Base de dados : MEDLINE
Pesquisa : G05.360.340.024 [Categoria DeCS]
Referências encontradas : 125 [refinar]
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  1 / 125 MEDLINE  
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[PMID]:28977568
[Au] Autor:Hong S; Kim D
[Ad] Endereço:Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea.
[Ti] Título:Computational characterization of chromatin domain boundary-associated genomic elements.
[So] Source:Nucleic Acids Res;45(18):10403-10414, 2017 Oct 13.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Topologically associated domains (TADs) are 3D genomic structures with high internal interactions that play important roles in genome compaction and gene regulation. Their genomic locations and their association with CCCTC-binding factor (CTCF)-binding sites and transcription start sites (TSSs) were recently reported. However, the relationship between TADs and other genomic elements has not been systematically evaluated. This was addressed in the present study, with a focus on the enrichment of these genomic elements and their ability to predict the TAD boundary region. We found that consensus CTCF-binding sites were strongly associated with TAD boundaries as well as with the transcription factors (TFs) Zinc finger protein (ZNF)143 and Yin Yang (YY)1. TAD boundary-associated genomic elements include DNase I-hypersensitive sites, H3K36 trimethylation, TSSs, RNA polymerase II, and TFs such as Specificity protein 1, ZNF274 and SIX homeobox 5. Computational modeling with these genomic elements suggests that they have distinct roles in TAD boundary formation. We propose a structural model of TAD boundaries based on these findings that provides a basis for studying the mechanism of chromatin structure formation and gene regulation.
[Mh] Termos MeSH primário: Cromatina/genética
Mapeamento Cromossômico/métodos
Biologia Computacional/métodos
Genoma Humano
Elementos Reguladores de Transcrição
[Mh] Termos MeSH secundário: Algoritmos
Sítios de Ligação
Cromatina/metabolismo
Bases de Dados Genéticas
Regulação da Expressão Gênica
Componentes Genômicos
Seres Humanos
Regiões Promotoras Genéticas
[Pt] Tipo de publicação:EVALUATION STUDIES; JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Chromatin)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171031
[Lr] Data última revisão:
171031
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171005
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkx738


  2 / 125 MEDLINE  
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[PMID]:28192430
[Au] Autor:Santesmasses D; Mariotti M; Guigó R
[Ad] Endereço:Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.
[Ti] Título:Computational identification of the selenocysteine tRNA (tRNASec) in genomes.
[So] Source:PLoS Comput Biol;13(2):e1005383, 2017 Feb.
[Is] ISSN:1553-7358
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Selenocysteine (Sec) is known as the 21st amino acid, a cysteine analogue with selenium replacing sulphur. Sec is inserted co-translationally in a small fraction of proteins called selenoproteins. In selenoprotein genes, the Sec specific tRNA (tRNASec) drives the recoding of highly specific UGA codons from stop signals to Sec. Although found in organisms from the three domains of life, Sec is not universal. Many species are completely devoid of selenoprotein genes and lack the ability to synthesize Sec. Since tRNASec is a key component in selenoprotein biosynthesis, its efficient identification in genomes is instrumental to characterize the utilization of Sec across lineages. Available tRNA prediction methods fail to accurately predict tRNASec, due to its unusual structural fold. Here, we present Secmarker, a method based on manually curated covariance models capturing the specific tRNASec structure in archaea, bacteria and eukaryotes. We exploited the non-universality of Sec to build a proper benchmark set for tRNASec predictions, which is not possible for the predictions of other tRNAs. We show that Secmarker greatly improves the accuracy of previously existing methods constituting a valuable tool to identify tRNASec genes, and to efficiently determine whether a genome contains selenoproteins. We used Secmarker to analyze a large set of fully sequenced genomes, and the results revealed new insights in the biology of tRNASec, led to the discovery of a novel bacterial selenoprotein family, and shed additional light on the phylogenetic distribution of selenoprotein containing genomes. Secmarker is freely accessible for download, or online analysis through a web server at http://secmarker.crg.cat.
[Mh] Termos MeSH primário: Mapeamento Cromossômico/métodos
Marcadores Genéticos/genética
Genoma/genética
Ensaios de Triagem em Larga Escala/métodos
RNA de Transferência Aminoácido-Específico/genética
Aminoacil-RNA de Transferência/genética
[Mh] Termos MeSH secundário: Algoritmos
Componentes Genômicos/genética
Selenocisteína
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Genetic Markers); 0 (RNA, Transfer, Amino Acid-Specific); 0 (RNA, Transfer, Amino Acyl); 0 (selenocysteinyl-tRNA); 0 (tRNA, selenocysteine-); 0CH9049VIS (Selenocysteine)
[Em] Mês de entrada:1706
[Cu] Atualização por classe:170619
[Lr] Data última revisão:
170619
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170214
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pcbi.1005383


  3 / 125 MEDLINE  
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[PMID]:28087711
[Au] Autor:Narendra V; Bulajic M; Dekker J; Mazzoni EO; Reinberg D
[Ad] Endereço:Howard Hughes Medical Institute, New York, New York 10016, USA.
[Ti] Título:CTCF-mediated topological boundaries during development foster appropriate gene regulation.
[So] Source:Genes Dev;30(24):2657-2662, 2016 Dec 15.
[Is] ISSN:1549-5477
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The genome is organized into repeating topologically associated domains (TADs), each of which is spatially isolated from its neighbor by poorly understood boundary elements thought to be conserved across cell types. Here, we show that deletion of CTCF (CCCTC-binding factor)-binding sites at TAD and sub-TAD topological boundaries that form within the HoxA and HoxC clusters during differentiation not only disturbs local chromatin domain organization and regulatory interactions but also results in homeotic transformations typical of Hox gene misregulation. Moreover, our data suggest that CTCF-dependent boundary function can be modulated by competing forces, such as the self-assembly of polycomb domains within the nucleus. Therefore, CTCF boundaries are not merely static structural components of the genome but instead are locally dynamic regulatory structures that control gene expression during development.
[Mh] Termos MeSH primário: Diferenciação Celular/genética
Regulação da Expressão Gênica no Desenvolvimento/genética
Componentes Genômicos/genética
Proteínas Repressoras/genética
Proteínas Repressoras/metabolismo
[Mh] Termos MeSH secundário: Animais
Padronização Corporal/genética
Fator de Ligação a CCCTC
Células Cultivadas
Células-Tronco Embrionárias
Deleção de Genes
Proteínas de Homeodomínio/genética
Proteínas de Homeodomínio/metabolismo
Camundongos
Domínios Proteicos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (CCCTC-Binding Factor); 0 (Ctcf protein, mouse); 0 (Homeodomain Proteins); 0 (Repressor Proteins)
[Em] Mês de entrada:1706
[Cu] Atualização por classe:171116
[Lr] Data última revisão:
171116
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170115
[St] Status:MEDLINE
[do] DOI:10.1101/gad.288324.116


  4 / 125 MEDLINE  
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[PMID]:27556533
[Au] Autor:Blaimer BB; Lloyd MW; Guillory WX; Brady SG
[Ad] Endereço:Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, United States of America.
[Ti] Título:Sequence Capture and Phylogenetic Utility of Genomic Ultraconserved Elements Obtained from Pinned Insect Specimens.
[So] Source:PLoS One;11(8):e0161531, 2016.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Obtaining sequence data from historical museum specimens has been a growing research interest, invigorated by next-generation sequencing methods that allow inputs of highly degraded DNA. We applied a target enrichment and next-generation sequencing protocol to generate ultraconserved elements (UCEs) from 51 large carpenter bee specimens (genus Xylocopa), representing 25 species with specimen ages ranging from 2-121 years. We measured the correlation between specimen age and DNA yield (pre- and post-library preparation DNA concentration) and several UCE sequence capture statistics (raw read count, UCE reads on target, UCE mean contig length and UCE locus count) with linear regression models. We performed piecewise regression to test for specific breakpoints in the relationship of specimen age and DNA yield and sequence capture variables. Additionally, we compared UCE data from newer and older specimens of the same species and reconstructed their phylogeny in order to confirm the validity of our data. We recovered 6-972 UCE loci from samples with pre-library DNA concentrations ranging from 0.06-9.8 ng/µL. All investigated DNA yield and sequence capture variables were significantly but only moderately negatively correlated with specimen age. Specimens of age 20 years or less had significantly higher pre- and post-library concentrations, UCE contig lengths, and locus counts compared to specimens older than 20 years. We found breakpoints in our data indicating a decrease of the initial detrimental effect of specimen age on pre- and post-library DNA concentration and UCE contig length starting around 21-39 years after preservation. Our phylogenetic results confirmed the integrity of our data, giving preliminary insights into relationships within Xylocopa. We consider the effect of additional factors not measured in this study on our age-related sequence capture results, such as DNA fragmentation and preservation method, and discuss the promise of the UCE approach for large-scale projects in insect phylogenomics using museum specimens.
[Mh] Termos MeSH primário: Sequência Conservada
Componentes Genômicos
Genoma de Inseto
Insetos/classificação
Insetos/genética
Análise de Sequência de DNA
[Mh] Termos MeSH secundário: Animais
Biologia Computacional/métodos
Filogenia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1707
[Cu] Atualização por classe:171116
[Lr] Data última revisão:
171116
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160825
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0161531


  5 / 125 MEDLINE  
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[PMID]:27525861
[Au] Autor:Lian S; Tu Y; Wang Y; Chen X; Wang L
[Ad] Endereço:School of Physics and Electronic Engineering, Xinyang Normal University, Xinyang City, China.
[Ti] Título:A repetitive sequence assembler based on next-generation sequencing.
[So] Source:Genet Mol Res;15(3), 2016 Jul 25.
[Is] ISSN:1676-5680
[Cp] País de publicação:Brazil
[La] Idioma:eng
[Ab] Resumo:Repetitive sequences of variable length are common in almost all eukaryotic genomes, and most of them are presumed to have important biomedical functions and can cause genomic instability. Next-generation sequencing (NGS) technologies provide the possibility of identifying capturing these repetitive sequences directly from the NGS data. In this study, we assessed the performances in identifying capturing repeats of leading assemblers, such as Velvet, SOAPdenovo, SGA, MSR-CA, Bambus2, ALLPATHS-LG, and AByss using three real NGS datasets. Our results indicated that most of them performed poorly in capturing the repeats. Consequently, we proposed a repetitive sequence assembler, named NGSReper, for capturing repeats from NGS data. Simulated datasets were used to validate the feasibility of NGSReper. The results indicate that the completeness of capturing repeat is up to 99%. Cross validation was performed in three real NGS datasets, and extensive comparisons indicate that NGSReper performed best in terms of completeness and accuracy in capturing repeats. In conclusion, NGSReper is an appropriate and suitable tool for capturing repeats directly from NGS data.
[Mh] Termos MeSH primário: Sequenciamento de Nucleotídeos em Larga Escala/métodos
Sequências Repetitivas de Ácido Nucleico/genética
[Mh] Termos MeSH secundário: Algoritmos
Componentes Genômicos
Genoma Humano
Seres Humanos
Análise de Sequência de DNA/métodos
Software
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1703
[Cu] Atualização por classe:170321
[Lr] Data última revisão:
170321
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160816
[St] Status:MEDLINE
[do] DOI:10.4238/gmr.15038790


  6 / 125 MEDLINE  
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[PMID]:27146967
[Au] Autor:Evtushenko EV; Levitsky VG; Elisafenko EA; Gunbin KV; Belousov AI; Safár J; Dolezel J; Vershinin AV
[Ad] Endereço:Institute of Molecular and Cellular Biology, Siberian Branch of the RAS, Novosibirsk, Russia.
[Ti] Título:The expansion of heterochromatin blocks in rye reflects the co-amplification of tandem repeats and adjacent transposable elements.
[So] Source:BMC Genomics;17:337, 2016 05 04.
[Is] ISSN:1471-2164
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: A prominent and distinctive feature of the rye (Secale cereale) chromosomes is the presence of massive blocks of subtelomeric heterochromatin, the size of which is correlated with the copy number of tandem arrays. The rapidity with which these regions have formed over the period of speciation remains unexplained. RESULTS: Using a BAC library created from the short arm telosome of rye chromosome 1R we uncovered numerous arrays of the pSc200 and pSc250 tandem repeat families which are concentrated in subtelomeric heterochromatin and identified the adjacent DNA sequences. The arrays show significant heterogeneity in monomer organization. 454 reads were used to gain a representation of the expansion of these tandem repeats across the whole rye genome. The presence of multiple, relatively short monomer arrays, coupled with the mainly star-like topology of the monomer phylogenetic trees, was taken as indicative of a rapid expansion of the pSc200 and pSc250 arrays. The evolution of subtelomeric heterochromatin appears to have included a significant contribution of illegitimate recombination. The composition of transposable elements (TEs) within the regions flanking the pSc200 and pSc250 arrays differed markedly from that in the genome a whole. Solo-LTRs were strongly enriched, suggestive of a history of active ectopic exchange. Several DNA motifs were over-represented within the LTR sequences. CONCLUSION: The large blocks of subtelomeric heterochromatin have arisen from the combined activity of TEs and the expansion of the tandem repeats. The expansion was likely based on a highly complex network of recombination mechanisms.
[Mh] Termos MeSH primário: Elementos de DNA Transponíveis
Amplificação de Genes
Heterocromatina/genética
Secale/genética
Sequências de Repetição em Tandem
[Mh] Termos MeSH secundário: Cromossomos Artificiais Bacterianos
Cromossomos de Plantas/genética
Biblioteca Gênica
Componentes Genômicos
Hibridização in Situ Fluorescente
Análise de Sequência com Séries de Oligonucleotídeos
Filogenia
Análise de Sequência de DNA
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (DNA Transposable Elements); 0 (Heterochromatin)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:171118
[Lr] Data última revisão:
171118
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160506
[St] Status:MEDLINE
[do] DOI:10.1186/s12864-016-2667-5


  7 / 125 MEDLINE  
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[PMID]:26992416
[Au] Autor:Costantini M; Greif G; Alvarez-Valin F; Bernardi G
[Ad] Endereço:Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy maria.costantini@szn.it gbernardi@uniroma3.it.
[Ti] Título:The Anolis Lizard Genome: An Amniote Genome without Isochores?
[So] Source:Genome Biol Evol;8(4):1048-55, 2016 Apr 13.
[Is] ISSN:1759-6653
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Two articles published 5 years ago concluded that the genome of the lizard Anolis carolinensis is an amniote genome without isochores. This claim was apparently contradicting previous results on the general presence of an isochore organization in all vertebrate genomes tested (including Anolis). In this investigation, we demonstrate that the Anolis genome is indeed heterogeneous in base composition, since its macrochromosomes comprise isochores mainly from the L2 and H1 families (a moderately GC-poor and a moderately GC-rich family, respectively), and since the majority of the sequenced microchromosomes consists of H1 isochores. These families are associated with different features of genome structure, including gene density and compositional correlations (e.g., GC3 vs flanking sequence GC and intron GC), as in the case of mammalian and avian genomes. Moreover, the assembled Anolis chromosomes have an enormous number of gaps, which could be due to sequencing problems in GC-rich regions of the genome. In conclusion, the Anolis genome is no exception to the general rule of an isochore organization in the genomes of vertebrates (and other eukaryotes).
[Mh] Termos MeSH primário: Componentes Genômicos
Lagartos/genética
[Mh] Termos MeSH secundário: Animais
Composição de Bases
Mapeamento Cromossômico
Evolução Molecular
Isocoros
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Isochores)
[Em] Mês de entrada:1703
[Cu] Atualização por classe:170313
[Lr] Data última revisão:
170313
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160320
[St] Status:MEDLINE
[do] DOI:10.1093/gbe/evw056


  8 / 125 MEDLINE  
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[PMID]:26582634
[Au] Autor:Heitkam T; Petrasch S; Zakrzewski F; Kögler A; Wenke T; Wanke S; Schmidt T
[Ad] Endereço:Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany.
[Ti] Título:Next-generation sequencing reveals differentially amplified tandem repeats as a major genome component of Northern Europe's oldest Camellia japonica.
[So] Source:Chromosome Res;23(4):791-806, 2015 Dec.
[Is] ISSN:1573-6849
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Northern Europe's oldest and largest Camellia japonica growing at the Pillnitz Castle (Germany) for over 200 years is of botanical and cultural importance and is a reference for C. japonica molecular scale analysis. In order to provide a fundament for genome analysis of the genus Camellia, we characterize the C. japonica tandem repeat fraction, constituting 12.5 % of the Pillnitz camellia's genome. A genomic library of the Pillnitz C. japonica was produced and Illumina sequenced to generate 36 Gb of paired-end reads. We performed graph-based read clustering implemented in the RepeatExplorer pipeline to estimate the C. japonica repeat fraction of 73 %. This enabled us to identify and characterize the most prominent satellite DNAs, Camellia japonica satellite 1-4 (CajaSat1-CajaSat4), and the 5S ribosomal DNA (rDNA) by bioinformatics, fluorescent in situ and Southern hybridization. Within the Camellia genus, satellite spreading, array expansion and formation of higher-order structures highlight different modes of repeat evolution. The CajaSat satellites localize at prominent chromosomal sites, including (peri)centromeres and subtelomeres of all chromosomes, thus serving as chromosomal landmarks for their identification. This work provides an insight into the C. japonica chromosome organization and significantly expands the Camellia genomic knowledge, also with respect to the tea plant Camellia sinensis.
[Mh] Termos MeSH primário: Camellia/genética
Componentes Genômicos
Genoma de Planta
Sequências de Repetição em Tandem
[Mh] Termos MeSH secundário: Sequência de Bases
Cromossomos de Plantas
Sequência Consenso
Metilação de DNA
DNA Satélite
Sequenciamento de Nucleotídeos em Larga Escala
Dados de Sequência Molecular
Alinhamento de Sequência
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (DNA, Satellite)
[Em] Mês de entrada:1609
[Cu] Atualização por classe:171018
[Lr] Data última revisão:
171018
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:151120
[St] Status:MEDLINE
[do] DOI:10.1007/s10577-015-9500-x


  9 / 125 MEDLINE  
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[PMID]:26553646
[Au] Autor:Keinath MC; Timoshevskiy VA; Timoshevskaya NY; Tsonis PA; Voss SR; Smith JJ
[Ad] Endereço:Department of Biology, University of Kentucky, Lexington, KY, 40506, USA.
[Ti] Título:Initial characterization of the large genome of the salamander Ambystoma mexicanum using shotgun and laser capture chromosome sequencing.
[So] Source:Sci Rep;5:16413, 2015 Nov 10.
[Is] ISSN:2045-2322
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Vertebrates exhibit substantial diversity in genome size, and some of the largest genomes exist in species that uniquely inform diverse areas of basic and biomedical research. For example, the salamander Ambystoma mexicanum (the Mexican axolotl) is a model organism for studies of regeneration, development and genome evolution, yet its genome is ~10× larger than the human genome. As part of a hierarchical approach toward improving genome resources for the species, we generated 600 Gb of shotgun sequence data and developed methods for sequencing individual laser-captured chromosomes. Based on these data, we estimate that the A. mexicanum genome is ~32 Gb. Notably, as much as 19 Gb of the A. mexicanum genome can potentially be considered single copy, which presumably reflects the evolutionary diversification of mobile elements that accumulated during an ancient episode of genome expansion. Chromosome-targeted sequencing permitted the development of assemblies within the constraints of modern computational platforms, allowed us to place 2062 genes on the two smallest A. mexicanum chromosomes and resolves key events in the history of vertebrate genome evolution. Our analyses show that the capture and sequencing of individual chromosomes is likely to provide valuable information for the systematic sequencing, assembly and scaffolding of large genomes.
[Mh] Termos MeSH primário: Ambystoma mexicanum/genética
Cromossomos
Genoma
Genômica
Sequenciamento de Nucleotídeos em Larga Escala
[Mh] Termos MeSH secundário: Animais
Galinhas/genética
Mapeamento Cromossômico
Feminino
Componentes Genômicos
Genômica/métodos
Sequências Repetitivas de Ácido Nucleico
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.
[Em] Mês de entrada:1609
[Cu] Atualização por classe:170220
[Lr] Data última revisão:
170220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:151111
[St] Status:MEDLINE
[do] DOI:10.1038/srep16413


  10 / 125 MEDLINE  
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[PMID]:26378165
[Au] Autor:Hahn CM; Iwanowicz LR; Cornman RS; Conway CM; Winton JR; Blazer VS
[Ad] Endereço:West Virginia University, School of Natural Resources, Morgantown, West Virginia, USA U.S. Geological Survey, Leetown Science Center, Kearneysville, West Virginia, USA.
[Ti] Título:Characterization of a Novel Hepadnavirus in the White Sucker (Catostomus commersonii) from the Great Lakes Region of the United States.
[So] Source:J Virol;89(23):11801-11, 2015 Dec.
[Is] ISSN:1098-5514
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:UNLABELLED: The white sucker Catostomus commersonii is a freshwater teleost often utilized as a resident sentinel. Here, we sequenced the full genome of a hepatitis B-like virus that infects white suckers from the Great Lakes Region of the United States. Dideoxy sequencing confirmed that the white sucker hepatitis B virus (WSHBV) has a circular genome (3,542 bp) with the prototypical codon organization of hepadnaviruses. Electron microscopy demonstrated that complete virions of approximately 40 nm were present in the plasma of infected fish. Compared to avi- and orthohepadnaviruses, sequence conservation of the core, polymerase, and surface proteins was low and ranged from 16 to 27% at the amino acid level. An X protein homologue common to the orthohepadnaviruses was not present. The WSHBV genome included an atypical, presumptively noncoding region absent in previously described hepadnaviruses. Phylogenetic analyses confirmed WSHBV as distinct from previously documented hepadnaviruses. The level of divergence in protein sequences between WSHBV and other hepadnaviruses and the identification of an HBV-like sequence in an African cichlid provide evidence that a novel genus of the family Hepadnaviridae may need to be established that includes these hepatitis B-like viruses in fishes. Viral transcription was observed in 9.5% (16 of 169) of white suckers evaluated. The prevalence of hepatic tumors in these fish was 4.9%, and only 2.4% of fish were positive for both virus and hepatic tumors. These results are not sufficient to draw inferences regarding the association of WSHBV and carcinogenesis in white sucker. IMPORTANCE: We report the first full-length genome of a hepadnavirus from fishes. Phylogenetic analysis of this genome indicates divergence from genomes of previously described hepadnaviruses from mammalian and avian hosts and supports the creation of a novel genus. The discovery of this novel virus may better our understanding of the evolutionary history of hepatitis B-like viruses of other hosts. In fishes, knowledge of this virus may provide insight regarding possible risk factors associated with hepatic neoplasia in the white sucker. This may also offer another model system for mechanistic research.
[Mh] Termos MeSH primário: Cipriniformes/virologia
Doenças dos Peixes/epidemiologia
Doenças dos Peixes/virologia
Genoma Viral/genética
Vírus da Hepatite B/genética
Neoplasias Hepáticas/veterinária
[Mh] Termos MeSH secundário: Animais
Sequência de Bases
Sequência Conservada/genética
Evolução Molecular
Componentes Genômicos
Great Lakes Region
Vírus da Hepatite B/classificação
Neoplasias Hepáticas/epidemiologia
Neoplasias Hepáticas/virologia
Microscopia Eletrônica/veterinária
Dados de Sequência Molecular
Filogenia
Análise de Sequência de DNA/veterinária
Especificidade da Espécie
Vírion/ultraestrutura
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.
[Em] Mês de entrada:1603
[Cu] Atualização por classe:170220
[Lr] Data última revisão:
170220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:150918
[St] Status:MEDLINE
[do] DOI:10.1128/JVI.01278-15



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