Identification and expression pattern analysis of a Moso Bamboo LTR retrotransposon / 生物工程学报

To develop more active LTR retrotransposons in Phyllostachys edulis, a Ph. edulis LTR retrotransposon (Ph-LTR2) was identified, and the expression pattern of the transposon under stress was systematically analyzed. Ph-LTR2 transposon is 6 030 bp in length and belongs to the Reina subfamily in the Ty3-Gypsy family. With the similarity of 96.41% of both LTR sequences, the Ph-LTR2 transposon inserted the moso bamboo genome about 61.92 thousand years ago. There are 5 copies identified in the genome. The Ph-LTR2 transposon domain includes GAG (gag protein) protein domain, PR (Proteases) protein domain, RT (Reverse transcriptase) protein domain, RH (Ribonuclease H) protein domain, INT (Integrase) protein domain and CHR (Chromatin organization modifier) protein domain. The expression patterns of INT, RT and RH were detected by real-time quantitative PCR. The three domains were found to have specific expression patterns at different tissues of the bamboo. Under the conditions of low/high temperature, methylation inhibitors treatments, irradiation and high salt stress, transcription levels of the three domains of the Ph-LTR2 transposon increased with different degrees. Specifically, after treatment with low/high temperature and methylation inhibitors, the transcription level was up-regulated; after low dose radiation treatment and low concentration of salt solution treatment, the transcription level was also increased, but the expression level decreased with increasing dose of radiation and concentration of salt solution. These results indicate that the expression pattern of the Ph-LTR2 transposon responds to the changes of the external environment, but the exact mechanism is not yet known. The results of this study laid a certain theoretical foundation for the development of the genetic tool based on Ph-LTR2 transposons.

Plant active LTR retrotransposons: a review / 生物工程学报

Long terminal repeat (LTR) retrotransposons are mobile DNA sequences that ubiquitously exist in eukaryotic genomes. They replicate themselves in the genome by copy-paste mechanism with RNA as medium. In higher plants, many active LTR retrotransposons have been applied to analyze molecular marker technology, genetic tagging, insertion mutation and gene function. Here, we systematically review the characteristics of plant active LTR retrotransposons, including their structures, copy numbers and distributions. We further analyzed the gag (group-specific antigen) and pol (polymerase) sequence features of different plants active LTR retrotransposons and the distribution patterns of the cis-acting elements in LTR regions. The results show that autonomous active LTR retrotransposons must contain LTR regions and code Gag, Pr, Int, Rt, Rh proteins. Both LTR regions are highly homologous with each other and contain many cis-regulatory elements; RVT and RNase_H1_RT domain are essential for Rt and Rh protein respectively. These results provide the basis for subsequent identification of plant active LTR retrotransposons and their functional analysis.

Fatores genéticos e clínicos relacionados à infecção pelo HIV-1 e HTLV-1 / genetic and clinical factors related to HIV-1 and HTLV-1

Nesta tese foram realizados três trabalhos distintos sendo que todos envolvem identificar possíveis fatores genéticos ou clínicos relacionados com a infecção pelo HIV-1 ou pelo HTLV-1 ou por ambos. No primeiro trabalho nós objetivamos identificar mutações que poderiam estar relacionadas com o desenvolvimento da TSP/HAM ou carga proviral. Para isto sequenciamos a região LTR5’ do HTLV-1 por Ion Torrent para verificar mutações com baixa frequência. Nós encontramos mutações em 52 posições que estavam presentes em mais de um indivíduo, porém apenas 11 destas estavam presentes em TFBS previamente descritos.Três mutações que não estavam presentes em TFBS previamente descritos foram statisticamente significantes quando comparadas entre os grupos," sendo" que" estes" sítios" podem" ser" importantes" para"a"mediação" da" transcrição" viral."No" segundo" estudo" nós" objetivamos determinar a prevalência do genótipo selvagem em Hlabisa, Kwazulu-Natal na África do Sul além de identificar possíveis fatores associados a presença deste genótipo em 220 pacientes submetidos a ART. O genótipo selvagem foi detectado em 28 amostras (12,7%). Selecionamos 11 pacientes para realizar o sequenciamento pelo Ion Torrent, nove confirmaram não ter mutações de resistência aos antirretrovirais em alta frequência. Foi encontrada uma alta contagem de CD4+ no início da terapia associado a falha terapêutica assim como uma alta carga viral antes da genotipagem e não foi encontrado associação entre aderência a terapia auto-reportada e a presença do genótipo selvagem. Aproximadamente um em cada oito adultos que falham a terapia possuem o genótipo selvagem sendo este dado confirmado através de sequenciamento de nova geração. Devido ao alto número de genótipos selvagem encontrados, o teste de resistência genotípica deve ser solicitado para se obter um melhor desfecho clinico em níveis individuais e populacionais. No terceiro estudo nós analisamos as diferenças na contagem de linfócitos T CD4+ entre indivíduos infectados apenas com o HIV-1 e indivíduos coinfectados HIV-1/HTLV-1 com falha terapêutica, além de analisarmos a soroprevalência do HTLV-1 em indivíduos infectados pelo HIV-1. Foram encontrados oito pacientes coinfectados (2,1%) dos 381 pacientes analisados. Nós não observamos nenhuma diferença estatística quando analisamos transversalmente os dados clínicos dos pacientes, exceto na primeira contagem de linfócitos T CD4+ após o início do tratamento que estava maior nos indivíduos coinfectados (p=0.03). A análise multivariada longitudinal mostrou que a media de linfócitos T CD4+ ao longo do tratamento, foi estatisticamente maior nos pacientes coinfectados levando em consideração características demográficas, carga viral, fatores relacionados a terapia, entre outros. Nos pacientes coinfectados também não foram encontrados marcadores de HLA relacionados com os supressores de elite do HIV-1. Os dados deste trabalho sugerem que os pacientes coinfectados em terapia ntirretroviral deveriam ter um acompanhamento clínico diferenciado dos indivíduos apenas infectados pelo HIV-1, pois a coinfecção poderia estar levando ao aumento do número dos linfócitos T CD4+ sem um possível ganho de resposta imune.

We performed three studies to analyze risk factors associated with retroviruses infections. In the first study we attempted to analyze mutations related to TSP/HAM development or proviral load. For that purpose we have sequenced the LTR 5’ region of HTLV-1 by Ion Torrent. We found that mutations in 52 positions were present in more than one individual, but only 11 were present in the previously described TFBS. Three mutations that were not present in the previously described TFBS were statistically significant comparing groups. Despite the absence of previously described TFBS, these sites might be important for the viral transcription. In the second study we analyzed the prevalence of HIV-1 wild type genotype in adults failing first-line ART. A total of 220 adults were included. The wild type genotype was detected by population sequencing in 28 (12.7%). No major drug resistance mutations were detected by deep sequencing for 81.8% (9/11) of those sampled. Higher baseline CD4+ cell count was associated with a greater likelihood of wild type genotype as was a higher viral load prior to resistance testing but there was no evidence of an association between selfreported adherence and the presence of wild type genotype. Approximately one in eight adults failing first-line ART had wild type genotype and this result was confirmed trough deep sequencing in some samples. Access to genotypic resistance testing may be required in this region to achieve optimal individual-level and population-level outcomes. In the third study we proposed to verify the prevalence of HTLV-1 and to statistically assess differences in CD4+ counts between HTLV-1/HIV-1 co-infected and HIV-1 mono-infected patients living in rural KwaZulu-Natal. The HTLV-1 seroprevalence was 2.1% (8 out 381 patients). The patients were grouped by HTLV-1/HIV-1 co-infected and HIV-1 mono-infected status for the statistical analysis...

Transposable Elements and Genome Size Variations in Plants

Although the number of protein-coding genes is not highly variable between plant taxa, the DNA content in their genomes is highly variable, by as much as 2,056-fold from a 1C amount of 0.0648 pg to 132.5 pg. The mean 1C-value in plants is 2.4 pg, and genome size expansion/contraction is lineage-specific in plant taxonomy. Transposable element fractions in plant genomes are also variable, as low as ~3% in small genomes and as high as ~85% in large genomes, indicating that genome size is a linear function of transposable element content. Of the 2 classes of transposable elements, the dynamics of class 1 long terminal repeat (LTR) retrotransposons is a major contributor to the 1C value differences among plants. The activity of LTR retrotransposons is under the control of epigenetic suppressing mechanisms. Also, genome-purging mechanisms have been adopted to counter-balance the genome size amplification. With a wealth of information on whole-genome sequences in plant genomes, it was revealed that several genome-purging mechanisms have been employed, depending on plant taxa. Two genera, Lilium and Fritillaria, are known to have large genomes in angiosperms. There were twice times of concerted genome size evolutions in the family Liliaceae during the divergence of the current genera in Liliaceae. In addition to the LTR retrotransposons, non-LTR retrotransposons and satellite DNAs contributed to the huge genomes in the two genera by possible failure of genome counter-balancing mechanisms.

Down-regulation of HIV-1 Infection by Inhibition of the MAPK Signaling Pathway / 中国病毒学·英文版

The human immunodeficiency virus type 1(HIV-1)can interact with and exploit the host cellular machinery to replicate and propagate itself.Numerous studies have shown that the Mitogen-activated protein kinase(MAPK)signal pathway can positively regulate the replication of HIV-1,but exactly how each MAPK pathway affects HIV-1 infection and replication is not understood.In this study,we used the Extracellular signal-regulated kinase(ERK)pathway inhibitor,PD98059,the Jun N-terminal kinase(JNK)pathway inhibitor,SP600125,and the p38 pathway inhibitor,SB203580,to investigate the roles of these pathways in HIV-1replication.We found that application of PD98059 results in a strong VSV-G pseudotyped HIV-1NL4-3 luciferase reporter virus and HIV-1NL4-3 virus inhibition activity.In addition,SB203580 and SP600125 also elicited marked VSV-G pseudotyped HIV-1NL4-3 luciferase reporter virus inhibition activity but no HIV-1NL4-3 virus inhibition activity.We also found that SB203580 and SP600125 can enhance the HIV-1 inhibition activity of PD98059when cells were treated with all three MAPK pathway inhibitors in combination.Finally,we show that HIV-1virus inhibition activity of the MAPK pathway inhibitors was the result of the negative regulation of HIV-1 LTR promoter activity.

Boty-II, a novel LTR retrotransposon in Botrytis cinerea B05.10 revealed by genomic sequence

Botrytis cinerea is a necrotrophic pathogen causing pre- and post-harvest diseases in at least 235 plant species. It manifests extraordinary genotype and phenotype variation. One of the causes of this variation is transposable elements. Two transposable elements have been discovered in this fungus, the retrotransposon (Boty), and the transposon (Flipper). In this work, two complete (Boty-II-76 and Boty-II-103) and two partial (Boty-II-95 and Boty-II-141) long terminal repeat (LTR) retrotransposons were identified by an in silico genomic sequence analysis. Boty-II-76 and Boty-II-103 contain 6439 bp nucleotides with a pair of LTRs at both ends, and an internal deduced pol gene encoding a polyprotein with reverse transcriptase and DDE integrase domains. They are flanked by 5 bp direct repeats (ACCAT, CTTTC). In Boty-II-141, two LTRs at both ends, and a partial internal pol gene encoding a protein with a DDE integrase domain were identified. In Boty-II-95, a right LTR and a partial internal pol gene encoding a protein with no conserved domains were identified. Boty-II uses a self-priming mechanism to initiate synthesis of reverse transcripts. The sequence of the presumed primer binding site for first-strand reverse transcription is 5’-TTGTACCAT-3’. The polypurine-rich sequence for plus-strand DNA synthesis is 5’-GCCTTGAGCGGGGGGTAC-3’. Fourteen Boty-II LTRs that contain 125-158 bp nucleotides and share 69.1 ~ 100 percent identities with the short inverted terminal repeats of 5 bp (TGTCA…TGACA) were discovered. Analysis of structural features and phylogeny revealed that Boty-II is a novel LTR retrotransposon. It could potentially be used as a novel molecular marker for the investigation of genetic variation in B. cinerea.

Identification of hRad21-Binding Sites in Human Chromosome

The aim of this study is to identify hRad21-binding sites in human chromosome, the core component of cohesin complex that held sister chromatids together. After chromatin immunoprecipitation with an hRad21 antibody, it was cloned the recovered DNA and sequenced 30 independent clones. Among them, 20 clones (67%) contained repetitive elements including short interspersed transposable elements (SINE or Alu elements), long terminal repeat (LTR) and long interspersed transposable elements (LINE), fourteen of these twenty (70%) repeats clones had Alu elements, which could be categorized as the old and the young Alu Subfamily, eleven of the fourteen (73%) Alu elements belonged to the old Alu Subfamily, and only three Alu elements were categorized as young Alu subfamily. There is no CpG island within these selected clones. Association of hRad21 with Alu was confirmed by chromatin immunoprecipitation-PCR using conserved Alu primers. The primers were designed in the flanking region of Alu, and the specific Alu element was shown in the selected clone. From these experiments, it was demonstrated that hRad21 could bind to SINE, LTRs, and LINE as well as Alu.

Evolutionary course of CsRn1 long-terminal-repeat retrotransposon and its heterogeneous integrations into the genome of the liver fluke, Clonorchis sinensis

The evolutionary course of the CsRn1 long-terminal-repeat (LTR) retrotransposon was predicted by conducting a phylogenetic analysis with its paralog LTR sequences. Based on the clustering patterns in the phylogenetic tree, multiple CsRn1 copies could be grouped into four subsets, which were shown to have different integration times. Their differential sequence divergences and heterogeneous integration patterns strongly suggested that these subsets appeared sequentially in the genome of C. sinensis. Members of recently expanding subset showed the lowest level of divergence in their LTR and reverse transcriptase gene sequences. They were also shown to be highly polymorphic among individual genomes of the trematode. The CsRn1 element exhibited a preference for repetitive, agenic chromosomal regions in terms of selecting integration targets. Our results suggested that CsRn1 might induce a considerable degree of intergenomic variation and, thereby, have influenced the evolution of the C. sinensis genome.

Divergent long-terminal-repeat retrotransposon families in the genome of Paragonimus westermani

To gain information on retrotransposons in the genome of Paragonimus westermani, PCR was carried out with degenerate primers, specific to protease and reverse transcriptase (rt) genes of long-terminal-repeat (LTR) retrotransposons. The PCR products were cloned and sequenced, after which 12 different retrotransposon-related sequences were isolated from the trematode genome. These showed various degrees of identity to the polyprotein of divergent retrotransposon families. A phylogenetic analysis demonstrated that these sequences could be classified into three different families of LTR retrotransposons, namely, Xena, Bel, and Gypsy families. Of these, two mRNA transcripts were detected by reverse transcriptase-PCR, showing that these two elements preserved their mobile activities. The genomic distributions of these two sequences were found to be highly repetitive. These results suggest that there are diverse retrotransposons including the ancient Xena family in the genome of P. westermani, which may have been involved in the evolution of the host genome.

A Human Immunodeficiency Virus Type 1 (HIV-1) Tat Cofactor Absent in Rodent Cells is a TAR-associated Factor

BACKGROUND: Although Tat plays a role as a potent transactivator in the viral gene expression from the Human Immunodeficiency Virus type 1 long terminal repeat (HIV-1 LTR), it does not function efficiently in rodent cells implying the absence of a human specific factor essential for Tat-medicated transactivation in rodent cells. In previous experiments, we demonstrated that one of chimeric forms of TAR (transacting responsive element) of HIV-1 LTR compensated the restriction in rodent cells. METHODS: To characterize the nature of the compensation, we tested the effects of several upstream binding factors of HIV-1 LTR by simple substitution, and also examined the role of the configuration of the upstream binding factor(s) indirectly by constructing spacing mutants that contained insertions between Sp1 and TATA box on Tat-mediated transactivation. RESULTS: Human Sp1 had no effect whereas its associated factors displayed differential effects in human and rodent cells. In addition, none of the spacing mutants tested overcame the restriction in rodent cells. Rather, when the secondary structure of the chimeric HIV-1 TAR construct was destroyed, the compensation in rodent cells was disappeared. Interestingly, the proper interaction between Sp1 and TATA box binding proteins, which is essential for Tat-dependent transcription, was dispensable in rodent cells. CONCLUSION: This result suggests that the human-specific Tat cofactor acts to allow Tat to interact effectively in a ribonucleoprotein complex that includes Tat, cellular factors, and TAR RNA, rather than be associated with the HIV-1 LTR upstream DNA binding factors.

A Human Immunodeficiency Virus Type 1 (HIV-1) Tat Cofactor Absent in Rodent Cells is a TAR-associated Factor

BACKGROUND: Although Tat plays a role as a potent transactivator in the viral gene expression from the Human Immunodeficiency Virus type 1 long terminal repeat (HIV-1 LTR), it does not function efficiently in rodent cells implying the absence of a human specific factor essential for Tat-medicated transactivation in rodent cells. In previous experiments, we demonstrated that one of chimeric forms of TAR (transacting responsive element) of HIV-1 LTR compensated the restriction in rodent cells. METHODS: To characterize the nature of the compensation, we tested the effects of several upstream binding factors of HIV-1 LTR by simple substitution, and also examined the role of the configuration of the upstream binding factor(s) indirectly by constructing spacing mutants that contained insertions between Sp1 and TATA box on Tat-mediated transactivation. RESULTS: Human Sp1 had no effect whereas its associated factors displayed differential effects in human and rodent cells. In addition, none of the spacing mutants tested overcame the restriction in rodent cells. Rather, when the secondary structure of the chimeric HIV-1 TAR construct was destroyed, the compensation in rodent cells was disappeared. Interestingly, the proper interaction between Sp1 and TATA box binding proteins, which is essential for Tat-dependent transcription, was dispensable in rodent cells. CONCLUSION: This result suggests that the human-specific Tat cofactor acts to allow Tat to interact effectively in a ribonucleoprotein complex that includes Tat, cellular factors, and TAR RNA, rather than be associated with the HIV-1 LTR upstream DNA binding factors.