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Terminal Repeat Sequences (1):
Recent article
Terminal Repeat Sequences
Abstract
We conduct an in silico analysis of the distribution and abundance of the full complement of 1045 copies in the updated AgamP3 assembly. Chromosomal distribution of Ty3/gypsy elements is inversely related to arm length, with densities being greatest on the X, and greater on the short versus long arm...
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PMID: 21283637
PDF is available here.
PDF is available here.
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Abstract
We demonstrate that RNAi also functions to repress genomic elements other than constitutive heterochromatin. Using DNA adenine methyltransferase identification (DamID), we show that the RNAi proteins Dcr1 and Rdp1 physically associate with some euchromatic genes, noncoding RNA genes and retrotranspo...
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PMID: 21151114
PDF is available here.
PDF is available here.
Abstract
We performed evolution experiments with Saccharomyces cerevisiae (yeast) in nitrogen-limited chemostat cultures. We used DNA microarrays to identify copy-number variation associated with adaptation and observed frequent amplifications and deletions at the GAP1 locus. GAP1 encodes the general amino a...
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PMID: 20937885
PDF is available here.
PDF is available here.
Abstract
We sequenced the long terminal repeats and part of the env region of enFeLVs in domestic cats and five wild species. A total of 305 enFeLV sequences were generated across 17 individuals, demonstrating considerable diversity within two major clades. Distinct proliferations of enFeLVs occurred before...
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PMID: 20615520
PDF is available here.
PDF is available here.
Abstract
We characterized the functional domains of BFV BTas. BTas contains two major functional domains: the N-terminal DNA-binding domain (residues 1-133) and the C-terminal activation domain (residues 198-249). The complete BTas responsive regions were mapped to the positions -380/-140 of LTR and 9205/927...
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PMID: 20615521
PDF is available here.
PDF is available here.
Abstract
We show that an LTR retrotransposon of ERV-9 human endogenous retrovirus located 40-70 kb upstream of the human fetal gamma- and adult beta-globin genes serves a long-range, host function. The ERV-9 LTR contains multiple CCAAT and GATA motifs and competitively recruits a high concentration of NF-Y a...
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PMID: 20615953
PDF is available here.
PDF is available here.
Journal of Bacteriology (192)13 2010
Abstract
We have analyzed the effects of IR mutations on both major transposition steps, the circle formation and integration of the abutted ends, characteristic for IS30. Several mutants show strikingly different phenotypes if the mutations are present at one or both ends and differentially influence the tr...
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PMID: 20418401
PDF is available here.
PDF is available here.
Journal of Virology (84)13 2010
Abstract
We minimized by setting up a split-packaging system expressing the necessary viral proteins in trans. Moreover, intact LTRs containing transcriptional elements are capable of activating cellular genes. By removing most of these transcriptional elements, we were able to generate a self-inactivating (...
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PMID: 20410274
PDF is available here.
PDF is available here.
Cell Stem Cell (6)5 2010
Abstract
We investigated paradigms of viral extinction. We show that trophectoderm stem cells do not silence retroviral transcription, whereas extraembryonic endoderm stem cells aggressively extinguish proviral transcription, even more rapidly than do embryonic stem cells. By using a short hairpin RNA librar...
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PMID: 20452320
PDF is available here.
PDF is available here.
Abstract
Two genotypes of porcine circovirus (PCV) have been described, the non-pathogenic PCV1 and the pathogenic PCV2 in pigs. PCV-ORF1 encodes Rep and Rep' proteins which have identical N-terminal sequence (RepN) within each PCV strain, but RepN has only 88% similarity between PCV1 and PCV2. Purified RepN...
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PMID: 20152863
PDF is available here.
PDF is available here.
Abstract
We demonstrated that TCS prevents HIV-1 DNA integration in a dose dependent manner in cell culture. At the same condition, TCS fails to induce obvious cytotoxicity and is also unable to interference viral early events such as viral entry, uncoating or reverse transcription. The HIV-1 integrase can i...
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PMID: 19669933
PDF is available here.
PDF is available here.
médecine/sciences (26)4 2010
Abstract
We described the characterization of a novel viral protein that we have termed HBZ for HTLV-1 bZIP factor. This viral factor is encoded on the antisense strand of HTLV-1 proviral DNA, demonstrating the existence of antisense transcription from a promoter located in the 3' LTR. HBZ can negatively con...
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PMID: 20412744
PDF is available here.
PDF is available here.
Abstract
Retrotransposons constitute a major proportion of the Triticeae genomes. Genome-scale studies have revealed their role in evolution affecting both genome structure and function and their potential for the development of novel markers. In this study, family members of an LTR copia ret...
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PMID: 20127492
PDF is available here.
PDF is available here.
Abstract
We constructed a full-length infectious BAC clone of MDV-GX0101 strain and deleted the LTR sequences by BAC mutagenesis. The pathogenic properties of the LTR-deleted virus were evaluated in infected SPF birds. The study demonstrated that the LTR-deleted virus had a stronger inhibitory effect on the...
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PMID: 19962172
PDF is available here.
PDF is available here.
Avian Pathology (39)1 2010
Abstract
An outbreak of acute respiratory disease in layers was diagnosed as being of dual nature due to fowlpox and infectious laryngotracheitis using a multidisciplinary approach including virus isolation, histopathology, electron microscopy and polymerase chain reaction (PCR). The diagnosis was based on v...
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PMID: 20390533
PDF is available here.
PDF is available here.
Genes & Development (24)3 2010
Abstract
We use pluripotent embryonic stem (ES) cells to demonstrate an unexpected redundancy between Polycomb-repressive complex 1 (PRC1) and PRC2 during the formation of differentiated cells. ES cells lacking the function of either PRC1 or PRC2 can differentiate into cells of the three germ layers, whereas...
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PMID: 20123906
PDF is available here.
PDF is available here.
Abstract
We showed that the solitary LTR residing in the KIAA1245/NBPF gene subfamily displayed high enhancer activity in a transformed embryonal carcinoma cell line Tera1. In this study, we performed a functional dissection of the LTR and studied its deletion series. Using transient transfection assay, we c...
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PMID: 20873221
PDF is available here.
PDF is available here.
Genetika (Moskva) (46)1 2010
Abstract
Species-specific LTR retrotransposons were first cloned in five rare relic species of drug plants located in the Perm' region. Sequences of LTR retrotransposons were used for PCR analysis based on amplification of repeated sequences from LTR or other sites of retrotransposons (IRAP). Genetic diversi...
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PMID: 20198878
PDF is available here.
PDF is available here.
Abstract
We report that the transcription of the telomeric retroelements SART1 and TRAS1 is suppressed by the silkworm Piwi subfamily proteins BmAgo3 and Siwi. The silkworm Piwi subfamily was found to be expressed predominantly in the gonads and early embryo, as in other model organisms, but in BmN4 cultured...
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PMID: 19943120
PDF is available here.
PDF is available here.
Abstract
A long-range PCR method directed at the Myxoma virus (MV) left hand and right hand terminal inverted repeats (TIRs) for rapid amplification of genomic DNA and MV isolate differentiation by restriction fragment length polymorphism (RFLP) analysis is described. The efficacy of this method was tested b...
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PMID: 19591871
PDF is available here.
PDF is available here.
Biochemistry (Washington) (48)30 2009
Abstract
We report the biochemical study of two copies of the Pacmmar element (Pacmmar1.1 and Pacmmar1.2), isolated from the coastal crab Pachygrapsus marmoratus. These two copies present an open reading frame encoding a putative active transposase. Using an in vitro transposition assay, we show that Pacmmar...
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PMID: 19530701
PDF is available here.
PDF is available here.
Bioinformatics (25)10 2009
Abstract
MOTIVATION: The large number of sequenced genomes required the development of software that reconstructs the consensus sequences of transposons and other repetitive elements. However, the available tools usually focus on the accurate identification of raw repeats and provide no information about the...
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PMID: 19349283
PDF is available here.
PDF is available here.
Abstract
We developed a quantitative assay based on real-time reverse transcriptase--PCR on low-density arrays to evaluate alterations of gene expression in individual primary T-cell clones. We show that the Moloney leukemia virus long terminal repeat (LTR) enhancer has the strongest activity in both a gamma...
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PMID: 19293778
PDF is available here.
PDF is available here.
FASEB Journal (23)5 2009
Abstract
We show that some full-length copies of tirant are present in heterochromatic regions in Drosophila simulans and that when tested in vitro, these copies have a functional promoter. However, when inserted in heterochromatic regions, tirant copies are inactive in vivo, and only transcription of euchro...
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PMID: 19141532
PDF is available here.
PDF is available here.
Immunogenetics (61)4 2009
Abstract
Our study shows that the nucleotide variations of the MER9-LTR DNA sequences are additional informative markers in fine mapping HLA-A genomic haplotypes for future population, evolutionary, and disease studies....
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PMID: 19294374
PDF is available here.
PDF is available here.
Abstract
mortality and tumor rates of GX0101 were 28.6% and 7.1% for SPF chickens viccinated against Marek's disease virus. Mortality and tumor rates of vvMd5 were 63.1% and 19.0% in the same viccinated SPF chickens. Mortality and tumor rates of GX0101 were lower than that of vvMd5. However, horizontal trans...
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PMID: 19621645
PDF is available here.
PDF is available here.
Avian Diseases (53)1 2009
Abstract
A total of 15 Mycoplasma gallisepticum (MG) isolates from Chinese poultry farms and three reference strains (S6, BG44T, and F36) were characterized by nested polymerase chain reaction and sequence analysis for two identical and directly repeated sequences, DR-1 and DR-2, within the putative cytadhes...
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PMID: 19432015
PDF is available here.
PDF is available here.
Genetika (Moskva) (45)2 2009
Abstract
Using a model system in which the expression of the reporter gene lacZ is under the control of five deleted variants of the copia retrotransposon regulatory region, which includes the 5'-long terminal repeat (LTR) and the 5'-untranslated region (5'-UTR), their contribution to the control of retrotra...
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PMID: 19334610
PDF is available here.
PDF is available here.
Molecules and Cells (27)1 2009
Abstract
Porcine endogenous retroviruses (PERVs) gamma1 in the pig genome have the potential to act as harmful factors in xenotransplantation (pig-to-human). Long terminal repeats (LTRs) are known to be strong promoter elements that could control the transcription activity of PERV elements and the adjacent f...
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PMID: 19214442
PDF is available here.
PDF is available here.
Abstract
Non-long terminal repeat (non-LTR) retrotransposons have contributed to shaping the structure and function of genomes. Fungi have small genomes, usually with limited amounts of repetitive DNA. In silico approach has been used to survey the non-LTR elements in 57 fungal genomes. More than 100 novel n...
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PMID: 18677522
PDF is available here.
PDF is available here.
Abstract
We have conditionally ablated the Rbpj gene in the mammary glands of mice expressing whey acidic protein (Wap)-Int3. Interestingly, Rbpj knockout mice (Wap-Cre(+)/Rbpj(-/-)/Wap-Int3) have normal mammary gland development, suggesting that the effect of endogenous Notch signaling on mammary gland deve...
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PMID: 18836481
PDF is available here.
PDF is available here.
Abstract
We report here the first complete HTLV-4 sequence obtained by PCR-based genome walking using uncultured peripheral blood lymphocyte DNA from an HTLV-4-infected person. The HTLV-4(1863LE) genome is 8791-bp long and is equidistant from HTLV-1, HTLV-2, and HTLV-3 sharing only 62-71% nucleotide identity...
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PMID: 19187529
PDF is available here.
PDF is available here.
Abstract
We have identified an LTR-retrotransposon, that we named Route66, with more than 95% sequence identity between rice and Sorghum. Using a combination of in silico and molecular approaches, we are able to present a substantial phylogenetic evidence that Route66 has been transferred horizontally betwee...
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PMID: 19291296
PDF is available here.
PDF is available here.
Genome Biology (10)1 2009
Abstract
Our analyses show that the platypus has significantly fewer repeats of certain classes in the regions of the genome that have become imprinted in therian mammals. The accumulation of repeats, especially long terminal repeats and DNA elements, in therian imprinted genes and gene clusters is coinciden...
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PMID: 19121219
PDF is available here.
PDF is available here.
Journal of Virology (83)2 2009
Abstract
The nucleotide sequence of the highly divergent small-ruminant lentivirus genotype E has been determined. The full genome consists of 8,418 nucleotides and lacks two large portions corresponding nearly to the entire dUTPase subunit of the pol and vpr-like accessory genes. Moreover, the 70-bp repeat...
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PMID: 18987157
PDF is available here.
PDF is available here.
Biophysical Journal (95)12 2008
Abstract
We have created a model polyQ protein in which the repeat location mimics the flexible environment of the polyQ tract in the disease proteins. Our model protein recapitulates the aggregation features observed with the clinical proteins and allows structural characterization. With the use of NMR spec...
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PMID: 18849414
PDF is available here.
PDF is available here.
Plant Physiology (148)4 2008
Abstract
We present an analysis of retrotransposons in soybean (Glycine max). Analysis of approximately 3.7 megabases (Mb) of genomic sequence, including 0.87 Mb of pericentromeric sequence, uncovered 45 intact long terminal repeat (LTR)-retrotransposons. The ratio of intact elements to solo LTRs was 8:1, on...
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PMID: 18952860
PDF is available here.
PDF is available here.
Abstract
We report the fixation of a non-LTR retroelement in five species (Drosophila littoralis, Drosophila virilis, Drosophila lummei, Drosophila americana and Drosophila novamexicana) of the virilis group of Drosophila. In most species, this TE insertion is being lost through the accumulation of small del...
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PMID: 18775768
PDF is available here.
PDF is available here.
Journal of Virology (82)24 2008
Abstract
The molecular mechanisms utilized by human immunodeficiency virus (HIV) to enter latency are poorly understood. Following the infection of Jurkat T cells with lentiviral vectors that express Tat in cis, gene expression is progressively silenced. Silencing is greatly enhanced when the lentiviral vect...
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PMID: 18829756
PDF is available here.
PDF is available here.
Journal of Nutrition (138)12 2008
Abstract
We demonstrate that the covalent binding of the vitamin biotin to lysine-12 in histone H4 (H4K12bio) and lysine-9 in histone H2A (H2AK9bio), mediated by holocarboxylase synthetase (HCS), is an epigenetic mechanism to repress retrotransposon transcription in human and mouse cell lines and in primary...
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PMID: 19022951
PDF is available here.
PDF is available here.
Abstract
A copia-like retrotransposon referred to as PyRE1G1 was isolated from the genome of the red alga Porphyra yezoensis. PyRE1G1 is 4807 bp in length, with 204 bp long terminal repeats (LTRs) at both ends. PyRE1G1 has an open reading frame of 1401 residues encoding gag, protease, integrase, reverse tran...
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PMID: 18708130
PDF is available here.
PDF is available here.
Abstract
We found that the addition of target DNA to the mixture of nonmodified Au-NRs suspension and label-free probe DNA in high ionic strength buffer leads to a color change from red to light purple in less than 5 min, displaying strong plasmon resonance light scattering (PRLS) signals. Mechanism investig...
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PMID: 18937420
PDF is available here.
PDF is available here.
Abstract
The presence of the micropia retroelement from the Ty1-copia family of LTR retroelements was investigated in three species of the Drosophila cardini group. Southern blot analysis suggested the existence of at least four micropia copies in the genomes of D. cardinoides, D. neocardini and D. polymorph...
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PMID: 18259879
PDF is available here.
PDF is available here.
Plant Journal (56)4 2008
Abstract
We have combined a search of chromodomain-containing Gypsy retroelements in Physcomitrella genomic sequences and an experimental investigation of diverse moss species. The computer-based mining of the chromodomain-containing LTR retrotransposons allowed us to describe four different elements from Ph...
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PMID: 18643967
PDF is available here.
PDF is available here.
Abstract
We investigated whether HIV plays a direct role in HPV-associated oral carcinogenesis by using HIV-1 transactivator protein (Tat), which is known to have oncogenic properties. We found that HIV-1 Tat not only increased the expression of HPV-16 E6 and E7 oncogenes in human oral keratinocytes harborin...
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PMID: 18813791
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)17 2008
Abstract
We examined the conservation and divergence of different types of alternative poly(A) sites across human, mouse, rat and chicken. We found that the 3'-most poly(A) sites tend to be more conserved than upstream ones, whereas poly(A) sites located upstream of the 3'-most exon, also termed intronic pol...
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PMID: 18757892
PDF is available here.
PDF is available here.
Journal of Virology (82)19 2008
Abstract
We characterize the promoters of the spliced version of the HBZ gene (sHBZ) and the unspliced version of the HBZ gene (usHBZ) by luciferase assay. Both promoters were TATA-less and contained initiators and downstream promoter elements. Detailed studies of the promoter for the sHBZ gene showed that S...
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PMID: 18653454
PDF is available here.
PDF is available here.
Journal of General Virology (89)Pt 10 2008
Abstract
We aimed to determine the commonality of this phenomenon and analysed FWPVs collected from 128 poultry flocks and birds over the last 10 years. Various fragments of both viruses were amplified and sequenced at the FWPV integration site, located between FWPV open reading frames 201 and 203. Seven iso...
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PMID: 18796713
PDF is available here.
PDF is available here.
Abstract
The frequency and HLA-A allelic associations of a HERVK9 DNA structural polymorphism located in close proximity to the highly polymorphic HLA-A gene within the major histocompatibility complex (MHC) genomic region were determined in Japanese, African Americans, and Australian Caucasians to better un...
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PMID: 18757922
PDF is available here.
PDF is available here.
Abstract
Mouse mammary tumor virus has served as a major model for the study of breast cancer since its discovery 1920's as a milk-transmitted agent. Much is known about in vivo infection by this virus, which initially occurs in lymphocytes that then carry virus to mammary tissue. In addition to the virion p...
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PMID: 18661104
PDF is available here.
PDF is available here.
Abstract
We previously discovered that Ty1 transcription is activated under conditions of severe adenine starvation. The mechanism of activation is independent of the Bas1 transcriptional activator of the de novo AMP biosynthesis pathway and probably involves chromatin remodeling at the Ty1 promoter. Here, w...
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PMID: 18591253
PDF is available here.
PDF is available here.
Abstract
We carried out a genetic characterization of a large set of HTLV-1 strains (n = 65) of descendants of Amerindians from this region. The LTR and env regions were analyzed. The genetic analysis showed that all of these new HTLV-1 isolates from Argentina belong to the Transcontinental subgroup A of the...
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PMID: 18657044
PDF is available here.
PDF is available here.
Journal of Virology (82)17 2008
Abstract
We previously reported that a mutant Rous sarcoma virus (RSV) with an alternate polypurine tract (PPT), DuckHepBFlipPPT, had unexpectedly high titers and that the PPT was miscleaved primarily at one position following a GA dinucleotide by the RNase H of reverse transcriptase (RT). This miscleavage r...
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PMID: 18562520
PDF is available here.
PDF is available here.
Journal of Virology (82)18 2008
Abstract
We recently constructed an SIVmac variant that does not require the Tat-TAR interaction for transcription. We used this variant to study additional roles of TAR in SIVmac replication and generated mutants with a truncated TAR structure. We demonstrate that partial or nearly complete removal of TAR d...
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PMID: 18596090
PDF is available here.
PDF is available here.
Molecules and Cells (26)1 2008
Abstract
We characterized the human endogenous retrovirus (HERV-W) family in humans and primates. In silico expression data indicated that 22 complete HERV-W families from human chromosomes 1-3, 5-8, 10-12, 15, 19, and X are randomly expressed in various tissues. Quantitative real-time RT-PCR analysis of the...
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PMID: 18525236
PDF is available here.
PDF is available here.
Abstract
Under controlled conditions, little difference in silage quality and microbial composition were observed between ensiling systems and this was further reflected in the T-RFLP community analysis. SIGNIFICANCE AND IMPACT OF THE STUDY: T-RFLP proved a potentially useful tool to study the ensilage proce...
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PMID: 18422959
PDF is available here.
PDF is available here.
Journal of Gene Medicine (10)8 2008
Abstract
This assay system might provide a useful tool for selecting the appropriate vector structure, as well as for studying the molecular mechanism underlying the cis-activation by the viral LTR.
(c) 2008 John Wiley & Sons, Ltd....
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PMID: 18563862
PDF is available here.
PDF is available here.
Animal Genetics (39)4 2008
Abstract
We have herein identified nine non-LTR retrotransposons, among which several appear to exist outside the standard defined clades. Two Litopenaeus stylirostris elements were discovered through degenerate PCR amplification using previously defined non-LTR degenerate primers, and through primers design...
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PMID: 18557973
PDF is available here.
PDF is available here.
Journal of Parasitology (94)4 2008
Abstract
We were able to map these retrotransposons. Perere 03 was localized in the euchromatic regions of the short arm of chromosome 2 and Boudicca in the euchromatic regions of the short arm of chromosomes 2 and Z....
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PMID: 18576699
PDF is available here.
PDF is available here.
Journal of Virology (82)16 2008
Abstract
Feline immunodeficiency virus (FIV) causes progressive immunodeficiency in domestic cats, with clinical course dependent on virus strain. For example, clade A FIV-PPR is predominantly neurotropic and causes a mild disease in the periphery, whereas clade C FIV-C36 causes fulminant disease with CD4(+)...
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PMID: 18550665
PDF is available here.
PDF is available here.