Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Terminal Repeat Sequences”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,081 records · Page 60Linked to original sources
PubMed2006

Tracing the origin of Brazilian HTLV-1 as determined by analysis of host and viral genes.

We compared the genetic diversity of the Brazilian human T-cell lymphotropic virus type 1 isolates with those found in KwaZulu-Natal (KZN), South Africa, and with the genetic background of the hosts. The seroprevalence rate in KZN was 1.7%. All sequences belonged to the A subgroup. The presence of South African sequences in two different clusters from Brazil, and the finding of the beta-globin haplotype in infected hosts are consistent with the transmission of this virus from southern Africa to Brazil.

Brazil↗
PubMed2000

The 5' RNA terminus of spleen necrosis virus stimulates translation of nonviral mRNA.

The RU5 region at the 5' RNA terminus of spleen necrosis virus (SNV) has been shown to facilitate expression of human immunodeficiency virus type 1 (HIV) unspliced RNA independently of the Rev-responsive element (RRE) and Rev. The SNV sequences act as a distinct posttranscriptional control element to stimulate gag RNA nuclear export and association with polyribosomes. Here we sought to determine whether RU5 functions to neutralize the cis-acting inhibitory sequences (INSs) in HIV RNA that confer RRE/Rev dependence or functions as an independent stimulatory sequence. Experiments with HIV gag reporter plasmids that contain inactivated INS-1 indicated that neutralization of INSs does not account for RU5 function. Results with luciferase reporter gene (luc) plasmids further indicated that RU5 stimulates expression of a nonretroviral RNA that lacks INSs. Northern blot and RT-PCR analyses indicated that RU5 does not increase the steady-state levels or nuclear export of the luc transcript but rather that the U5 region facilitates efficient polyribosomal association of the mRNA. RU5 does not function as an internal ribosome entry site in bicistronic reporter plasmids, and it requires the 5'-proximal position for efficient function. Our results indicate that RU5 contains stimulatory sequences that function in a 5'-proximal position to enhance initiation of translation of a nonretroviral reporter gene RNA. We speculate that RU5 evolved to overcome the translation-inhibitory effect of the highly structured encapsidation signal and other replication motifs in the 5' untranslated region of the retroviral RNA.

5' Untranslated Regions↗
PubMed2001

Molecular biology and pathogenesis of the human T-cell leukaemia/lymphotropic virus Type-1 (HTLV-1).

Retroviruses are associated with a variety of diseases, including immunological and neurological disorders, and various forms of cancer. In humans, the Human T-cell Leukaemia/Lymphotropic virus type 1 (HTLV-1), which belongs to the Oncovirus family, is the aetiological agent of two diverse diseases: Adult T-cell leukaemia/lymphoma (ATLL) (Poiesz et al. 1980; Hinuma et al. 1981; Yoshida et al. 1982), as well as the neurological disorder tropical spastic paraparesis/HTLV-1-associated myelopathy (TSP/HAM) (Gessain et al. 1985; Rodgers-Johnson et al. 1985; Osame et al. 1986). HTLV-1 is the only human retrovirus known to be the aetiological agent of cancer. A genetically related virus, HTLV-2, has been identified and isolated (Kalyanaraman et al. 1982). However, there has been no demonstration of a definitive aetiological role for HTLV-2 in human disease to date. Simian T-cell lymphotropic viruses types 1 and 2 (STLV-1 and -2) and bovine leukaemia virus (BLV) have also been classified in same group, Oncoviridae, based upon their similarities in genetic sequence and structure to HTLV-1 and -2 (Burny et al. 1988; Dekaban et al. 1995; Slattery et al. 1999). This article will focus on HTLV-1, reviewing its discovery, molecular biology, and its role in disease pathogenesis.

Animals↗
PubMed2001

Development of simple sequence repeat markers from bacterial artificial chromosomes without subcloning.

Simple sequence repeats (SSRs) were isolated from pearl millet bacterial artificial clones (BACs) without any subcloning steps. SSR sequences were targeted using 3' end-anchored SSR primers. Flanking sequences were isolated by suppression PCR. In this pilot study, 25 SSR markers have been developed from 40 BAC pools, comprising a total of 384 clones. This novel way to develop new markers has the added advantage that mapping the SSR markers will anchor individual BACs to the genetic maps and, thus, facilitate the construction of BAC contigs.

Chromosomes, Artificial, Bacterial↗
PubMedDate not supplied

Involvement of protein-DNA interaction in adeno-associated virus Rep78-mediated inhibition of HIV-1.

OBJECTIVE: It has been well documented by several laboratories that adeno-associated virus (AAV) is able to inhibit HIV-1 replication and gene expression. This effect has been mapped to the AAV-encoded Rep78 protein. However, the mechanism by which Rep78 is able to inhibit HIV-1 is unclear. As Rep78 is a DNA binding transcription factor, the objective of this study was to investigate where Rep78 might bind within the HIV-1 long terminal repeat (LTR) sequences and to judge the importance of this protein-DNA interaction. STUDY DESIGN/METHODS: Rep78's binding to HIV-LTR DNA was analyzed by electrophoretic mobility shift assay (EMSA). The importance of this protein-DNA interaction was analyzed using a Rep78 mutant defective for binding HIV-LTR DNA in an assay for monitoring gene expression (chloramphenicol acetyltransferase [CAT] assay). RESULTS: The preferred site for Rep78 binding was found to be adjacent to the HIV-LTR TATA box, within nt -54 to -34 relative to the site of transcription initiation. Furthermore, a Rep78 mutant with substitutions at amino acid residues 64 and 65 which was found defective for binding HIV-LTR DNA, was also found to be defective for inhibition of tat transactivated HIV-LTR gene expression. CONCLUSION: These data strongly suggest that Rep78's DNA binding ability is important for its mechanism of inhibition. Furthermore, the TATA box region of the HIV-LTR, to which Rep78 preferentially binds, is a likely target through which the inhibition takes place.

DNA, Viral↗
PubMed2002

Amplification and detection of transposon insertion flanking sequences using fluorescent muAFLP.

The amplification of transposon insertionflanking sequences is the basis of a variety of techniques usedfor the detection and characterization of specific transposon insertion events. We have developed a method for the efficient size determination and quantification of amplified genomic sequences thatflank Mutator (Mu) transposon insertions in maize. Using this detection method, we have been able to optimize Mu insertion site amplification and to assess amplification from increasingly complex templates representing increasing numbers of Mu-active maize plants. This detection method should be applicablefor the characterization of transposon or transgene insertion events in a wide variety of organisms.

DNA Primers↗
PubMed2005

Improved rapid amplification of cDNA ends (RACE) for mapping both the 5' and 3' terminal sequences of paramyxovirus genomes.

Rapid amplification of cDNA ends (RACE) is a powerful PCR-based technique for determination of RNA terminal sequences. However, most of the RACE methods reported in the literature are developed specifically for the mapping of eukaryotic transcripts with 3' poly-A tail and 5' cap structure. In this study, an improved RACE strategy was developed which allows both 5' and 3' RACE of paramyxovirus genomic RNA using the same set of common molecular biology reagents without having to rely on expensive RACE kits. Mapping of RNA genome terminal sequences is an essential part of characterizing novel paramyxoviruses since these sequences contain important signals for genome replication and transcription, and are important molecular markers for studying virus evolution. The usefulness of this strategy was demonstrated by rapid characterization of both genome ends for a novel paramyxovirus recently isolated from human kidney primary cells. The RACE strategy described in this paper is simple, cost-effective and can be used to map genome ends of any RNA viruses.

DNA Primers↗
PubMed2004

Identification of cis sequences required for lytic DNA replication and packaging of murine gammaherpesvirus 68.

Human gammaherpesviruses are associated with lymphomas and other malignancies. Murine gammaherpesvirus 68 (MHV-68) infection of mice has emerged as a model for understanding gammaherpesvirus pathogenesis in vivo. In contrast to human gammaherpesviruses, MHV-68 replicates in permissive cell lines in a robust manner, presenting an efficient model to study the basic mechanisms for DNA replication and recombination processes. In addition, MHV-68 also infects a broad range of cells of different tissue types and from different host species, and the viral genome persists as an episome in infected cells. These features make MHV-68 an attractive system on which to build gene delivery vectors. We have therefore undertaken a study to identify the cis elements required for MHV-68 genome replication and packaging. Here we report that an 8.4-kb MHV-68 genomic fragment between ORF66 and ORF73 conferred on the plasmid the ability to replicate; replication required the presence of either de novo viral infection or viral reactivation from latency. We further mapped the origin of lytic replication (oriLyt) to a 1.25-kb region. Moreover, we demonstrated that the terminal repeat of the viral genome is sufficient for packaging of the replicated oriLyt plasmid into mature viral particles. Functional identification of the MHV-68 oriLyt and packaging signal has laid a foundation for investigating the mechanisms controlling gammaherpesvirus DNA replication during the viral lytic phase and will also serve as a base on which to design gene delivery vectors.

Animals↗
PubMed1985

Polymorphism of the 3' open reading frame of the virus associated with the acquired immune deficiency syndrome, human T-lymphotropic virus type III.

The genome of the virus associated with the acquired immune deficiency syndrome (AIDS), human T-lymphotropic virus type III (HTLV-III), includes two open reading frames, not found in other retroviruses. One of these, designated 3' open reading frame (3'orf) is 648 base pairs (bp) in length, and overlaps with the 3' long terminal repeat (LTR) sequences. Sequences of additional HTLV-III clones were determined in order to estimate the level and location of variation within 3'orf, to gain some insight into the function of its protein product. Newly determined sequences are reported for 3'orf of two unintegrated clones of HTLV-III and three cDNA clones made from virion RNA derived from the same cell line infected with pooled blood samples of different patients with AIDS or AIDS-related complex symptoms (ARC). In addition, sequences for 3'orf were derived from an unintegrated viral clone derived from a different cell line infected with a distinct isolate from a single patient. These sequences are compared to those previously reported for six other viral clones. Sequences of 3'orf differ among clones by 1.1-10.4% bp and 2.4-17.0% of predicted amino acids. This represents significantly greater sequence variation than is found in the entire genome on average. Moreover, a functional proviral clone has a termination codon at amino acid residue 124 of this open reading frame. This raises questions concerning the structure, and regulation of expression of the protein encoded by 3'orf.

Acquired Immunodeficiency Syndrome↗
PubMed1986

[Structure of long terminal repeats of transcriptionally active and inactive copies of the mobile dispersed gene MDG3 in Drosophila melanogaster].

The nucleotide sequences of long terminal repeats (LTRs) and adjacent regions are determined in the transcribed and non-transcribed variants of a mobile dispersed genetic element MDG3. MDG3 is similar to other mdg elements. A 4 bp duplication of the host DNA is generated upon its integration. MDG3 is flanked by a 5 bp inverted repeat. The length of the LTRs varies in different MDG3 variants, the difference being connected mainly with duplications of certain sequences in U3 and R regions. The copies with 267 bp LTR are the most abundant ones and perfectly conservative in their primary structure. They are transcribed in 67J25D cell culture and are not transcribed in Kc cell line, where another variant with LTR length 293 bp is transcriptionally active. S1-mapping of transcription initiation and termination sites has demonstrated that in both MDG3 variants they are situated in the same positions, and the LTR itself may be subdivided into U3, R and U5 regions, like retroviral LTRs. Possible factors involved in the regulation of mdg transcription are discussed.

Animals↗
PubMedDate not supplied

Integration, expression and germ-line transmission of foreign growth hormone genes in medaka (Oryzias latipes).

Gene constructs consisting of human growth hormone (hGH) gene driven by promoter/regulatory sequence of mouse metallothionein (mMT), viral thymidine kinase (vTK), rat cholecystokinin (rCCK), or chicken beta-actin (cBA) gene were injected into the cytoplasm of fertilized medaka eggs via the micropyle. More than 49% of the injected embryos survived at hatching. Up to 26% of the survivors showed integration of the introduced gene construct, as determined by polymerase chain reaction analysis and subsequent confirmation by Southern blot hybridization of the genomic DNA. A significant fraction of F1 progeny, derived from crosses between transgenic founders and the nontransgenic individuals, inherited the transgene. Expression of hGH gene was also observed in some of the P1 founders and F1 transgenic progeny carrying mMT-hCG or cBA-hGH gene. Furthermore, the growth performance of the P1 mMT-hGH and cBA-hGH transgenic founders and F1 cBA-hGH F1 transgenic progeny was significantly greater than their full sibling, nontransgenic individuals. In addition to the microinjection experiment, a gene construct containing the long-terminal repeat (LTR) sequence of avian Rous sarcoma virus (RSV) and rainbow trout (rt) GH2 cDNA was introduced into embryos of medaka by electroporation using an exponential decay electroporator. Approximately 70% of the electroporated embryos survived at hatching, and 20% of the survived individuals integrated RSVLTR-rtGH2 cDNA into their genomes. These two techniques will greatly enhance the ability to study regulation of gene expression in transgenic animals during differentiation and development.

Animals↗
PubMed1999

Telomere fluorescence measurements in granulocytes and T lymphocyte subsets point to a high turnover of hematopoietic stem cells and memory T cells in early childhood.

To study telomere length dynamics in hematopoietic cells with age, we analyzed the average length of telomere repeat sequences in diverse populations of nucleated blood cells. More than 500 individuals ranging in age from 0 to 90 yr, including 36 pairs of monozygous and dizygotic twins, were analyzed using quantitative fluorescence in situ hybridization and flow cytometry. Granulocytes and naive T cells showed a parallel biphasic decline in telomere length with age that most likely reflected accumulated cell divisions in the common precursors of both cell types: hematopoietic stem cells. Telomere loss was very rapid in the first year, and continued for more than eight decades at a 30-fold lower rate. Memory T cells also showed an initial rapid decline in telomere length with age. However, in contrast to naive T cells, this decline continued for several years, and in older individuals lymphocytes typically had shorter telomeres than did granulocytes. Our findings point to a dramatic decline in stem cell turnover in early childhood and support the notion that cell divisions in hematopoietic stem cells and T cells result in loss of telomeric DNA.

Adolescent↗
PubMed1994

Marek's disease virus type 1-specific phosphorylated proteins pp38 and pp24 with common amino acid termini are encoded from the opposite junction regions between the long unique and inverted repeat sequences of viral genome.

The nucleotide sequence of the junction region between the long unique (UL) and terminal inverted repeat (TRL) sequences of Marek's disease (MD) virus type 1 (MDV1) DNA revealed the presence of a rightward open reading frame of 155 amino acids. The ORF inserted into an eukaryotic expression vector transiently expressed an antigen in the cytoplasm of COS7 cells which reacted with the monoclonal antibody M21 against an MDV1-specific phosphorylated protein complex consisting of at least the proteins pp38 and pp24. In addition, RNA synthesized in vitro from the ORF under the control of the T7 promoter was translated in vitro using rabbit reticulocyte lysates. A polypeptide of about 24 kDa was immunoprecipitated with M21 antibody. Thus, the MDV1-specific phosphorylated proteins pp38 and pp24 with common amino termini are encoded in the opposite junction regions between the UL and IRL and between the UL and TRL, respectively, of the MDV1 genome. The pp38 gene is transcribed leftward from the viral genome, while the pp24 gene was shown here to be transcribed rightward in a MD tumor cell line as well as in cells productively infected with MDV1.

Amino Acid Sequence↗
PubMed1999

[Cloning of 0-17.5 mu and sequencing of 0-4.8 mu of the lefe and DNA of the Ad7 vaccine strain left end].

OBJECTIVE: Cloning of 0-17.5 mu DNA fragment of adenovirus 7 vaccine strain and sequencing of 0-4.8 mu fragment (1,737 bp). METHODS: Isolating and purifying Ad7 vaccine genome from the A549 cultured cells, putting 0.3-17.5 mu fragment into pAd7T plasmid, then sequencing the 0-4.8 mu fragment including inverted terminal repeats (ITR), packaging sequence and Ela region. RESULTS: We obtained 0-17.5 mu fragment of Ad7 vaccine strain genome and sequenced its left terminal 1,737 bp. Sequence analysis showed that the Ad7 vaccine strain Ela region encodes 6,300, 24,000 and 28,000 proteins. Compared with equivalent region of Ad7 Gomen strain, they share the homology of the nucleotide sequence 98.9%, 97.3%, 97.5% and the homology of the deduced amino acid sequence 96.6%, 96.5%, and 96.9% respectively. When compared with Ad7 Grider strain, they share the homology of the nucleotide sequence 100%, 99.7%, 99.7% and the homology of the deduced amino acid sequence 100%, 99.1%, and 99.2% respectively. CONCLUSION: The Ad7 vaccine strain left terminal 1,737 bp nucleotide sequence showed a high homology with corresponding region of Ad7 Gomen strain and Grider strain.

Adenoviridae↗
PubMed2005

Cryptic promoter activity in the coding region of the HMG-CoA reductase gene in Fusarium graminearum.

Head blight or scab disease caused by Fusarium graminearum poses a major threat to wheat and barley production in North America and other countries. To better understand the molecular mechanisms of F. graminearum pathogenesis, we have generated a collection of random insertional mutants. In mutant 222, one of the transformants significantly reduced in virulence, the transforming vector was inserted at amino acid 269 of the hydroxymethyl-glutaryl CoA reductase gene (HMR1) that encodes a key enzyme in sterol and isoprenoid biosynthesis. The N-terminal transmembrane domains of HMR1 were disrupted, but the C-terminal catalytic domain was intact in mutant 222. We failed to isolate mutants deleted of the HMR1 gene, suggesting that HMR1 is an essential gene. Mutants deleted of the N-terminal 254 amino acids of HMR1 were viable and phenotypically similar to mutant 222. In both mutant 222 and the hmr1Delta254 mutants, a 3-kb truncated HMR1 transcript was detectable by northern blot analyses. In the wild-type strain, only the 5-kb messenger was observed. The initiation site of truncated HMR1 transcripts was determined by 5'-RACE to be 507bp upstream from the catalytic subunit. When a HMR1 fragment corresponding to the DNA sequence of HMR1269-641 was translationally fused to a promoter-less GFP construct, green fluorescent signals were detectable in vegetative hyphae of the resulting transformants. These data indicate that this region of HMR1 ORF has cryptic promoter activity and can express the catalytic domain in hmr1 mutants deleted of its N-terminal portion. Our results also illustrate the importance of the HMR1 gene and the function of its transmembrane domains in F. graminearum.

Acyl Coenzyme A↗
PubMed2004

Reduced Myc overexpression and normal B-cell differentiation mediate resistance to avian leukosis virus lymphomagenesis.

Avian leukosis virus (ALV) induces bursal lymphoma in tumor-susceptible chicken strains after proviral integration within the c-myc gene, and subsequent expansion of Myc-overexpressing lymphocytes within transformed follicles. Line 6(3) strain chickens are resistant to ALV tumorigenesis, largely failing to develop Myc-transformed follicles, although they show similar levels of ALV infection and integration as lymphoma-susceptible strains. Immunohistochemical analysis determined that the transformed follicles that do arise in lymphoma-resistant birds show much lower and more variable Myc overexpression than those of susceptible birds. This reduced Myc overexpression fails to block B-cell differentiation in resistant birds, while high Myc consistently blocks development at a late embryo stage in susceptible birds. This failure of Myc to block differentiation results in a normal pattern of posthatching bursal emigration in resistant transformed follicles, while transformed follicles of susceptible birds grow rapidly due to blocked emigration. Forced Myc overexpression produces transformed follicles in resistant birds, indicating that resistant lymphocytes can tolerate high Myc expression. The coding sequence and expression of the endogenous c-myc gene is the same in resistant and susceptible birds, suggesting that genetic resistance is instead mediated by reduced ALV LTR enhancer-driven transcription in the target lymphocytes of resistant birds.

Animals↗
PubMed2003

On the genomic location of the exuperantia1 gene in Drosophila miranda: the limits of in situ hybridization experiments.

In situ hybridization to Drosophila polytene chromosomes is a powerful tool for determining the chromosomal location of genes. Using in situ hybridization experiments, Yi and Charlesworth recently reported the transposition of the exuperantia1 gene (exu1) from a neo-sex chromosome to the ancestral X chromosome of Drosophila miranda, close to exuperantia2 (exu2). By characterizing sequences flanking exu1, however, we found the position of exu1 to be conserved on the neo-sex chromosome. Further, the exu2 gene was found to be tandemly duplicated on the X chromosome of D. miranda. The misleading hybridization signal of exu1 may be caused by multiple copies of exu2, which interfere with the hybridization of the exu1 probe to its genomic position on the neo-X chromosome. This suggests that flanking DNA should be used to confirm the positions of members of gene families.

Animals↗
PubMed2000

Establishment and characterization of molecular clones of porcine endogenous retroviruses replicating on human cells.

The use of pig xenografts is being considered to alleviate the shortage of allogeneic organs for transplantation. In addition to the problems overcoming immunological and physiological barriers, the existence of numerous porcine microorganisms poses the risk of initiating a xenozoonosis. Recently, different classes of type C porcine endogenous retoviruses (PERV) which are infectious for human cells in vitro have been partially described. We therefore examined whether completely intact proviruses exist that produce infectious and replication-competent virions. Several proviral PERV sequences were cloned and characterized. One molecular PERV class B clone, PERV-B(43), generated infectious particles after transfection into human 293 cells. A second clone, PERV-B(33), which was highly homologous to PERV-B(43), showed a G-to-A mutation in the first start codon (Met to Ile) of the env gene, preventing this provirus from replicating. However, a genetic recombinant, PERV-B(33)/ATG, carrying a restored env start codon, became infectious and could be serially passaged on 293 cells similar to virus clone PERV-B(43). PERV protein expression was detected 24 to 48 h posttransfection (p. t.) using cross-reacting antiserum, and reverse transcriptase activity was found at 12 to 14 days p.t. The transcriptional start and stop sites as well as the splice donor and splice acceptor sites of PERV mRNA were mapped, yielding a subgenomic env transcript of 3. 1 kb. PERV-B(33) and PERV-B(43) differ in the number of copies of a 39-bp segment in the U3 region of the long terminal repeat. Strategies to identify and to specifically suppress or eliminate those proviruses from the pig genome might help in the production of PERV-free animals.

Animals↗