nested events...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28420154/mechanisms-of-ltr-retroelement-transposition-lessons-from-drosophila-melanogaster
#5
REVIEW
Lidia Nefedova, Alexander Kim
Long terminal repeat (LTR) retrotransposons occupy a special place among all mobile genetic element families. The structure of LTR retrotransposons that have three open reading frames is identical to DNA forms of retroviruses that are integrated into the host genome. Several lines of evidence suggest that LTR retrotransposons share a common ancestry with retroviruses and thus are highly relevant to understanding mechanisms of transposition. Drosophila melanogaster is an exceptionally convenient model for studying the mechanisms of retrotransposon movement because many such elements in its genome are transpositionally active...
April 16, 2017: Viruses
https://www.readbyqxmd.com/read/28416702/massive-horizontal-transfer-of-transposable-elements-in-insects
#6
Jean Peccoud, Vincent Loiseau, Richard Cordaux, Clément Gilbert
Horizontal transfer (HT) of genetic material is central to the architecture and evolution of prokaryote genomes. Within eukaryotes, the majority of HTs reported so far are transfers of transposable elements (TEs). These reports essentially come from studies focusing on specific lineages or types of TEs. Because of the lack of large-scale survey, the amount and impact of HT of TEs (HTT) in eukaryote evolution, as well as the trends and factors shaping these transfers, are poorly known. Here, we report a comprehensive analysis of HTT in 195 insect genomes, representing 123 genera and 13 of the 28 insect orders...
April 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28415970/drosophila-melanogaster-retrotransposon-and-inverted-repeat-derived-endogenous-sirnas-are-differentially-processed-in-distinct-cellular-locations
#7
Andrew W Harrington, Michael R McKain, Daniel Michalski, Kaylyn M Bauer, Joshua M Daugherty, Mindy Steiniger
BACKGROUND: Endogenous small interfering (esi)RNAs repress mRNA levels and retrotransposon mobility in Drosophila somatic cells by poorly understood mechanisms. 21 nucleotide esiRNAs are primarily generated from retrotransposons and two inverted repeat (hairpin) loci in Drosophila culture cells in a Dicer2 dependent manner. Additionally, proteins involved in 3' end processing, such as Symplekin, CPSF73 and CPSR100, have been recently implicated in the esiRNA pathway. RESULTS: Here we present evidence of overlap between two essential RNA metabolic pathways: esiRNA biogenesis and mRNA 3' end processing...
April 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28414318/initial-sites-of-hepadnavirus-integration-into-host-genome-in-human-hepatocytes-and-in-the-woodchuck-model-of-hepatitis-b-associated-hepatocellular-carcinoma
#8
R Chauhan, N D Churchill, P M Mulrooney-Cousins, T I Michalak
Hepatitis B virus (HBV) and the closely related woodchuck hepatitis virus (WHV) are potent carcinogens that trigger development of primary hepatocellular carcinoma (HCC). The initial sites of hepadnavirus-host genome integration, their diversity and kinetics of formation can be central to virus persistence and the initiation and progression of HCC. To recognize the nature of the very early virus-host interactions, we explored de novo infection of human hepatocyte-like HepaRG cells with authentic HBV and naive woodchucks with WHV...
April 17, 2017: Oncogenesis
https://www.readbyqxmd.com/read/28413161/rapid-and-recent-evolution-of-ltr-retrotransposons-drives-rice-genome-evolution-during-the-speciation-of-aa-genome-oryza-species
#9
Qun-Jie Zhang, Li-Zhi Gao
The dynamics of LTR retrotransposons and their contribution to genome evolution during plant speciation have remained largely unanswered. Here, we perform a genome-wide comparison of all eight Oryza AA- genome species, and identify 3,911 intact LTR retrotransposons classified into 790 families. The top 44 most abundant LTR retrotransposon families show patterns of rapid and distinct diversification since the species split over the last ~4.8 Myr. Phylogenetic and read depth analyses of 11 representative retrotransposon families further provide a comprehensive evolutionary landscape of these changes...
April 16, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28409117/searching-for-active-mobile-genetic-elements-in-dsrna-fraction-of-pinus-sylvestris-having-witches-broom-abnormalities
#10
A A Pochtovyy, O Yu Baranov, I E Rubel', O A Razumova, V E Padutov, A V Khromov, A V Makhotenko, A P Tkachuk, V V Makarov, V A Gushchin
The most common type of coniferous mobile genetic elements are retrotransposons. Despite of their early positive impact on evolution of modern coniferous species they can have a significant negative impact for Forestry and breeding. Breaking genomic structural integrity mobile elements can cause phenotypic defects of plants. In this regard, the study of the diversity of coniferous mobile genetic elements is particularly interesting. In the present paper, we describe mobile genetic elements in dsRNA fraction of Pinus sylvestris having witches broom abnormalities...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28408706/embryo-culture-in-presence-of-oviductal-fluid-induces-dna-methylation-changes-in-bovine-blastocysts
#11
Antonio Daniel Barrera, Elina Vanesa García, Meriem Hamdi, Maria-Jesús Sánchez Calabuig, Angela Patricia Lopez-Cardona, Noelia Fonseca Balvís, Dimitrios Rizos, Alfonso Gutierrez-Adan
During the transit through the oviduct, the early embryo initiates an extensive DNA methylation reprogramming of its genome. Given that these epigenetic modifications are susceptible to environmental factors, components present in the oviductal milieu could affect the DNA methylation marks of the developing embryo. The aim of this study was to examine if culture of bovine embryos with oviductal fluid (OF) can induce DNA methylation changes at specific genomic regions in the resulting blastocysts. In vitro produced zygotes were cultured in medium with 3 mg/mL bovine serum albumin (BSA) or 1...
April 13, 2017: Reproduction: the Official Journal of the Society for the Study of Fertility
https://www.readbyqxmd.com/read/28407808/nested-pcr-assay-for-detection-of-schistosoma-japonicum-infection-in-domestic-animals
#12
Xin Zhang, Chuan-Chuan He, Jin-Ming Liu, Hao Li, Ke Lu, Zhi-Qiang Fu, Chuan-Gang Zhu, Yi-Ping Liu, Lai-Bao Tong, De-Bao Zhou, Li Zha, Yang Hong, Ya-Mei Jin, Jiao-Jiao Lin
BACKGROUND: Schistosomiasis japonica is a common zoonosis. Domestic animals are the primary source of infection and play an important role in disease transmission. The prevalence and infectivity of this disease in domestic animals in China have significantly decreased and, for this reason, diagnostics with a higher sensitivity have become increasingly necessary. It was reported that polymerase chain reaction (PCR)-based methods could be used to detect schistosome infection in humans and animals and presented a high sensitivity and specificity...
April 13, 2017: Infectious Diseases of Poverty
https://www.readbyqxmd.com/read/28406973/tre5-a-retrotransposition-profiling-reveals-putative-rna-polymerase-iii-transcription-complex-binding-sites-on-the-dictyostelium-extrachromosomal-rdna-element
#13
Thomas Spaller, Marco Groth, Gernot Glöckner, Thomas Winckler
The amoeba Dictyostelium discoideum has a haploid genome in which two thirds of the DNA encodes proteins. Consequently, the space available for selfish mobile elements to expand without excess damage to the host genome is limited. The non-long terminal repeat retrotransposon TRE5-A maintains an active population in the D. discoideum genome and apparently adapted to this gene-dense environment by targeting positions ~47 bp upstream of tRNA genes that are devoid of protein-coding regions. Because only ~24% of tRNA genes are associated with a TRE5-A element in the reference genome, we evaluated whether TRE5-A retrotransposition is limited to this subset of tRNA genes...
2017: PloS One
https://www.readbyqxmd.com/read/28405714/recessive-male-sterility-in-cabbage-brassica-oleracea-var-capitata-caused-by-loss-of-function-of-bocyp704b1-due-to-the-insertion-of-a-ltr-retrotransposon
#14
Jia-Lei Ji, Li-Mei Yang, Zhi-Yuan Fang, Mu Zhuang, Yang-Yong Zhang, Hong-Hao Lv, Yu-Mei Liu, Zhan-Sheng Li
The LTR-retrotransposon insertion in BoCYP704B1 is proved to be the primary cause of the male sterility in cabbage. Effective allele-specific markers were developed for marker-assisted selection of male sterile gene. 83121A is a spontaneous male sterile mutant identified from cabbage. Genetic analysis indicated that male sterility is controlled by a single recessive gene. Pollen wall formation in the 83121A mutant was severely defective, with a lack of sporopollenin or exine. To understand the mechanisms of male sterility in 83121A, transcription analysis using RNA-Seq was carried out in the buds of the male sterile line 83121A and the male fertile line 83121B, which are near-isogenic lines differing only in the fertility trait...
April 12, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28403818/srnas-as-possible-regulators-of-retrotransposon-activity-in-cryptococcus-gattii-vgii
#15
Patrícia Aline Gröhs Ferrareze, Rodrigo Silva Araujo Streit, Francine Melise Dos Santos, Augusto Schrank, Livia Kmetzsch, Marilene Henning Vainstein, Charley Christian Staats
BACKGROUND: The absence of Argonaute genes in the fungal pathogen Cryptococcus gattii R265 and other VGII strains indicates that yeasts of this genotype cannot have a functional RNAi pathway, an evolutionarily conserved gene silencing mechanism performed by small RNAs. The success of the R265 strain as a pathogen that caused the Pacific Northwest and Vancouver Island outbreaks may imply that RNAi machinery loss could be beneficial under certain circumstances during evolution. As a result, a hypermutant phenotype would be created with high rates of genome retrotransposition, for instance...
April 12, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28398238/ltr-retrotransposons-from-bdelloid-rotifers-capture-additional-orfs-shared-between-highly-diverse-retroelement-types
#16
Fernando Rodriguez, Aubrey W Kenefick, Irina R Arkhipova
Rotifers of the class Bdelloidea, microscopic freshwater invertebrates, possess a highlydiversified repertoire of transposon families, which, however, occupy less than 4% of genomic DNA in the sequenced representative Adineta vaga. We performed a comprehensive analysis of A. vaga retroelements, and found that bdelloid long terminal repeat (LTR)retrotransposons, in addition to conserved open reading frame (ORF) 1 and ORF2 corresponding to gag and pol genes, code for an unusually high variety of ORF3 sequences...
April 11, 2017: Viruses
https://www.readbyqxmd.com/read/28394277/structure-of-ty1-internally-initiated-rna-influences-restriction-factor-expression
#17
Leszek Błaszczyk, Marcin Biesiada, Agniva Saha, David J Garfinkel, Katarzyna J Purzycka
The long-terminal repeat retrotransposon Ty1 is the most abundant mobile genetic element in many Saccharomyces cerevisiae isolates. Ty1 retrotransposons contribute to the genetic diversity of host cells, but they can also act as an insertional mutagen and cause genetic instability. Interestingly, retrotransposition occurs at a low level despite a high level of Ty1 RNA, even though S. cerevisiae lacks the intrinsic defense mechanisms that other eukaryotes use to prevent transposon movement. p22 is a recently discovered Ty1 protein that inhibits retrotransposition in a dose-dependent manner...
April 10, 2017: Viruses
https://www.readbyqxmd.com/read/28394248/highest-diploid-number-among-gymnotiformes-first-cytogenetic-insights-into-rhabdolichops-sternopygidae
#18
Pablo Suárez, Inaê Cristina Guerreiro Pinto Barroso, Danillo Dos Santos Silva, Susana S R Milhomem, Diogo Cavalcanti Cabral-de-Mello, Cesar Martins, Julio Cesar Pieczarka, Cleusa Yoshiko Nagamachi
We report the first comparative cytogenetic analysis of two species from electrogenic fish of genus Rhabdolichops (Sternopygidae, Gymnotiformes): Rhabdolichops troscheli and Rhabdolichops cf eastwardi. R. troscheli has 2n = 54 (fundamental number [FN] = 66), whereas R. cf. eastwardi has 2n = 74 (FN = 78). C-banding revealed centromeric constitutive heterochromatin in both species. Ag-NORs mapped on pair 6 in R. troscheli and pair 30 in R. cf eastwardi. Fluorescense in situ hybridization with 18S rDNA probes confirmed the Ag-NOR staining results and revealed additional (presumably silent) ribosomal genes on pairs 12, 13, 21, 23, 26, and 27 in R...
April 10, 2017: Zebrafish
https://www.readbyqxmd.com/read/28390408/a-comprehensive-hybridization-model-allows-whole-herv-transcriptome-profiling-using-high-density-microarray
#19
Jérémie Becker, Philippe Pérot, Valérie Cheynet, Guy Oriol, Nathalie Mugnier, Marine Mommert, Olivier Tabone, Julien Textoris, Jean-Baptiste Veyrieras, François Mallet
BACKGROUND: Human endogenous retroviruses (HERVs) have received much attention for their implications in the etiology of many human diseases and their profound effect on evolution. Notably, recent studies have highlighted associations between HERVs expression and cancers (Yu et al., Int J Mol Med 32, 2013), autoimmunity (Balada et al., Int Rev Immunol 29:351-370, 2010) and neurological (Christensen, J Neuroimmune Pharmacol 5:326-335, 2010) conditions. Their repetitive nature makes their study particularly challenging, where expression studies have largely focused on individual loci (De Parseval et al...
April 8, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28387035/the-frenemies-within-viruses-retrotransposons-and-plasmids-that-naturally-infect-saccharomyces-yeasts
#20
Paul A Rowley
Viruses are a major focus of current research efforts because of their detrimental impact on humanity and their ubiquity within the environment. Bacteriophages have long been used to study host-virus interactions within microbes, but it is often forgotten that the single-celled eukaryote Saccharomyces cerevisiae and related species are infected with double-stranded RNA viruses, single stranded RNA viruses, LTR-retrotransposons and double-stranded DNA plasmids. These intracellular nucleic acid elements have some similarities to higher eukaryotic viruses, i...
April 7, 2017: Yeast
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