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Long Terminal Repeat (long + terminal_repeat)
Selected AbstractsGenome-wide Characterization of Long Terminal Repeat -retrotransposons in Apple Reveals the Differences in Heterogeneity and Copy Number between Ty1 -copia and Ty3 -gypsy RetrotransposonsJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 9 2008Hai-Yue Sun Abstract The conserved domains of reverse transcriptase (RT) genes of Ty1- copia and Ty3- gypsy groups of long terminal repeat (LTR) retrotransposons were isolated from the Malus domestica genome using degenerate oligonucleotide primers. Sequence analysis showed that 45% of Ty1- copia and 63% of Ty3- gypsy RT sequences contained premature stop codons and/or indels disrupting the reading frame. High heterogeneity among RT sequences of both Ty1- copia and Ty3- gypsy group retrotransposons was observed, but Ty3- gypsy group retrotransposons in the apple genome are less heterogeneous than Ty1- copia elements. Retrotransposon copy number was estimated by dot blot hybridizations for Ty1- copia (,5 000) and Ty3- gypsy (,26 000). All elements of the two types of LTR retrotransposons comprise approximately 38% of the M. domestica genome, with the Ty3- gypsy group contribution being higher (33.5%) than the Ty1- copia one (4.6%). Transcription was not detected by reverse transcription-polymerase chain reaction for either Ty1- copia or Ty3- gypsy retrotransposons in the leaves of plants in vitro or in leaf explants cultured on medium supplemented with high concentration benzylaminopurine. This research reveals the differences in heterogeneity and copy number between Ty1- copia and Ty3- gypsy retrotransposons in the apple genome. Ty1- copia retrotransposon has higher heterogeneity than Ty3- gypsy retrotransposon, but the latter has a higher copy number, which implies that Ty3- gypsy retrotransposons may play a more important role in the apple genome evolution. [source] Effects of structural variations of APOBEC3A and APOBEC3B genes in chronic hepatitis B virus infectionHEPATOLOGY RESEARCH, Issue 12 2009Hiromi Abe Aim:, Human APOBEC3 deaminases induce G to A hypermutation in nascent DNA strand of hepatitis B virus (HBV) genomes and seem to operate as part of the innate antiviral immune system. We analyzed the importance of APOBEC3A (A3A) and APOBEC3B (A3B) proteins, which are potent inhibitors of adeno-associated-virus and long terminal repeat (LTR)-retrotransposons, in chronic HBV infection. Methods:, We focused on the common deletion polymorphism that spans from the 3, part of A3A gene to the 3, portion of A3B gene. An association study was carried out in 724 HBV carriers and 469 healthy control subjects. We also analyzed hypermutated genomes detected in deletion and insertion (non-deletion) homozygous patients to determine the effect of APOBEC3 gene deletion. Further, we performed functional analysis of A3A gene by transient transfection experiments. Results:, The association study showed no significant association between deletion polymorphism and chronic HBV carrier state. Context analysis also showed a negligible effect for the deletion. Rather, mild liver fibrosis was associated with APOBEC gene deletion homozygosity, suggesting that A3B deletion is not responsible for chronic HBV infection. Functional analysis of A3A showed that overexpression of A3A induced hypermutation in HBV genome, although the levels of hypermutants were less than those introduced by A3G. However, overexpression of A3A did not decrease replicative intermediates of HBV. Conclusion:, These results suggest that A3A and A3B play little role in HBV elimination through anti-viral defense mechanisms. The significance of hypermutation induced by A3A should be investigated further. [source] Nicotinamide phosphoribosyltransferase/sirtuin 1 pathway is involved in human immunodeficiency virus type 1 Tat-mediated long terminal repeat transactivationJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 6 2010Hong-Sheng Zhang Abstract Tat is a multifunctional transactivator encoded by human immunodeficiency virus type 1 (HIV-1). Tat transactivating activity is controlled by nicotinamide adenine nucleotide+ (NAD+)-dependent deacetylase sirtuin 1 (SIRT1). Nicotinamide phosphoribosyltransferase (Nampt) is a rate-limiting enzyme in the conversion of nicotinamide into NAD+, which is crucial for SIRT1 activation. Thus, the effect of Nampt on Tat-regulated SIRT activity was studied in Hela-CD4-,-gal (MAGI) cells. We demonstrated that Tat caused NAD+ depletion and inhibited Nampt mRNA and protein expression in MAGI cells. Resveratrol reversed Tat-induced NAD+ depletion and inhibition of Nampt mRNA and protein expression. Further investigation revealed that Tat-induced inhibition of SIRT1 activity was potentiated in Nampt-knockdown by Nampt siRNA compared to treatment with Tat alone. Nampt siRNA potentiated Tat-induced HIV-1 transactivation in MAGI cells. Altogether, these results indicate that Nampt is critical in the regulation of Tat-induced inhibition of SIRT1 activity and long terminal repeat (LTR) transactivation. Nampt/SIRT1 pathway could be a novel therapeutic tool for the treatment of HIV-1 infection. J. Cell. Biochem. 110: 1464,1470, 2010. © 2010 Wiley-Liss, Inc. [source] Genome-wide Characterization of Long Terminal Repeat -retrotransposons in Apple Reveals the Differences in Heterogeneity and Copy Number between Ty1 -copia and Ty3 -gypsy RetrotransposonsJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 9 2008Hai-Yue Sun Abstract The conserved domains of reverse transcriptase (RT) genes of Ty1- copia and Ty3- gypsy groups of long terminal repeat (LTR) retrotransposons were isolated from the Malus domestica genome using degenerate oligonucleotide primers. Sequence analysis showed that 45% of Ty1- copia and 63% of Ty3- gypsy RT sequences contained premature stop codons and/or indels disrupting the reading frame. High heterogeneity among RT sequences of both Ty1- copia and Ty3- gypsy group retrotransposons was observed, but Ty3- gypsy group retrotransposons in the apple genome are less heterogeneous than Ty1- copia elements. Retrotransposon copy number was estimated by dot blot hybridizations for Ty1- copia (,5 000) and Ty3- gypsy (,26 000). All elements of the two types of LTR retrotransposons comprise approximately 38% of the M. domestica genome, with the Ty3- gypsy group contribution being higher (33.5%) than the Ty1- copia one (4.6%). Transcription was not detected by reverse transcription-polymerase chain reaction for either Ty1- copia or Ty3- gypsy retrotransposons in the leaves of plants in vitro or in leaf explants cultured on medium supplemented with high concentration benzylaminopurine. This research reveals the differences in heterogeneity and copy number between Ty1- copia and Ty3- gypsy retrotransposons in the apple genome. Ty1- copia retrotransposon has higher heterogeneity than Ty3- gypsy retrotransposon, but the latter has a higher copy number, which implies that Ty3- gypsy retrotransposons may play a more important role in the apple genome evolution. [source] HTLV-II infection associated with a chronic neurodegenerative disease: Clinical and molecular analysisJOURNAL OF MEDICAL VIROLOGY, Issue 2 2002Edimilson A. Silva Abstract HTLV II is a retrovirus endemic in some Amerindian tribes and spread worldwide with a high prevalence among intravenous drug abusers. It has three different genetic subtypes a, b, and d, defined mainly by the long terminal repeat (LTR) region. HTLV II has been associated with a neurodegenerative disease in few cases. We describe the first well-documented case in Brazil where the virus is endemic in isolated ethnic groups. The patient is a 55-year-old woman with a chronic and painful syndrome characterized by spastic paraparesis, hyperactive reflexes and spastic bladder. Somatosensory evoked potential indicates a thoracic spinal cord lesion. Computer tomography showed periventricular demyelination. Enzyme-linked immunosorbent assay was positive for HTLV I/II whereas the discriminatory Western blot was indeterminate. Molecular analysis of the Tax region revealed a HTLV II pattern that was also confirmed through sequencing the LTR region. Phylogenetic analysis of the LTR sequence shows an HTLV IIa subtype that clustered with the virus isolated from Kayapo Indians and Brazilian urban intravenous drug users. Indeterminate Western blots are frequently found using commercial kits, therefore we recommend that all cases in which a myelopathy is associated with an indeterminate serological result should be evaluated by PCR to determine the actual number of HTLV II associated myelopathy cases. J. Med. Virol. 66:253,257, 2002. © 2002 Wiley-Liss, Inc. [source] Tight control of transgene expression by lentivirus vectors containing second-generation tetracycline-responsive promotersTHE JOURNAL OF GENE MEDICINE, Issue 6 2005Krzysztof Pluta Abstract Background The goal of this study was to design improved regulatable lentivirus vector systems. The aim was to design tetracycline (tet)-regulatable lentivirus vectors based on the Tet-on system displaying low background expression in the absence of the doxycycline (DOX) inducer and high transgene expression levels in the presence of DOX. Methods We constructed a binary lentivirus vector system that is composed of a self-inactivating (SIN) lentivirus vector bearing inducible first- or second-generation tet-responsive promoter elements (TREs) driving expression of a transgene and a second lentivirus vector encoding a reverse tetracycline-controlled transactivator (rtTA) that activates transgene expression from the TRE in the presence of DOX. Results We evaluated a number of different rtTAs and found rtTA2S -M2 to induce the highest levels of transgene expression. Regulated transgene expression was stable in human breast carcinoma cells implanted into nude mice for up to 11 weeks. In an attempt to minimize background expression levels, the chicken ,-globin cHS4 insulator element was cloned into the 3, long terminal repeat (LTR) of the transgene transfer vector. The cHS4 insulator element reduced background expression but expression levels following DOX addition were lower than those observed with vectors lacking an insulator sequence. In a second strategy, vectors bearing second-generation TREs harboring repositioned tetracycline operator elements were used. Such vectors displayed greatly reduced leakiness in the absence of DOX and induced transgene expression levels were up to 522-fold above those seen in the absence of DOX. Conclusions Inducible lentivirus vectors bearing insulators or second-generation TREs will likely prove useful for applications demanding the lowest levels of background expression. Copyright © 2005 John Wiley & Sons, Ltd. [source] Role of mitogen-activated protein kinases, nuclear factor-,B, and interferon regulatory factor 3 in Toll-like receptor 4-mediated activation of HIV long terminal repeatAPMIS, Issue 2 2009RANDI S. BERG Monocytes/macrophages are known to represent a potential reservoir of human immunodeficiency virus type 1 (HIV-1), which ensures continuous replication of the virus in patients on highly active antiretroviral therapy (HAART). Infected macrophages are a highly productive source of HIV-1 during infections with common opportunistic pathogens. Previous studies report that toll like receptors (TLR)s play a role in HIV-1 replication in macrophages. Here, we investigate the three main pathways activated through TLR4 and the interactions with the HIV-1 long terminal repeat (LTR), using human embryonic kidney (HEK) 293 cells expressing TLR4 and transfected with a luciferase reporter under the control of the HIV-1 LTR. Here, we demonstrate, that TLR4-mediated activation of HIV-LTR is largely governed by the nuclear factor-,B pathway. Neither of the mitogen-activated protein kinases ERK1/2, JNK, or p38 nor the transcription factor interferon regulatory factor 3 were involved in the direct transactivation of HIV-LTR through stimulation of TLR4. [source] Genetic variability of Old Portuguese bread wheat cultivars assayed by IRAP and REMAP markersANNALS OF APPLIED BIOLOGY, Issue 3 2010A. Carvalho Retrotransposons (RTNs) constitute informative molecular markers for plant species as a result of their ability of integrating into a multitude of loci throughout the genome and thereby generating insertional polymorphisms between individuals. Inter-retrotransposon amplified polymorphisms (IRAPs) and the retrotransposon-microsatellite amplified polymorphisms (REMAPs) are marker systems based on long terminal repeats (LTRs) RTNs, developed for plants, that have been widely used for evolution, genetic diversity, DNA fingerprinting of cultivars and varieties, genetic mapping linkage and for detection of genetic rearrangements induced by polyploidisation. In the present study, we aimed to analyse the genetic variability among 48 Old Portuguese bread wheat cultivars using both IRAP and REMAP markers. Five IRAP and six REMAP primer combinations were used. IRAP produced 103 polymorphic fragments in a total of 113 bands. On average, 22.6 bands were amplified per IRAP primer combination. The bands ranged in size from 250 to 5000 bp. The REMAP primer combinations allowed the amplification of 53 bands, 51 of them polymorphic. An average of 8.8 REMAP bands was scored per primer combination. The REMAP bands ranged from 250 to 3000 bp. Both marker systems presented high percentages of polymorphism. However, IRAP markers were suitable for detecting genetic variability at the individual level and did not differentiate higher taxa. The REMAP maker system allowed the clustering by botanical variety and identified most of the homonym bread wheat cultivars. [source] | |||||||||||||