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  1 / 87806 MEDLINE  
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[PMID]:29409851
[Au] Autor:Tan M; Li G; Qi S; Liu X; Chen X; Ma J; Zhang D; Han M
[Ad] Endereço:College of Horticulture, Northwest A & F University, Yangling, Shaanxi 712100, China.
[Ti] Título:Identification and expression analysis of the IPT and CKX gene families during axillary bud outgrowth in apple (Malus domestica Borkh.).
[So] Source:Gene;651:106-117, 2018 Apr 20.
[Is] ISSN:1879-0038
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Cytokinins (CKs) play a crucial role in promoting axillary bud outgrowth and targeting the control of CK metabolism can be used to enhance branching in plants. CK levels are maintained mainly by CK biosynthesis (isopentenyl transferase, IPT) and degradation (dehydrogenase, CKX) genes in plants. A systematic study of the IPT and CKX gene families in apple, however, has not been conducted. In the present study, 12 MdIPTs and 12 MdCKXs were identified in the apple genome. Systematic phylogenetic, structural, and synteny analyses were performed. Expression analysis of these genes in different tissues was also assessed. MdIPT and MdCKX genes exhibit distinct expression patterns in different tissues. The response of MdIPT, MdCKX, and MdPIN1 genes to various treatments (6-BA, decapitation and Lovastatin, an inhibitor of CKs synthesis) that impact branching were also investigated. Results indicated that most of the MdIPT and MdCKX, and MdPIN1 genes were upregulated by 6-BA and decapitation treatment, but inhibited by Lovastatin, a compound that effectively suppresses axillary bud outgrowth induced by decapitation. These findings suggest that cytokinin biosynthesis is required for the activation of bud break and the export of auxin from buds in apple tree with intact primary shoot apex or decapitated apple tree. MdCKX8 and MdCKX10, however, exhibited little response to decapitation, but were significantly up-regulated by 6-BA and Lovastatin, a finding that warrants further investigation in order to understand their function in bud-outgrowth.
[Mh] Termos MeSH primário: Alquil e Aril Transferases/genética
Genes de Plantas
Malus/genética
Oxirredutases/genética
[Mh] Termos MeSH secundário: Arabidopsis/genética
Compostos de Benzil/farmacologia
Mapeamento Cromossômico
Cromossomos de Plantas
Evolução Molecular
Flores/genética
Perfilação da Expressão Gênica
Regulação da Expressão Gênica de Plantas
Genoma de Planta
Lovastatina/farmacologia
Malus/enzimologia
Malus/crescimento & desenvolvimento
Família Multigênica
Filogenia
Reguladores de Crescimento de Planta
Purinas/farmacologia
Sintenia
Regulação para Cima
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Benzyl Compounds); 0 (Plant Growth Regulators); 0 (Purines); 9LHU78OQFD (Lovastatin); EC 1.- (Oxidoreductases); EC 1.5.99.12 (cytokinin oxidase); EC 2.5.- (Alkyl and Aryl Transferases); EC 2.5.1.27 (adenylate isopentenyltransferase); KXG6A989PS (benzylaminopurine)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180208
[St] Status:MEDLINE


  2 / 87806 MEDLINE  
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[PMID]:29244014
[Au] Autor:Aganezov SS; Alekseyev MA
[Ad] Endereço:Princeton University, 35 Olden St., Princeton, 08450, NJ, USA. aganezov@cs.princeton.edu.
[Ti] Título:CAMSA: a tool for comparative analysis and merging of scaffold assemblies.
[So] Source:BMC Bioinformatics;18(Suppl 15):496, 2017 Dec 06.
[Is] ISSN:1471-2105
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Despite the recent progress in genome sequencing and assembly, many of the currently available assembled genomes come in a draft form. Such draft genomes consist of a large number of genomic fragments (scaffolds), whose positions and orientations along the genome are unknown. While there exists a number of methods for reconstruction of the genome from its scaffolds, utilizing various computational and wet-lab techniques, they often can produce only partial error-prone scaffold assemblies. It therefore becomes important to compare and merge scaffold assemblies produced by different methods, thus combining their advantages and highlighting present conflicts for further investigation. These tasks may be labor intensive if performed manually. RESULTS: We present CAMSA-a tool for comparative analysis and merging of two or more given scaffold assemblies. The tool (i) creates an extensive report with several comparative quality metrics; (ii) constructs the most confident merged scaffold assembly; and (iii) provides an interactive framework for a visual comparative analysis of the given assemblies. Among the CAMSA features, only scaffold merging can be evaluated in comparison to existing methods. Namely, it resembles the functionality of assembly reconciliation tools, although their primary targets are somewhat different. Our evaluations show that CAMSA produces merged assemblies of comparable or better quality than existing assembly reconciliation tools while being the fastest in terms of the total running time. CONCLUSIONS: CAMSA addresses the current deficiency of tools for automated comparison and analysis of multiple assemblies of the same set scaffolds. Since there exist numerous methods and techniques for scaffold assembly, identifying similarities and dissimilarities across assemblies produced by different methods is beneficial both for the developers of scaffold assembly algorithms and for the researchers focused on improving draft assemblies of specific organisms.
[Mh] Termos MeSH primário: Mapeamento Cromossômico/métodos
Genômica/métodos
Software
[Mh] Termos MeSH secundário: Algoritmos
Genoma
Alinhamento de Sequência
Análise de Sequência de DNA
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180307
[Lr] Data última revisão:
180307
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171216
[St] Status:MEDLINE
[do] DOI:10.1186/s12859-017-1919-y


  3 / 87806 MEDLINE  
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[PMID]:28459939
[Au] Autor:Moyers BT; Owens GL; Baute GJ; Rieseberg LH
[Ad] Endereço:Department of Botany and Biodiversity Research Centre, University of British Columbia, Room 3529-6270 University Blvd, Vancouver, BC V6T 1Z4, Canada.
[Ti] Título:The genetic architecture of UV floral patterning in sunflower.
[So] Source:Ann Bot;120(1):39-50, 2017 Jul 01.
[Is] ISSN:1095-8290
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Background and Aims: The patterning of floral ultraviolet (UV) pigmentation varies both intra- and interspecifically in sunflowers and many other plant species, impacts pollinator attraction, and can be critical to reproductive success and crop yields. However, the genetic basis for variation in UV patterning is largely unknown. This study examines the genetic architecture for proportional and absolute size of the UV bullseye in Helianthus argophyllus , a close relative of the domesticated sunflower. Methods: A camera modified to capture UV light (320-380 nm) was used to phenotype floral UV patterning in an F 2 mapping population, then quantitative trait loci (QTL) were identified using genotyping-by-sequencing and linkage mapping. The ability of these QTL to predict the UV patterning of natural population individuals was also assessed. Key Results: Proportional UV pigmentation is additively controlled by six moderate effect QTL that are predictive of this phenotype in natural populations. In contrast, UV bullseye size is controlled by a single large effect QTL that also controls flowerhead size and co-localizes with a major flowering time QTL in Helianthus . Conclusions: The co-localization of the UV bullseye size QTL, flowerhead size QTL and a previously known flowering time QTL may indicate a single highly pleiotropic locus or several closely linked loci, which could inhibit UV bullseye size from responding to selection without change in correlated characters. The genetic architecture of proportional UV pigmentation is relatively simple and different from that of UV bullseye size, and so should be able to respond to natural or artificial selection independently.
[Mh] Termos MeSH primário: Flores/anatomia & histologia
Helianthus/genética
Pigmentação/genética
Locos de Características Quantitativas
Raios Ultravioleta
[Mh] Termos MeSH secundário: Mapeamento Cromossômico
Flores/genética
Genótipo
Fenótipo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1712
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170502
[St] Status:MEDLINE
[do] DOI:10.1093/aob/mcx038


  4 / 87806 MEDLINE  
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[PMID]:28449073
[Au] Autor:Berlin S; Hallingbäck HR; Beyer F; Nordh NE; Weih M; Rönnberg-Wästljung AC
[Ad] Endereço:Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, P.O. Box 7080, SE-750 07 Uppsala, Sweden.
[Ti] Título:Genetics of phenotypic plasticity and biomass traits in hybrid willows across contrasting environments and years.
[So] Source:Ann Bot;120(1):87-100, 2017 Jul 01.
[Is] ISSN:1095-8290
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Background and Aims: Phenotypic plasticity can affect the geographical distribution of taxa and greatly impact the productivity of crops across contrasting and variable environments. The main objectives of this study were to identify genotype-phenotype associations in key biomass and phenology traits and the strength of phenotypic plasticity of these traits in a short-rotation coppice willow population across multiple years and contrasting environments to facilitate marker-assisted selection for these traits. Methods: A hybrid Salix viminalis × ( S. viminalis × Salix schwerinii ) population with 463 individuals was clonally propagated and planted in three common garden experiments comprising one climatic contrast between Sweden and Italy and one water availability contrast in Italy. Several key phenotypic traits were measured and phenotypic plasticity was estimated as the trait value difference between experiments. Quantitative trait locus (QTL) mapping analyses were conducted using a dense linkage map and phenotypic effects of S. schwerinii haplotypes derived from detected QTL were assessed. Key Results: Across the climatic contrast, clone predictor correlations for biomass traits were low and few common biomass QTL were detected. This indicates that the genetic regulation of biomass traits was sensitive to environmental variation. Biomass QTL were, however, frequently shared across years and across the water availability contrast. Phenology QTL were generally shared between all experiments. Substantial phenotypic plasticity was found among the hybrid offspring, that to a large extent had a genetic origin. Individuals carrying influential S. schwerinii haplotypes generally performed well in Sweden but less well in Italy in terms of biomass production. Conclusions: The results indicate that specific genetic elements of S. schwerinii are more suited to Swedish conditions than to those of Italy. Therefore, selection should preferably be conducted separately for such environments in order to maximize biomass production in admixed S. viminalis × S. schwerinii populations.
[Mh] Termos MeSH primário: Biomassa
Meio Ambiente
Fenótipo
Salix/genética
[Mh] Termos MeSH secundário: Mapeamento Cromossômico
Estudos de Associação Genética
Itália
Locos de Características Quantitativas
Salix/crescimento & desenvolvimento
Suécia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1712
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170428
[St] Status:MEDLINE
[do] DOI:10.1093/aob/mcx029


  5 / 87806 MEDLINE  
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[PMID]:29351563
[Au] Autor:Ates D; Aldemir S; Alsaleh A; Erdogmus S; Nemli S; Kahriman A; Ozkan H; Vandenberg A; Tanyolac B
[Ad] Endereço:Department of Bioengineering, Faculty of Engineering, Ege University, Bornova, Izmir, Turkey.
[Ti] Título:A consensus linkage map of lentil based on DArT markers from three RIL mapping populations.
[So] Source:PLoS One;13(1):e0191375, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Lentil (Lens culinaris ssp. culinaris Medikus) is a diploid (2n = 2x = 14), self-pollinating grain legume with a haploid genome size of about 4 Gbp and is grown throughout the world with current annual production of 4.9 million tonnes. MATERIALS AND METHODS: A consensus map of lentil (Lens culinaris ssp. culinaris Medikus) was constructed using three different lentils recombinant inbred line (RIL) populations, including "CDC Redberry" x "ILL7502" (LR8), "ILL8006" x "CDC Milestone" (LR11) and "PI320937" x "Eston" (LR39). RESULTS: The lentil consensus map was composed of 9,793 DArT markers, covered a total of 977.47 cM with an average distance of 0.10 cM between adjacent markers and constructed 7 linkage groups representing 7 chromosomes of the lentil genome. The consensus map had no gap larger than 12.67 cM and only 5 gaps were found to be between 12.67 cM and 6.0 cM (on LG3 and LG4). The localization of the SNP markers on the lentil consensus map were in general consistent with their localization on the three individual genetic linkage maps and the lentil consensus map has longer map length, higher marker density and shorter average distance between the adjacent markers compared to the component linkage maps. CONCLUSION: This high-density consensus map could provide insight into the lentil genome. The consensus map could also help to construct a physical map using a Bacterial Artificial Chromosome library and map based cloning studies. Sequence information of DArT may help localization of orientation scaffolds from Next Generation Sequencing data.
[Mh] Termos MeSH primário: Lens (Planta)/genética
[Mh] Termos MeSH secundário: Mapeamento Cromossômico/métodos
Sequência Consenso
DNA de Plantas/genética
Ligação Genética
Genoma de Planta
Polimorfismo de Nucleotídeo Único
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (DNA, Plant)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180305
[Lr] Data última revisão:
180305
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180120
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0191375


  6 / 87806 MEDLINE  
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[PMID]:29272270
[Au] Autor:Badet T; Voisin D; Mbengue M; Barascud M; Sucher J; Sadon P; Balagué C; Roby D; Raffaele S
[Ad] Endereço:LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France.
[Ti] Título:Parallel evolution of the POQR prolyl oligo peptidase gene conferring plant quantitative disease resistance.
[So] Source:PLoS Genet;13(12):e1007143, 2017 12.
[Is] ISSN:1553-7404
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Plant pathogens with a broad host range are able to infect plant lineages that diverged over 100 million years ago. They exert similar and recurring constraints on the evolution of unrelated plant populations. Plants generally respond with quantitative disease resistance (QDR), a form of immunity relying on complex genetic determinants. In most cases, the molecular determinants of QDR and how they evolve is unknown. Here we identify in Arabidopsis thaliana a gene mediating QDR against Sclerotinia sclerotiorum, agent of the white mold disease, and provide evidence of its convergent evolution in multiple plant species. Using genome wide association mapping in A. thaliana, we associated the gene encoding the POQR prolyl-oligopeptidase with QDR against S. sclerotiorum. Loss of this gene compromised QDR against S. sclerotiorum but not against a bacterial pathogen. Natural diversity analysis associated POQR sequence with QDR. Remarkably, the same amino acid changes occurred after independent duplications of POQR in ancestors of multiple plant species, including A. thaliana and tomato. Genome-scale expression analyses revealed that parallel divergence in gene expression upon S. sclerotiorum infection is a frequent pattern in genes, such as POQR, that duplicated both in A. thaliana and tomato. Our study identifies a previously uncharacterized gene mediating QDR against S. sclerotiorum. It shows that some QDR determinants are conserved in distantly related plants and have emerged through the repeated use of similar genetic polymorphisms at different evolutionary time scales.
[Mh] Termos MeSH primário: Resistência à Doença/genética
Serina Endopeptidases/genética
[Mh] Termos MeSH secundário: Arabidopsis/genética
Ascomicetos/genética
Ascomicetos/patogenicidade
Mapeamento Cromossômico
Regulação da Expressão Gênica de Plantas
Estudo de Associação Genômica Ampla
Doenças das Plantas/genética
Imunidade Vegetal/genética
Proteínas de Plantas/genética
Serina Endopeptidases/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Plant Proteins); EC 3.4.21.- (Serine Endopeptidases); EC 3.4.21.26 (prolyl oligopeptidase)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180227
[Lr] Data última revisão:
180227
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171223
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pgen.1007143


  7 / 87806 MEDLINE  
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[PMID]:29355683
[Au] Autor:Yang C; Wu J; Zhang X; Wen L; Sun J; Cheng Y; Tang X; Liang B; Chen G; Zhou F; Cui Y; Zhang A; Zhang X; Zheng X; Yang S; Sun L
[Ad] Endereço:Institute of Dermatology and Department of Dermatology of the First Affiliated Hospital, Anhui Medical University, Hefei 230032, China; Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei 230032, China.
[Ti] Título:Fine-mapping analysis of the MHC region for vitiligo based on a new Han-MHC reference panel.
[So] Source:Gene;648:76-81, 2018 Mar 30.
[Is] ISSN:1879-0038
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Vitiligo is an immune-related disease with patchy depigmentation of skin and hair caused by selective destruction of melanocytes. In recent decades, many studies have shown the association between vitiligo and HLA genes; however, the results of Han Chinese are scarce. In this study, we performed a fine-mapping analysis of the MHC region in 2818 Han Chinese subjects through a widely used HLA imputation method with a newly built large-scale Han-MHC reference panel. Three new four-digit HLA alleles (HLA-DQB1 ∗ 02:02, HLA-DQA1 ∗ 02:01 and HLA-DPB1 ∗ 17:01) were identified to be associated with the risk of vitiligo, and four previously reported alleles were confirmed. Further conditional analysis revealed that two important variants, HLA-DQß1 amino acid position 135 (OR = 1.79, P = 1.87 × 10 ) and HLA-B amino acid positions 45-46 (OR = 1.44, P = 5.61 × 10 ), conferred most of the MHC associations. Three-dimension ribbon models showed that the former is located within the ß2 domain of the HLA-DQß1 molecule, and the latter lies in the α1 domain of the HLA-B molecule, while both are involved in specific antigen presenting process. Finally, we summarized all significant signals in the MHC region to clarify their complex relationships, and 8.60% of phenotypic variance could be explained based on all reported variants in Han Chinese so far. Our findings highlight the complex genetic architecture of the MHC region for vitiligo in Han Chinese population and expand our understanding of the roles of HLA coding variants in the etiology of vitiligo.
[Mh] Termos MeSH primário: Predisposição Genética para Doença/genética
Antígenos HLA/genética
Polimorfismo de Nucleotídeo Único
Vitiligo/genética
[Mh] Termos MeSH secundário: Alelos
Grupo com Ancestrais do Continente Asiático/genética
China
Mapeamento Cromossômico/métodos
Frequência do Gene
Predisposição Genética para Doença/etnologia
Haplótipos
Seres Humanos
Desequilíbrio de Ligação
Modelos Logísticos
Fatores de Risco
Vitiligo/etnologia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (HLA Antigens)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180226
[Lr] Data última revisão:
180226
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180123
[St] Status:MEDLINE


  8 / 87806 MEDLINE  
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[PMID]:29362361
[Au] Autor:Yousri NA; Fakhro KA; Robay A; Rodriguez-Flores JL; Mohney RP; Zeriri H; Odeh T; Kader SA; Aldous EK; Thareja G; Kumar M; Al-Shakaki A; Chidiac OM; Mohamoud YA; Mezey JG; Malek JA; Crystal RG; Suhre K
[Ad] Endereço:Genetic Medicine, Weill Cornell Medicine-Qatar, PO Box 24144, Doha, Qatar. nay2005@qatar-med.cornell.edu.
[Ti] Título:Whole-exome sequencing identifies common and rare variant metabolic QTLs in a Middle Eastern population.
[So] Source:Nat Commun;9(1):333, 2018 01 23.
[Is] ISSN:2041-1723
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Metabolomics-genome-wide association studies (mGWAS) have uncovered many metabolic quantitative trait loci (mQTLs) influencing human metabolic individuality, though predominantly in European cohorts. By combining whole-exome sequencing with a high-resolution metabolomics profiling for a highly consanguineous Middle Eastern population, we discover 21 common variant and 12 functional rare variant mQTLs, of which 45% are novel altogether. We fine-map 10 common variant mQTLs to new metabolite ratio associations, and 11 common variant mQTLs to putative protein-altering variants. This is the first work to report common and rare variant mQTLs linked to diseases and/or pharmacological targets in a consanguineous Arab cohort, with wide implications for precision medicine in the Middle East.
[Mh] Termos MeSH primário: Árabes
Exoma
Estudo de Associação Genômica Ampla
Metaboloma
Locos de Características Quantitativas
[Mh] Termos MeSH secundário: Adulto
Mapeamento Cromossômico
Estudos de Coortes
Consanguinidade
Feminino
Variação Genética
Genótipo
Sequenciamento de Nucleotídeos em Larga Escala
Seres Humanos
Masculino
Meia-Idade
Oriente Médio
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180222
[Lr] Data última revisão:
180222
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180125
[St] Status:MEDLINE
[do] DOI:10.1038/s41467-017-01972-9


  9 / 87806 MEDLINE  
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[PMID]:29335486
[Au] Autor:Ramírez F; Bhardwaj V; Arrigoni L; Lam KC; Grüning BA; Villaveces J; Habermann B; Akhtar A; Manke T
[Ad] Endereço:Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108, Freiburg, Germany.
[Ti] Título:High-resolution TADs reveal DNA sequences underlying genome organization in flies.
[So] Source:Nat Commun;9(1):189, 2018 01 15.
[Is] ISSN:2041-1723
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Despite an abundance of new studies about topologically associating domains (TADs), the role of genetic information in TAD formation is still not fully understood. Here we use our software, HiCExplorer (hicexplorer.readthedocs.io) to annotate >2800 high-resolution (570 bp) TAD boundaries in Drosophila melanogaster. We identify eight DNA motifs enriched at boundaries, including a motif bound by the M1BP protein, and two new boundary motifs. In contrast to mammals, the CTCF motif is only enriched on a small fraction of boundaries flanking inactive chromatin while most active boundaries contain the motifs bound by the M1BP or Beaf-32 proteins. We demonstrate that boundaries can be accurately predicted using only the motif sequences at open chromatin sites. We propose that DNA sequence guides the genome architecture by allocation of boundary proteins in the genome. Finally, we present an interactive online database to access and explore the spatial organization of fly, mouse and human genomes, available at http://chorogenome.ie-freiburg.mpg.de .
[Mh] Termos MeSH primário: Cromatina/ultraestrutura
Mapeamento Cromossômico/métodos
Cromossomos de Insetos/ultraestrutura
Drosophila melanogaster/genética
Genoma de Inseto
[Mh] Termos MeSH secundário: Animais
Evolução Biológica
Fator de Ligação a CCCTC/genética
Fator de Ligação a CCCTC/metabolismo
Cromatina/química
Montagem e Desmontagem da Cromatina
Cromossomos de Insetos/química
Proteínas de Ligação a DNA/genética
Proteínas de Ligação a DNA/metabolismo
Bases de Dados Genéticas
Proteínas de Drosophila/genética
Proteínas de Drosophila/metabolismo
Drosophila melanogaster/ultraestrutura
Proteínas do Olho/genética
Proteínas do Olho/metabolismo
Expressão Gênica
Seres Humanos
Camundongos
Conformação Molecular
Motivos de Nucleotídeos
Software
Fatores de Transcrição/genética
Fatores de Transcrição/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (BEAF-32 protein, Drosophila); 0 (CCCTC-Binding Factor); 0 (CTCF protein, Drosophila); 0 (Chromatin); 0 (DNA-Binding Proteins); 0 (Drosophila Proteins); 0 (Eye Proteins); 0 (M1BP protein, Drosophila); 0 (Transcription Factors)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180222
[Lr] Data última revisão:
180222
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180117
[St] Status:MEDLINE
[do] DOI:10.1038/s41467-017-02525-w


  10 / 87806 MEDLINE  
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[PMID]:29335463
[Au] Autor:Wang Q; Sun Q; Czajkowsky DM; Shao Z
[Ad] Endereço:Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 200240, Shanghai, China.
[Ti] Título:Sub-kb Hi-C in D. melanogaster reveals conserved characteristics of TADs between insect and mammalian cells.
[So] Source:Nat Commun;9(1):188, 2018 01 15.
[Is] ISSN:2041-1723
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Topologically associating domains (TADs) are fundamental elements of the eukaryotic genomic structure. However, recent studies suggest that the insulating complexes, CTCF/cohesin, present at TAD borders in mammals are absent from those in Drosophila melanogaster, raising the possibility that border elements are not conserved among metazoans. Using in situ Hi-C with sub-kb resolution, here we show that the D. melanogaster genome is almost completely partitioned into >4000 TADs, nearly sevenfold more than previously identified. The overwhelming majority of these TADs are demarcated by the insulator complexes, BEAF-32/CP190, or BEAF-32/Chromator, indicating that these proteins may play an analogous role in flies as that of CTCF/cohesin in mammals. Moreover, extended regions previously thought to be unstructured are shown to consist of small contiguous TADs, a property also observed in mammals upon re-examination. Altogether, our work demonstrates that fundamental features associated with the higher-order folding of the genome are conserved from insects to mammals.
[Mh] Termos MeSH primário: Cromatina/ultraestrutura
Mapeamento Cromossômico/métodos
Cromossomos de Insetos/ultraestrutura
Drosophila melanogaster/genética
Genoma de Inseto
Mamíferos/genética
[Mh] Termos MeSH secundário: Animais
Evolução Biológica
Fator de Ligação a CCCTC/genética
Fator de Ligação a CCCTC/metabolismo
Proteínas de Ciclo Celular/genética
Proteínas de Ciclo Celular/metabolismo
Cromatina/química
Montagem e Desmontagem da Cromatina
Proteínas Cromossômicas não Histona/genética
Proteínas Cromossômicas não Histona/metabolismo
Mapeamento Cromossômico/instrumentação
Cromossomos de Insetos/química
Proteínas de Ligação a DNA/genética
Proteínas de Ligação a DNA/metabolismo
Proteínas de Drosophila/genética
Proteínas de Drosophila/metabolismo
Drosophila melanogaster/ultraestrutura
Proteínas do Olho/genética
Proteínas do Olho/metabolismo
Expressão Gênica
Seres Humanos
Proteínas Associadas aos Microtúbulos/genética
Proteínas Associadas aos Microtúbulos/metabolismo
Conformação Molecular
Proteínas Associadas à Matriz Nuclear/genética
Proteínas Associadas à Matriz Nuclear/metabolismo
Proteínas Nucleares/genética
Proteínas Nucleares/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (BEAF-32 protein, Drosophila); 0 (CCCTC-Binding Factor); 0 (CP190 protein, Drosophila); 0 (CTCF protein, human); 0 (Cell Cycle Proteins); 0 (Chromatin); 0 (Chromosomal Proteins, Non-Histone); 0 (DNA-Binding Proteins); 0 (Drosophila Proteins); 0 (Eye Proteins); 0 (Microtubule-Associated Proteins); 0 (Nuclear Matrix-Associated Proteins); 0 (Nuclear Proteins); 0 (chromator protein, Drosophila); 0 (cohesins)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180222
[Lr] Data última revisão:
180222
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180117
[St] Status:MEDLINE
[do] DOI:10.1038/s41467-017-02526-9



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