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  1 / 1849 MEDLINE  
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[PMID]:28899944
[Au] Autor:Sakurai T; Nakagawa S; Bai H; Bai R; Kusama K; Ideta A; Aoyagi Y; Kaneko K; Iga K; Yasuda J; Miyazawa T; Imakawa K
[Ad] Endereço:Department of Occupational and Environment Health, Tokyo University of Science, Chiba 278-0022, Japan.
[Ti] Título:Novel endogenous retrovirus-derived transcript expressed in the bovine placenta is regulated by WNT signaling.
[So] Source:Biochem J;474(20):3499-3512, 2017 Oct 10.
[Is] ISSN:1470-8728
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Endogenous retroviruses (ERVs) are involved in placentation; perhaps, the most well-known s are the syncytins, actively transcribed genes involved in cell-cell fusion and possible morphological variations. However, ERVs other than syncytins that play an important role in placental development have not been well characterized. To identify genes expressed during the onset of placentation in the bovine species, we characterized the expression profiles of bovine conceptus transcripts during the peri-attachment period using RNA-seq analysis, and confirming some candidates through real-time PCR. Using and PCR analyses, we identified a novel proviral sequence derived from a region, designated bovine endogenous retroviruses (BERV)-K3, containing _p10 and _p24, zinc finger domain. Initial expression of this in bovine conceptuses was on day 20 (day 0 = day of estrus), soon after conceptus attachment to the endometrial epithelium, and its high placental expression was maintained up to the middle of pregnancy. The transcript was also found in the uterine luminal and glandular epithelia, liver, kidney, intestine, and skin. is located on chromosome 7 and integrated within , from which noncoding RNA could be transcribed. Furthermore, the expression of endogenous in bovine trophoblast cell lines was induced by a WNT agonist, a signaling system common to genes expressed in placentas. These data support the argument that during the evolutionary process, mammals incorporated not only similar sequences, but also s unique to individual species. BERV-K3 is in the latter case, likely providing functions unique to ruminant gestation.
[Mh] Termos MeSH primário: Retrovirus Endógenos/genética
Regulação da Expressão Gênica no Desenvolvimento
Placenta/fisiologia
Transcrição Genética/fisiologia
Via de Sinalização Wnt/fisiologia
[Mh] Termos MeSH secundário: Animais
Bovinos
Feminino
Gravidez
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171024
[Lr] Data última revisão:
171024
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170914
[St] Status:MEDLINE
[do] DOI:10.1042/BCJ20170531


  2 / 1849 MEDLINE  
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[PMID]:28858759
[Au] Autor:Mercorio R; Bonzini M; Angelici L; Iodice S; Delbue S; Mariani J; Apostoli P; Pesatori AC; Bollati V
[Ad] Endereço:EPIGET LAB, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Via san Barnaba 8, 20122 Milan, Italy.
[Ti] Título:Effects of metal-rich particulate matter exposure on exogenous and endogenous viral sequence methylation in healthy steel-workers.
[So] Source:Environ Res;159:452-457, 2017 11.
[Is] ISSN:1096-0953
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Inhaled particles have been shown to produce systemic changes in DNA methylation. Global hypomethylation has been associated to viral sequence reactivation, possibly linked to the activation of pro-inflammatory pathways occurring after exposure. This observation provides a rationale to investigate viral sequence (both exogenous and endogenous) methylation in association to metal-rich particulate matter exposure. To verify this hypothesis, we chose the Wp promoter of the Epstein-Barr Virus (EBV-Wp) and the promoter of the human-endogenous-retrovirus w (HERV-w), respectively as a paradigm of an exogenous and an endogenous retroviral sequence, to be investigated by bisulfite PCR Pyrosequencing. We enrolled 63 male workers in an electric furnace steel plant, exposed to high level of metal-rich particulate matter. RESULTS: Comparing samples obtained in the first day of a work week (time 0-baseline, after 2 days off work) and the samples obtained after 3 days of work (time 1-post exposure), the mean methylation of EBV-Wp was significantly higher at baseline compared to post-exposure (mean = 56.7%5mC; mean = 47.9%5mC; p-value = 0.009), whereas the mean methylation of HERV-w did not significantly differ. Individual exposure to inhalable particles and metals was estimated based on measures in all working areas and time spent by the study subjects in each area. In a regression model adjusted for age, body mass index and smoking, PM and metal components had a positive association with EBV-Wp methylation (i.e. PM10: ß = 5.99, p-value < 0.038; nickel: ß = 17.82, p-value = 0.02; arsenic: ß = 13.59, p-value < 0.015). CONCLUSIONS: The difference observed comparing baseline and post-exposure samples may be suggestive of a rapid change in EBV methylation induced by air particles, while correlation between EBV methylation and PM/metal exposure may represent a more stable adaptive mechanism. Future studies investigating a larger panel of viral sequences could better elucidate possible mechanisms and their role in pro-inflammatory pathways leading to systemic health effects.
[Mh] Termos MeSH primário: Poluentes Atmosféricos/toxicidade
Metilação de DNA/efeitos dos fármacos
Metalurgia
Metais/toxicidade
Exposição Ocupacional
Material Particulado/toxicidade
[Mh] Termos MeSH secundário: Adulto
DNA Viral/metabolismo
Retrovirus Endógenos/efeitos dos fármacos
Retrovirus Endógenos/metabolismo
Herpesvirus Humano 4/efeitos dos fármacos
Herpesvirus Humano 4/metabolismo
Seres Humanos
Itália
Masculino
Meia-Idade
Reação em Cadeia da Polimerase
Regiões Promotoras Genéticas
Aço
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Air Pollutants); 0 (DNA, Viral); 0 (Metals); 0 (Particulate Matter); 12597-69-2 (Steel)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171120
[Lr] Data última revisão:
171120
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170901
[St] Status:MEDLINE


  3 / 1849 MEDLINE  
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[PMID]:28821995
[Au] Autor:Bergallo M; Montanari P; Mareschi K; Merlino C; Berger M; Bini I; Daprà V; Galliano I; Fagioli F
[Ad] Endereço:Department of Public Health and Pediatric Sciences, University of Turin, Medical School, 10136, Turin, Italy. Massimiliano.bergallo@unito.it.
[Ti] Título:Expression of the pol gene of human endogenous retroviruses HERV-K and -W in leukemia patients.
[So] Source:Arch Virol;162(12):3639-3644, 2017 Dec.
[Is] ISSN:1432-8798
[Cp] País de publicação:Austria
[La] Idioma:eng
[Ab] Resumo:The human endogenous retroviruses (HERVs) are a family of endogenous retroviruses that integrated into the germ cell DNA of primates over 30 million years ago. HERV expression seems impaired in several diseases, ranging from autoimmune to neoplastic disorders. The purpose of this study was to evaluate the overall endogenous retroviral transcription profile in bone marrow (BM) samples. A total of 30 paediatric high-risk leukaemia patients (lymphoid and myeloid malignancies) were tested for HERVs virus gene expression. Our findings show that HERV-K expression was significantly higher in leukaemia patients when compared to healthy donors of a similar median age. We observed a significantly high expression of HERV-K in acute lymphoblastic leukemia (ALL) patients. In this study, we also found a relative overexpression of the endogenous retrovirus HERV-K in BM cells from the majority of leukemia samples analyzed, in particular in ALL. This overexpression might be related to lymphatic leukemogenesis and it warrants further investigations.
[Mh] Termos MeSH primário: Retrovirus Endógenos/enzimologia
Expressão Gênica
Produtos do Gene pol/análise
Leucemia/patologia
[Mh] Termos MeSH secundário: Adolescente
Medula Óssea/patologia
Criança
Pré-Escolar
Feminino
Perfilação da Expressão Gênica
Seres Humanos
Lactente
Masculino
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Gene Products, pol)
[Em] Mês de entrada:1711
[Cu] Atualização por classe:171113
[Lr] Data última revisão:
171113
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170820
[St] Status:MEDLINE
[do] DOI:10.1007/s00705-017-3526-7


  4 / 1849 MEDLINE  
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[PMID]:28768854
[Au] Autor:Kawasaki J; Kawamura M; Ohsato Y; Ito J; Nishigaki K
[Ad] Endereço:Laboratory of Molecular Immunology and Infectious Disease, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan.
[Ti] Título:Presence of a Shared 5'-Leader Sequence in Ancestral Human and Mammalian Retroviruses and Its Transduction into Feline Leukemia Virus.
[So] Source:J Virol;91(20), 2017 Oct 15.
[Is] ISSN:1098-5514
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Recombination events induce significant genetic changes, and this process can result in virus genetic diversity or in the generation of novel pathogenicity. We discovered a new recombinant feline leukemia virus (FeLV) gene harboring an unrelated insertion, termed the X region, which was derived from endogenous gammaretrovirus 4 (FcERV-gamma4). The identified FcERV-gamma4 proviruses have lost their coding capabilities, but some can express their viral RNA in feline tissues. Although the X-region-carrying recombinant FeLVs appeared to be replication-defective viruses, they were detected in 6.4% of tested FeLV-infected cats. All isolated recombinant FeLV clones commonly incorporated a middle part of the FcERV-gamma4 5'-leader region as an X region. Surprisingly, a sequence corresponding to the portion contained in all X regions is also present in at least 13 endogenous retroviruses (ERVs) observed in the cat, human, primate, and pig genomes. We termed this shared genetic feature the commonly shared (CS) sequence. Despite our phylogenetic analysis indicating that all CS-sequence-carrying ERVs are classified as gammaretroviruses, no obvious closeness was revealed among these ERVs. However, the Shannon entropy in the CS sequence was lower than that in other parts of the provirus genome. Notably, the CS sequence of human endogenous retrovirus T had 73.8% similarity with that of FcERV-gamma4, and specific signals were detected in the human genome by Southern blot analysis using a probe for the FcERV-gamma4 CS sequence. Our results provide an interesting evolutionary history for CS-sequence circulation among several distinct ancestral viruses and a novel recombined virus over a prolonged period. Recombination among ERVs or modern viral genomes causes a rapid evolution of retroviruses, and this phenomenon can result in the serious situation of viral disease reemergence. We identified a novel recombinant FeLV gene that contains an unrelated sequence, termed the X region. This region originated from the 5' leader of FcERV-gamma4, a replication-incompetent feline ERV. Surprisingly, a sequence corresponding to the X region is also present in the 5' portion of other ERVs, including human endogenous retroviruses. Scattered copies of the ERVs carrying the unique genetic feature, here named the commonly shared (CS) sequence, were found in each host genome, suggesting that ancestral viruses may have captured and maintained the CS sequence. More recently, a novel recombinant FeLV hijacked the CS sequence from inactivated FcERV-gamma4 as the X region. Therefore, tracing the CS sequences can provide unique models for not only the modern reservoir of new recombinant viruses but also the genetic features shared among ancient retroviruses.
[Mh] Termos MeSH primário: Regiões 5´ não Traduzidas/genética
Retrovirus Endógenos/genética
Genes gag
Genoma Viral
Vírus da Leucemia Felina/genética
Recombinação Genética
[Mh] Termos MeSH secundário: Animais
Gatos/virologia
Evolução Molecular
Gammaretrovirus/genética
Seres Humanos/virologia
Leucemia Felina/virologia
Mamíferos/genética
Mamíferos/virologia
Filogenia
Provírus/genética
Provírus/fisiologia
RNA Viral/genética
Suínos/virologia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (5' Untranslated Regions); 0 (RNA, Viral)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171024
[Lr] Data última revisão:
171024
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170804
[St] Status:MEDLINE


  5 / 1849 MEDLINE  
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[PMID]:28700586
[Au] Autor:Ito J; Sugimoto R; Nakaoka H; Yamada S; Kimura T; Hayano T; Inoue I
[Ad] Endereço:Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, Japan.
[Ti] Título:Systematic identification and characterization of regulatory elements derived from human endogenous retroviruses.
[So] Source:PLoS Genet;13(7):e1006883, 2017 Jul.
[Is] ISSN:1553-7404
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Human endogenous retroviruses (HERVs) and other long terminal repeat (LTR)-type retrotransposons (HERV/LTRs) have regulatory elements that possibly influence the transcription of host genes. We systematically identified and characterized these regulatory elements based on publicly available datasets of ChIP-Seq of 97 transcription factors (TFs) provided by ENCODE and Roadmap Epigenomics projects. We determined transcription factor-binding sites (TFBSs) using the ChIP-Seq datasets and identified TFBSs observed on HERV/LTR sequences (HERV-TFBSs). Overall, 794,972 HERV-TFBSs were identified. Subsequently, we identified "HERV/LTR-shared regulatory element (HSRE)," defined as a TF-binding motif in HERV-TFBSs, shared within a substantial fraction of a HERV/LTR type. HSREs could be an indication that the regulatory elements of HERV/LTRs are present before their insertions. We identified 2,201 HSREs, comprising specific associations of 354 HERV/LTRs and 84 TFs. Clustering analysis showed that HERV/LTRs can be grouped according to the TF binding patterns; HERV/LTR groups bounded to pluripotent TFs (e.g., SOX2, POU5F1, and NANOG), embryonic endoderm/mesendoderm TFs (e.g., GATA4/6, SOX17, and FOXA1/2), hematopoietic TFs (e.g., SPI1 (PU1), GATA1/2, and TAL1), and CTCF were identified. Regulatory elements of HERV/LTRs tended to locate nearby and/or interact three-dimensionally with the genes involved in immune responses, indicating that the regulatory elements play an important role in controlling the immune regulatory network. Further, we demonstrated subgroup-specific TF binding within LTR7, LTR5B, and LTR5_Hs, indicating that gains or losses of the regulatory elements occurred during genomic invasions of the HERV/LTRs. Finally, we constructed dbHERV-REs, an interactive database of HERV/LTR regulatory elements (http://herv-tfbs.com/). This study provides fundamental information in understanding the impact of HERV/LTRs on host transcription, and offers insights into the transcriptional modulation systems of HERV/LTRs and ancestral HERVs.
[Mh] Termos MeSH primário: Retrovirus Endógenos/genética
Elementos Reguladores de Transcrição/genética
Fatores de Transcrição/genética
Transcrição Genética
[Mh] Termos MeSH secundário: Seres Humanos
Sequências Reguladoras de Ácido Nucleico/genética
Sequências Repetidas Terminais/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Transcription Factors)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170808
[Lr] Data última revisão:
170808
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170713
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pgen.1006883


  6 / 1849 MEDLINE  
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[PMID]:28656984
[Au] Autor:Mager DL; Lorincz MC
[Ad] Endereço:Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.
[Ti] Título:Epigenetic modifier drugs trigger widespread transcription of endogenous retroviruses.
[So] Source:Nat Genet;49(7):974-975, 2017 Jun 28.
[Is] ISSN:1546-1718
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:A study in this issue demonstrates that epigenome-modifying drugs used in cancer chemotherapy induce transcription from thousands of previously unannotated transcription start sites, most of which are derived from ancient endogenous retroviruses (ERVs). This work, coupled with previous related findings, suggests that induction of ERVs, rather than direct effects on specific genes, may have a central role in the cellular responses to such agents and, in turn, their therapeutic efficacy.
[Mh] Termos MeSH primário: Retrovirus Endógenos
Epigenômica
[Mh] Termos MeSH secundário: Seres Humanos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171026
[Lr] Data última revisão:
171026
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170629
[St] Status:MEDLINE
[do] DOI:10.1038/ng.3902


  7 / 1849 MEDLINE  
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[PMID]:28651004
[Au] Autor:Lemaître C; Tsang J; Bireau C; Heidmann T; Dewannieux M
[Ad] Endereço:CNRS, UMR 9196, Institut Gustave Roussy, Villejuif, France.
[Ti] Título:A human endogenous retrovirus-derived gene that can contribute to oncogenesis by activating the ERK pathway and inducing migration and invasion.
[So] Source:PLoS Pathog;13(6):e1006451, 2017 Jun.
[Is] ISSN:1553-7374
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Endogenous retroviruses are cellular genes of retroviral origin captured by their host during the course of evolution and represent around 8% of the human genome. Although most are defective and transcriptionally silenced, some are still able to generate retroviral-like particles and proteins. Among these, the HERV-K(HML2) family is remarkable since its members have amplified relatively recently and many of them still have full length coding genes. Furthermore, they are induced in cancers, especially in melanoma, breast cancer and germ cell tumours, where viral particles, as well as the envelope protein (Env), can be detected. Here we show that HERV-K(HML2) Env per se has oncogenic properties. Its expression in a non-tumourigenic human breast epithelial cell line induces epithelial to mesenchymal transition (EMT), often associated with tumour aggressiveness and metastasis. In our model, this is typified by key modifications in a set of molecular markers, changes in cell morphology and enhanced cell motility. Remarkably, microarrays performed in 293T cells reveal that HERV-K(HML2) Env is a strong inducer of several transcription factors, namely ETV4, ETV5 and EGR1, which are downstream effectors of the MAPK ERK1/2 and are associated with cellular transformation. We demonstrate that HERV-K(HML2) Env effectively activates the ERK1/2 pathway in our experimental setting and that this activation depends on the Env cytoplasmic tail. In addition, this phenomenon is very specific, being absent with every other retroviral Env tested, except for Jaagsiekte Sheep Retrovirus (JSRV) Env, which is already known to have transforming properties in vivo. Though HERV-K Env is not directly transforming by itself, the newly discovered properties of this protein may contribute to oncogenesis.
[Mh] Termos MeSH primário: Retrovirus Endógenos/genética
Transição Epitelial-Mesenquimal/genética
Sistema de Sinalização das MAP Quinases/genética
[Mh] Termos MeSH secundário: Animais
Neoplasias da Mama/genética
Transformação Celular Neoplásica/genética
Produtos do Gene env/genética
Seres Humanos
Retrovirus Jaagsiekte de Ovinos
Invasividade Neoplásica
Ovinos/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Gene Products, env)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170929
[Lr] Data última revisão:
170929
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170627
[St] Status:MEDLINE
[do] DOI:10.1371/journal.ppat.1006451


  8 / 1849 MEDLINE  
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[PMID]:28605635
[Au] Autor:Terry SN; Manganaro L; Cuesta-Dominguez A; Brinzevich D; Simon V; Mulder LCF
[Ad] Endereço:Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
[Ti] Título:Expression of HERV-K108 envelope interferes with HIV-1 production.
[So] Source:Virology;509:52-59, 2017 Sep.
[Is] ISSN:1096-0341
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The human endogenous retroviruses (HERV)-K of the HML-2 group include full-length or near full-length elements encoding functional proteins, and are classified as type-1 or type-2 (type-1 has a deletion in the 5' end of the env gene). Because proteins of different retroviruses can interact, we hypothesized that HERV-K envelope (Env) could influence HIV-1 replication. Here we describe the negative effect of envelope expression of certain type-2 HERV-Ks on HIV-1 production. All HIV-1 and SIV strains tested were susceptible to various degrees to inhibition by the HERV-K108 envelope. We identified four residues within HERV-K108 Env as being critical to inhibit HIV-1 production. No inhibition was observed on EGFP expression, indicating that HERV-K Env does not affect general protein production. These findings demonstrate that envelope proteins from some endogenous retroviruses can limit production of exogenous lentiviruses such as HIV-1. Future studies will elucidate the mechanism mediating HIV-1 inhibition by HERV Envs.
[Mh] Termos MeSH primário: Retrovirus Endógenos/genética
Expressão Gênica
HIV-1/crescimento & desenvolvimento
Proteínas do Envelope Viral/biossíntese
Interferência Viral
[Mh] Termos MeSH secundário: Análise Mutacional de DNA
Vírus da Imunodeficiência Símia/crescimento & desenvolvimento
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Viral Envelope Proteins)
[Em] Mês de entrada:1707
[Cu] Atualização por classe:170802
[Lr] Data última revisão:
170802
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170613
[St] Status:MEDLINE


  9 / 1849 MEDLINE  
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[PMID]:28472185
[Au] Autor:Ma Y; Liu R; Lv H; Han J; Zhong D; Zhang X
[Ad] Endereço:School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China.
[Ti] Título:A computational method for prediction of matrix proteins in endogenous retroviruses.
[So] Source:PLoS One;12(5):e0176909, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Human endogenous retroviruses (HERVs) encode active retroviral proteins, which may be involved in the progression of cancer and other diseases. Matrix protein (MA), in group-specific antigen genes (gag) of retroviruses, is associated with the virus envelope glycoproteins in most mammalian retroviruses and may be involved in virus particle assembly, transport and budding. However, the amount of annotated MAs in ERVs is still at a low level so far. No computational method to predict the exact start and end coordinates of MAs in gags has been proposed yet. In this paper, a computational method to identify MAs in ERVs is proposed. A divide and conquer technique was designed and applied to the conventional prediction model to acquire better results when dealing with gene sequences with various lengths. Initiation sites and termination sites were predicted separately and then combined according to their intervals. Three different algorithms were applied and compared: weighted support vector machine (WSVM), weighted extreme learning machine (WELM) and random forest (RF). G - mean (geometric mean of sensitivity and specificity) values of initiation sites and termination sites under 5-fold cross validation generated by random forest models are 0.9869 and 0.9755 respectively, highest among the algorithms applied. Our prediction models combine RF & WSVM algorithms to achieve the best prediction results. 98.4% of all the collected ERV sequences with complete MAs (125 in total) could be predicted exactly correct by the models. 94,671 HERV sequences from 118 families were scanned by the model, 104 new putative MAs were predicted in human chromosomes. Distributions of the putative MAs and optimizations of model parameters were also analyzed. The usage of our predicting method was also expanded to other retroviruses and satisfying results were acquired.
[Mh] Termos MeSH primário: Biologia Computacional
Retrovirus Endógenos/metabolismo
Proteínas da Matriz Viral/metabolismo
[Mh] Termos MeSH secundário: Animais
Seres Humanos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Viral Matrix Proteins)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170915
[Lr] Data última revisão:
170915
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170505
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0176909


  10 / 1849 MEDLINE  
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[PMID]:28472109
[Au] Autor:Tongyoo P; Avihingsanon Y; Prom-On S; Mutirangura A; Mhuantong W; Hirankarn N
[Ad] Endereço:Inter-Department Program of Biomedical Sciences, Faculty of Graduate School, Chulalongkorn University, Bangkok, Thailand.
[Ti] Título:EnHERV: Enrichment analysis of specific human endogenous retrovirus patterns and their neighboring genes.
[So] Source:PLoS One;12(5):e0177119, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Human endogenous retroviruses (HERVs) are flanked by long terminal repeats (LTRs), which contain the regulation part of the retrovirus. Remaining HERVs constitute 7% to 8% of the present day human genome, and most have been identified as solo LTRs. The HERV sequences have been associated with several molecular functions as well as certain diseases in human, but their roles in human diseases are yet to be established. We designed EnHERV to make accessible the identified endogenous retrovirus repetitive sequences from Repbase Update (a database of eukaryotic repetitive elements) that are present in the human genome. Defragmentation process was done to improve the RepeatMasker annotation output. The defragmented elements were used as core database in EnHERV. EnHERV is available at http://sysbio.chula.ac.th/enherv and can be searched using either gene lists of user interest or HERV characteristics. Besides the search function, EnHERV also provides an enrichment analysis function that allows users to perform enrichment analysis between selected HERV characteristics and user-input gene lists, especially genes with the expression profile of a certain disease. EnHERV will facilitate exploratory studies of specific HERV characteristics that control gene expression patterns related to various disease conditions. Here we analyzed 25 selected HERV groups/names from all four HERV superfamilies, using the sense and anti-sense directions of the HERV and gene expression profiles from 49 specific tissue and disease conditions. We found that intragenic HERVs were associated with down-regulated genes in most cancer conditions and in psoriatic skin tissues and associated with up-regulated genes in immune cells particularly from systemic lupus erythematosus (SLE) patients. EnHERV allowed the analysis of how different types of LTRs were differentially associated with specific gene expression profiles in particular disease conditions for further studies into their mechanisms and functions.
[Mh] Termos MeSH primário: Retrovirus Endógenos/genética
Genes Virais
[Mh] Termos MeSH secundário: Doenças Autoimunes/genética
Seres Humanos
Sequências Repetidas Terminais
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170915
[Lr] Data última revisão:
170915
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170505
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0177119



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