[Nuclear factor kappa B (NF-kappa B). I. Function and regulation].
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Animals↗
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Results for “Terminal Repeat Sequences”
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Identification of multiple Gypsy LTR-retrotransposon lineages in vertebrate genomes.
Gypsy LTR-retrotransposons have been identified in the genomes of many organisms, but only a small number of vertebrate examples have been reported to date. Here we show that members of this family are likely to be widespread in many vertebrate classes with the possible exceptions of mammals and birds. Phylogenetic analyses demonstrate that although there are several distinct lineages of vertebrate gypsy LTR-retrotransposons, the majority clusters into one monophyletic clade. Groups of fungal, plant, and insect elements were also observed, suggesting horizontal transfer between phyla may be infrequent. However, in contrast to this, there was little evidence to support sister relationships between elements derived from vertebrate and insect hosts. In fact, the majority of the vertebrate elements appeared to be most closely related to a group of gypsy LTR-retrotransposons present within fungi. This implies either that at least one horizontal transmission between these two phyla has occurred previously or that a gypsy LTR-retrotransposon lineage has been lost from insect taxa.
Animals↗
A detailed linkage map of lettuce based on SSAP, AFLP and NBS markers.
Molecular markers based upon a novel lettuce LTR retrotransposon and the nucleotide binding site-leucine-rich repeat (NBS-LRR) family of disease resistance-associated genes have been combined with AFLP markers to generate a 458 locus genetic linkage map for lettuce. A total of 187 retrotransposon-specific SSAP markers, 29 NBS-LRR markers and 242 AFLP markers were mapped in an F(2) population, derived from an interspecific cross between a Lactuca sativa cultivar commonly used in Europe and a wild Lactuca serriola isolate from Northern Europe. The cross has been designed to aid efforts to assess gene flow from cultivated lettuce into the wild in the perspective of genetic modification biosafety. The markers were mapped in nine major and one minor linkage groups spanning 1,266.1 cM, with an average distance of 2.8 cM between adjacent mapped markers. The markers are well distributed throughout the lettuce genome, with limited clustering of different marker types. Seventy-seven of the AFLP markers have been mapped previously and cross-comparison shows that the map from this study corresponds well with the previous linkage map.
Chromosome Mapping↗
Distribution of HERV-LTR elements in HLA-DQB1 alleles: comments on the article by Bieda et al.
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Diabetes Mellitus, Type 1↗
Immunohistochemical study of tau accumulation in early stages of Alzheimer-type neurofibrillary lesions.
Accumulation of abnormally phosphorylated tau results in the formation of neurofibrillary tangles (NFTs) in the neuronal cell soma and neuropil threads (NTs) in the cell processes. In the present study, we used immunohistochemistry to investigate serially cut thick tissue sections from the brains of patients with Alzheimer's disease (AD) and non-demented elderly subjects. In the early stages of neurofibrillary pathology, clusters of NTs occurred occasionally in the cerebral cortex. Each NTs cluster, the entire extent of which was observed in the serial sections, corresponded to a dendritic tree that was arborized from a tau-positive neuron. Adult human brain contains six tau isoforms with three having three carboxyl-terminal tandem repeat sequences that are encoded by exon 10 (3R-tau) and the other three having four repeat sequences (4R-tau). Three isoform patterns, 3R-tau(+)/4R-tau(-), 3R-tau(-)/4R-tau(+) and 3R-tau(+)/4R-tau(+), were seen in NFTs in early stage AD lesions. In an individual neuron, the isoform pattern was consistent between the NFTs in the cell soma and the NTs in the cell processes. The results of this study indicate that, in early stages of AD and age-associated neurofibrillary changes, tau accumulates simultaneously in the cell soma and cell processes of affected neurons. The process of AD and age-associated tau pathology is not tau-isoform-specific, but the ratio of 3R-tau and 4R-tau isoforms involved in the neurofibrillary changes varies and is specific to individual neurons.
Aged↗
Mechanisms regulating the copy numbers of six LTR retrotransposons in the genome of Drosophila melanogaster.
There has been debate over the mechanisms that control the copy number of transposable elements in the genome of Drosophila melanogaster. Target sites in D. melanogaster populations are occupied at low frequencies, suggesting that there is some form of selection acting against transposable elements. Three main theories have been proposed to explain how selection acts against transposable elements: insertions of a copy of a transposable element are selected against; chromosomal rearrangements caused by ectopic exchange between element copies are selected against; or the process of transposition itself is selected against. The three theories give different predictions for the pattern of transposable element insertions in the chromosomes of D. melanogaster. We analysed the abundance of six LTR (long terminal repeat) retrotransposons on the X and fourth chromosomes of multiple strains of D. melanogaster, which we compare with the predictions of each theory. The data suggest that no one theory can account for the insertion patterns of all six retrotransposons. Comparing our results with earlier work using these transposable element families, we find a significant correlation between studies in the particular model of copy number regulation supported by the proportion of elements on the X for the different transposable element families. This suggests that different retrotransposon families are regulated by different mechanisms.
Animals↗
Amplification of a long terminal repeat-like element on the Y chromosome of the platyfish, Xiphophorus maculatus.
The platyfish (Xiphophorus maculatus), in which sex chromosomes are evident from stable and predictable inheritance of sex, is one of the best-studied lower vertebrates with respect to sex determination. In order to identify the structural equivalent for this in the karyotype, which does not contain heteromorphic pairs of chromosomes, two sex-linked molecular probes were used for fluorescent in situ hybridization analysis. One probe, derived from the melanoma oncogene locus ONC-Xmrk, stained both the X and the Y chromosome. This cytogenetic analysis mapped the sex-determining locus to the subtelomeric region of a medium-sized telocentric chromosome. Another probe, a repetitive element (XIR), specifically labeled the Y chromosome in metaphase spreads and in interphase nuclei. The sex chromosomes of X. maculatus can be considered to be at an early stage of evolution of gonosomes. Expansion of the XIR repeat is obviously one of the earliest of the molecular events that lead to divergence of the Y chromosome and recombinational isolation of the sex-determining locus.
Alleles↗
Coordinating Y-chromosomal STR research for the Courts.
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Chromosome Mapping↗
Telomere shortening in gastric carcinoma with aging despite telomerase activation.
In the present study, we analyzed both telomere length and telomerase activity in surgical and autopsy samples of non-neoplastic mucosa and carcinomas of the stomach. Telomere length, determined by Southern blot analysis, demonstrated progressive shortening with age in non-neoplastic gastric mucosal specimens from 38 human subjects aged between 0 and 99 years, with an average annual loss rate of 46 base pairs (bp). The mean (+/- SD) telomere length in 21 gastric carcinomas was 7.0 +/- 1.6 x 10(3) base pairs (1.6 kbp). In 20 (95%) of the 21 subjects, the values were smaller than those in the nonneoplastic gastric mucosa (mean shortening 1.8 kbp), although a strong correlation was observed for the paired data (r = 0.69, P = 0.0004). Similarly, telomere lengths in carcinomas were shorter than those for intestinal metaplasia (a mean difference of 1.1 kbp). Telomerase activity, estimated using the telomeric repeat amplification protocol assay, was positive in 18 (86%) of the 21 gastric carcinomas, without significant differences among the three histological types (well, moderately, and poorly differentiated adenocarcinomas) or with sex or age. The results suggest that telomere length and possibly shortening rates vary with the individual, and that examination of both non-neoplastic mucosa and tumors is necessary to improve our understanding of the significance of telomerase in neoplasia.
Adenocarcinoma↗
Evidence for horizontal transfer of the LTR retrotransposon mdg3, which lacks an env gene.
Horizontal (interspecific) transfer is regarded as a possible strategy for the propagation of transposable elements through evolutionary time. To date, however, conclusive evidence that transposable elements are capable of horizontal transfer from one species to another has been limited to class II or DNA-type elements. We tested the possibility of such transfer for several Drosophila melanogaster LTR retrotransposons of the gypsy group in an experiment in which D. melanogaster and D. virilis somatic cell lines were used as donor and recipient cells, respectively. This approach was chosen in light of the high levels of LTR retrotransposon amplification and expression observed in cultured D. melanogaster cells. In the course of the experiment, parallel analysis for mdg1, mdg3, 17.6, 297, 412 and B104/roo retrotransposons was performed to detect their presence in the genome of recipient cells. Only the mdg3 retrotransposon, which lacks an env gene, was found to be transmitted into recipient cells. This model, based on the use of cultured cells, is a promising system for further investigating the mechanisms of LTR retrotransposon transfer.
Animals↗
Discovery and evolution of endogenous retroviruses in the genome of crab-eating macaque (Macaca fascicularis).
Endogenous retroviruses (ERVs) are a dynamic and biologically significant component of vertebrate genomes, with integration events spanning deep evolutionary time. The crab-eating macaque (Macaca fascicularis) is an important non-human primate model for biomedical research because of its close phylogenetic relationship to humans and its conservation status as an endangered species. However, the ERV complement of its genome has not been systematically characterized. Using the current highest-quality chromosome-level genome assembly for this species, we performed a genome-wide, homology-based survey of relatively intact ERV proviruses in M. fascicularis. We identified 106 proviral loci distributed across all chromosomes. Phylogenetic reconstruction based on conserved reverse transcriptase domains classified these elements into β-, γ-, and unclassified lineages, with β- and γ-retroviral lineages predominating. LTR divergence-based dating indicated that these proviruses represent multiple waves of historical retroviral activity and span a broad range of integration ages. This curated dataset provides a high-confidence reference set for investigating the evolutionary history and genomic impact of preserved ERV proviruses in an endangered primate model; however, it does not include degraded ERV fragments or solo LTRs.
Animals↗
A maize MuDR transposon promoter shows limited autoregulation.
Transgenic maize expressing luciferase under the control of the mudrB terminal inverted repeat promoter (TIRB) of the MuDR transposon was assayed for transgene expression in active and inactive Mutator lines. We find that active MuDR elements increase TIRB-luciferase expression by 2- to 10-fold, relative to nonMuDR or silenced MuDR lines, in embryonic leaves in 75% of plants tested. However, this increase does not persist in juvenile and adult leaves. In pollen, TIRB-luciferase expression is up to 100-fold higher than in leaves but is unaffected by the presence or absence of active MuDR. Because the MuRA transposase binds to a motif within TIRB, we hypothesize that MURA may act as a weak transcriptional activator of TIRB or may partly inhibit host-induced silencing of TIRB in active Mutator lines during the early stages of somatic growth. Our results contrast with those for the maize transposon Spm, in which the TNPA transposase acts as a repressor of the Spm promoter in active Spm lines.
DNA Transposable Elements↗
Effect of deletion and the site of insertion in double copy anti-tat retroviral vectors: viral titres and production of anti-tat mRNA.
In attempts to further develop murine leukemia virus (MLV) based retroviral vectors for gene therapy, we investigated vector production and antisense expression from retroviral constructs with U3 deletions or insertions. Promoter elements in the U3 region of the 3' LTR of the vector pLXSN were deleted and replaced with DNA encoding the HIV anti-tat gene under control of the tRNAmet promoter to produce a double copy self inactivating vector (DC-SIN). DC-SIN constructs were compared to vectors containing the anti-tat cassette inserted at 5 different sites of the U3 region (DC-insertions). Titres of DC-SIN and DC-insertion vectors were similar but approximately 10 fold lower than parental pLXSN. Cells transduced with DC-SIN and DC-insertion vectors all expressed anti-tat mRNA. Transcripts from the MLV-LTR were detected in cells transduced with DC-insertion but not DC-SIN vectors or a vector with the anti-tat cassette between CAAT and TATA boxes of the promoter, indicating inactivation of the viral promoter in the latter vectors. Cells transduced with constructs of either design showed comparable efficacy of protection against HIV challenge. Thus, no U3 insertion site was preferred for virus production. Insertion of a tRNA promoter between CAAT and TATA boxes and the DC-SIN design which would not introduce an active RNA pol II promoter into the genome are attractive for further development of safe gene therapy agents.
Genes, tat↗
Thermal blockage of viruslike particle formation for the yeast retrotransposon Ty3 reveals differences in the cellular stress response.
The long terminal repeat (LTR) retrotransposons of the yeast Saccharomyces cerevisiae are similar in their structures and life cycles to animal retroviruses. The yeast LTR retrotransposon Ty3 does not transpose under conditions where the cellular stress response is activated. During stress, mature Ty3 proteins, indicative of the formation of intracellular Ty3 viruslike particles (VLPs), do not accumulate. In order to examine the role of stress proteins in Ty3 transposition, a sensitive genetic assay was developed to measure VLP formation. The assay employs a Ty3 element marked with a mutant allele of the yeast HIS3 gene (his3AI). To create a stable His+ phenotype, Ty3 must form VLPs, reverse transcribe Ty3 RNA into cDNA, and then insert the cDNA into either chromosomal or plasmid DNA. Using this assay, thermal inhibition of Ty3 transposition was evident at temperatures as low as 30 degrees C. The level of production of mature Ty3 proteins parallels the transposition frequency. Although overexpression of the yeast UBP3 gene allows VLPs to form and transposition to occur in the constitutively stressed ssa1 ssa2 strain, it does not alleviate the inhibition of these processes during stress induced by heat or ethanol. This suggests that the genetic and physical modes of stress response induction are not equivalent.
Endopeptidases↗
Regulation of exogenous gene expression by superoxide.
PURPOSE: Regulation of gene expression after gene introduction is a problematic aspect of gene therapy. Transcription regulates gene-specific transcriptional factors, which bind to regulatory regions in the promoter. The cytomegalovirus long terminal repeat (CMV-LTR) has a TPA response element (TRE) as a binding site for activator protein 1 (AP-1), which is induced by oxidative stress. The purpose of this study was to regulate exogenous gene expression in a vector with CMV-LTR using oxygen radicals. METHODS: We used two plasmids (1) pQBI25 encoding CMV-LTR and red-shift green fluorescent protein (rsGFP) cDNA and (2) pRc/CMV-SOD encoding CMV-LTR and human Cu, Zn-superoxide dismutase (SOD) cDNA. FR cells were transfected with pQBI25 (FR-pQBI25 cells), and L2 cells were transfected with pRc/CMV-SOD (L2-pRc/CMV-SOD cells). Each type of cell was exposed to oxygen radicals using paraquat for 24 h. Levels of c-fos, c-jun and rsGFP mRNAs were determined using reverse transcription polymerase chain reaction (RT-PCR). Levels of rsGFP protein were measured by fluorometry. Total SOD activity was measured using the nitrite method. RESULTS: Levels of c-fos, c-jun (AP-1 composition protein) and rsGFP mRNA were induced significantly by oxygen radical exposure in FR-pQBI25 cells. A positive correlation was observed between levels of c-fos mRNA and rsGFP mRNA and also between levels of c-jun mRNA and rsGFP mRNA. Levels of rsGFP protein were also induced significantly. Total SOD activity was induced significantly by oxygen radical exposure in L2-pRc/CMV-SOD cells. CONCLUSIONS: This study suggests that gene expression driven by the CMV- LTR promoter may be regulated by oxygen radicals.
Animals↗
Development of an acid-soluble assay for measuring retrovirus integrase 3'-OH terminal nuclease activity.
A quantitative and efficient assay was developed to measure the 3'-OH terminal DNA endonuclease activity of the avian myeloblastosis virus (AMV) integrase protein. A retroviral-like linearized plasmid containing long terminal repeat (LTR) sequences at its recessed 3'-OH termini was filled in and labeled with the Escherichia coli Klenow DNA polymerase fragment. The 32P-labeled nucleotide was located at the penultimate position. The labeled linearized plasmid or restriction fragments derived from it were incubated with AMV IN and release of the label was quantitated by conversion to acid-soluble counts. The structure of the released product was characterized on 23% sequencing gels. Results indicate that AMV integration protein is functioning as an endonuclease releasing a dinucleotide and that the activity is stoichiometric with a preference for the cleavage of the U3 LTR terminus over that of the U5 LTR terminus.
Avian Myeloblastosis Virus↗
Molecular cloning of unintegrated closed circular DNA of porcine retrovirus.
Viral DNA of unintegrated closed circular form was isolated from a swine kidney cell line (SKL) which was infected with a porcine retrovirus Tsukuba-1 (PRetV) produced from a swine malignant lymphoma-derived cell line. Shimozuma-1 and cloned using a lambda phage vector, Charon 21A. One of ten independent clones contained the 8.3 kb DNA fragment as an insert, which was thought to be a full length of viral DNA molecule carrying a long terminal repeat (LTR) sequence. We have analyzed this insert by mapping the recognition sites of some restriction endonucleases by Southern blot hybridization with appropriate probes.
Animals↗
Site-specific rearrangements in the long terminal repeat of extra mouse mammary tumor proviruses in murine T-cell leukemias.
Extra MMTV proviruses in T-cell leukemias of GR and C57/BL10 mice contain alterations in their long terminal repeat (LTR) sequence. The four different leukemias studied contain different deletions, but common hallmarks were observed around the recombination sites. At the 5' end of the deletions we observed a common nonamer sequence, AGACAGGTG, in two leukemias and an almost identical sequence, AGAGCAGGTG, in two other leukemias. At the 3' end of the deletions we invariably found a common stretch of five nucleotides, TTAAA. Three of the four leukemias showed nonconserved crossover sites. The deletions in two leukemias were replaced with neighboring sequences, generating direct repeats. The MMTV LTR characteristic open reading frame and glucocorticoid response element were altered in all four rearranged MMTV LTRs. These results demonstrate site specific rearrangements in the LTR of extra MMTV proviruses in T-cell leukemias and suggest that these rearrangements might permit expression of MMTV in a new target cell.
Animals↗