Base de dados : MEDLINE
Pesquisa : D12.776.930 [Categoria DeCS]
Referências encontradas : 150967 [refinar]
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  1 / 150967 MEDLINE  
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[PMID]:29221486
[Au] Autor:Suzuki T; Maeda S; Furuhata E; Shimizu Y; Nishimura H; Kishima M; Suzuki H
[Ad] Endereço:Division of Genomic Technologies, RIKEN Center for Life Science Technologies (CLST), RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan.
[Ti] Título:A screening system to identify transcription factors that induce binding site-directed DNA demethylation.
[So] Source:Epigenetics Chromatin;10(1):60, 2017 12 08.
[Is] ISSN:1756-8935
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: DNA methylation is a fundamental epigenetic modification that is involved in many biological systems such as differentiation and disease. We and others recently showed that some transcription factors (TFs) are involved in the site-specific determination of DNA demethylation in a binding site-directed manner, although the reports of such TFs are limited. RESULTS: Here, we develop a screening system to identify TFs that induce binding site-directed DNA methylation changes. The system involves the ectopic expression of target TFs in model cells followed by DNA methylome analysis and overrepresentation analysis of the corresponding TF binding motif at differentially methylated regions. It successfully identified binding site-directed demethylation of SPI1, which is known to promote DNA demethylation in a binding site-directed manner. We extended our screening system to 15 master TFs involved in cellular differentiation and identified eight novel binding site-directed DNA demethylation-inducing TFs (RUNX3, GATA2, CEBPB, MAFB, NR4A2, MYOD1, CEBPA, and TBX5). Gene ontology and tissue enrichment analysis revealed that these TFs demethylate genomic regions associated with corresponding biological roles. We also describe the characteristics of binding site-directed DNA demethylation induced by these TFs, including the targeting of highly methylated CpGs, local DNA demethylation, and the overlap of demethylated regions between TFs of the same family. CONCLUSIONS: Our results show the usefulness of the developed screening system for the identification of TFs that induce DNA demethylation in a site-directed manner.
[Mh] Termos MeSH primário: Desmetilação
Fatores de Transcrição/metabolismo
[Mh] Termos MeSH secundário: Sítios de Ligação
Metilação de DNA
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Transcription Factors)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180310
[Lr] Data última revisão:
180310
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171210
[St] Status:MEDLINE
[do] DOI:10.1186/s13072-017-0169-6


  2 / 150967 MEDLINE  
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[PMID]:27777628
[Au] Autor:Brueckner L; van Arensbergen J; Akhtar W; Pagie L; van Steensel B
[Ad] Endereço:Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands.
[Ti] Título:High-throughput assessment of context-dependent effects of chromatin proteins.
[So] Source:Epigenetics Chromatin;9:43, 2016.
[Is] ISSN:1756-8935
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Chromatin proteins control gene activity in a concerted manner. We developed a high-throughput assay to study the effects of the local chromatin environment on the regulatory activity of a protein of interest. The assay combines a previously reported multiplexing strategy based on barcoded randomly integrated reporters with Gal4-mediated tethering. We applied the assay to heterochromatin protein 1a (HP1a), which is mostly known as a repressive protein but has also been linked to transcriptional activation. RESULTS: Recruitment to over 1000 genomic locations revealed that HP1a is a potent repressor able to silence even highly expressing reporter genes. However, the local chromatin context can modulate HP1a function. In pericentromeric regions, HP1a-induced repression was enhanced by twofold. In regions marked by a H3K36me3-rich chromatin signature, HP1a-dependent silencing was significantly decreased. We found no evidence for an activating function of HP1a in our experimental system. Furthermore, we did not observe stable transmission of repression over mitotic divisions after loss of targeted HP1a. CONCLUSIONS: The multiplexed tethered reporter assay should be applicable to a large number of chromatin proteins and will be a useful tool to dissect combinatorial regulatory interactions in chromatin.
[Mh] Termos MeSH primário: Cromatina/metabolismo
Proteínas Cromossômicas não Histona/genética
Proteínas de Drosophila/genética
[Mh] Termos MeSH secundário: Animais
Linhagem Celular
Proteínas Cromossômicas não Histona/metabolismo
Proteínas de Drosophila/metabolismo
Drosophila melanogaster/genética
Drosophila melanogaster/metabolismo
Inativação Gênica
Histonas/metabolismo
Plasmídeos/genética
Plasmídeos/metabolismo
Elongação da Transcrição Genética
Fatores de Transcrição/genética
Fatores de Transcrição/metabolismo
Transfecção
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Chromatin); 0 (Chromosomal Proteins, Non-Histone); 0 (Drosophila Proteins); 0 (GAL4 protein, Drosophila); 0 (Histones); 0 (Transcription Factors)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180310
[Lr] Data última revisão:
180310
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161026
[St] Status:MEDLINE


  3 / 150967 MEDLINE  
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[PMID]:29429191
[Au] Autor:Zhang YY; Lou HF; Wang CS; Zhang L
[Ad] Endereço:Deparment of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China; Beijing Key Laboratory of Nasal Diseases, Beijing Institude of Otorhinolaryngology, Beijing 100005, China.
[Ti] Título:[Mechanisms underlying glucocorticoid resistance in chronic rhinosinusitis with nasal polyps].
[So] Source:Zhonghua Er Bi Yan Hou Tou Jing Wai Ke Za Zhi;53(2):154-160, 2018 Feb 07.
[Is] ISSN:1673-0860
[Cp] País de publicação:China
[La] Idioma:chi
[Ab] Resumo:Chronic rhinosinusitis with nasal polyps (CRSwNP) is a chronic inflammatory disease that occurs in the nasal and sinus mucosa, which is a common disease in otorhinolaryngology. At present, CRSwNP can be effectively treated by glucocorticoids (GC). GC binds to GC receptors in the nasal mucosa, affects the expression of inflammatory genes, inhibits the activation and action of eosinophils, T cell-associated inflammatory responses in nasal polyps, as well as tissue remodeling. However, there are some patients fall reponse to GC, so called GC resistance. The study suggests that the possible mechanism of CRSwNP GC resistance is mainly related to GC receptor abnormal, the role of cytokines and transcription factors, such as Th cells and IL-8. In addition, MAPK-related kinases and histone deacetylase in the GC signaling pathway also play important roles in the GC resistance process. This paper reviews the mechanism of GC treatment of CRSwNP, the mechanism of GC resistance and alternative treatment of GC.
[Mh] Termos MeSH primário: Glucocorticoides/uso terapêutico
Erros Inatos do Metabolismo
Pólipos Nasais/tratamento farmacológico
Receptores de Glucocorticoides/deficiência
Rinite/tratamento farmacológico
Sinusite/tratamento farmacológico
[Mh] Termos MeSH secundário: Doença Crônica
Citocinas/metabolismo
Resistência a Medicamentos
Glucocorticoides/metabolismo
Seres Humanos
Mucosa Nasal/metabolismo
Pólipos Nasais/complicações
Rinite/complicações
Transdução de Sinais
Sinusite/complicações
Fatores de Transcrição/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Nm] Nome de substância:
0 (Cytokines); 0 (Glucocorticoids); 0 (Receptors, Glucocorticoid); 0 (Transcription Factors)
[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:180213
[St] Status:MEDLINE
[do] DOI:10.3760/cma.j.issn.1673-0860.2018.02.017


  4 / 150967 MEDLINE  
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[PMID]:29422671
[Au] Autor:Li C; Zhang B; Chen B; Ji L; Yu H
[Ad] Endereço:Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore.
[Ti] Título:Site-specific phosphorylation of TRANSPARENT TESTA GLABRA1 mediates carbon partitioning in Arabidopsis seeds.
[So] Source:Nat Commun;9(1):571, 2018 02 08.
[Is] ISSN:2041-1723
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Seed development is dependent on nutrients, such as a source of carbon, supplied by the parent plant. It remains largely unknown how these nutrients are distributed to zygotic and maternal tissues to coordinate storage of reserve compounds and development of protective tissues like seed coat. Here we show that phosphorylation of TRANSPARENT TESTA GLABRA1 (TTG1) is regulated by SHAGGY-like kinases 11/12 (SK11/12) and that this mediates carbon flow to fatty acid synthesis and seed coat traits in Arabidopsis seeds. SK11/12 phosphorylate TTG1 at serine 215, thus preventing TTG1 interaction with TRANSPARENT TESTA2. This compromises recruitment of TTG1 to the GLABRA2 locus and downregulates GLABRA2 expression, which enhances biosynthesis of fatty acids in the embryo, but reduces production of mucilage and flavonoid pigments in the seed coat. Therefore, site-specific phosphorylation of TTG1 by SK11/SK12 regulates carbon partitioning between zygotic and maternal sinks in seeds.
[Mh] Termos MeSH primário: Proteínas de Arabidopsis/genética
Arabidopsis/genética
Carbono/metabolismo
Regulação da Expressão Gênica de Plantas
Sementes/genética
[Mh] Termos MeSH secundário: Arabidopsis/crescimento & desenvolvimento
Arabidopsis/metabolismo
Proteínas de Arabidopsis/metabolismo
Ácidos Graxos/biossíntese
Flavonoides/biossíntese
Regulação da Expressão Gênica no Desenvolvimento
Quinase 3 da Glicogênio Sintase/genética
Quinase 3 da Glicogênio Sintase/metabolismo
Isoenzimas/genética
Isoenzimas/metabolismo
Mutação
Fenótipo
Fosforilação
Mucilagem Vegetal/biossíntese
Sementes/crescimento & desenvolvimento
Sementes/metabolismo
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 (Arabidopsis Proteins); 0 (Fatty Acids); 0 (Flavonoids); 0 (Isoenzymes); 0 (Plant Mucilage); 0 (TTG1 protein, Arabidopsis); 0 (TTG2 protein, Arabidopsis); 0 (Transcription Factors); 7440-44-0 (Carbon); EC 2.7.11.26 (ATSK11 protein, Arabidopsis); EC 2.7.11.26 (Glycogen Synthase Kinase 3)
[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:180210
[St] Status:MEDLINE
[do] DOI:10.1038/s41467-018-03013-5


  5 / 150967 MEDLINE  
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[PMID]:29205966
[Au] Autor:Deng XD; Zhang W; Zhang B; Ma Y; Muer CE; Zhang LX; Xie Y; Liu Y
[Ad] Endereço:Department of Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China.
[Ti] Título:[Expression of XPG Gene in Forensic Age Estimation].
[So] Source:Fa Yi Xue Za Zhi;32(6):415-419, 2016 Dec.
[Is] ISSN:1004-5619
[Cp] País de publicação:China
[La] Idioma:chi
[Ab] Resumo:OBJECTIVES: To explore the expression of xeroderma pigmentosum complementation group G ( ) gene in healthy Han population of different ages and to analysis the relationship between the mRNA and protein expression levels of XPG and age, which may provide a new molecular-biological indicator for forensic age determination. METHODS: Total 150 samples of peripheral blood were collected from healthy Han population of different ages. Total RNA of peripheral blood mononuclear cell (PBMC) were extracted by TRIzol method, and the relative expression of mRNA in PBMC was detected by quantitative real-time PCR, and the protein expression levels of XPG in plasma were detected by ELISA. RESULTS: The mRNA and protein expression levels of XPG in ≤18 years old group were significantly different from 19-45 years old group and ≥46 years old group ( <0.05), while there was no significant difference between 19-45 years old group and ≥46 years old group ( >0.05). No significant sex differences were observed in mRNA and protein expression levels of XPG ( >0.05). CONCLUSIONS: The relative expression level of mRNA in PBMC declines with the increase of age in younger age, while the protein expression level in plasma increases with age, and gene can be used as one of new markers for forensic age estimation.
[Mh] Termos MeSH primário: Fatores Etários
Proteínas de Ligação a DNA/genética
Endonucleases/genética
Proteínas Nucleares/genética
Fatores de Transcrição/genética
[Mh] Termos MeSH secundário: Adulto
Grupo com Ancestrais do Continente Asiático
Genética Forense
Seres Humanos
Leucócitos Mononucleares
Meia-Idade
RNA Mensageiro
Reação em Cadeia da Polimerase em Tempo Real
Adulto Jovem
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA excision repair protein ERCC-5); 0 (DNA-Binding Proteins); 0 (Nuclear Proteins); 0 (RNA, Messenger); 0 (Transcription Factors); EC 3.1.- (Endonucleases)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171206
[St] Status:MEDLINE
[do] DOI:10.3969/j.issn.1004-5619.2016.06.005


  6 / 150967 MEDLINE  
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[PMID]:27773872
[Au] Autor:Willmore-Payne C; Damjanovich-Colmenares K; Pasi AV; Werner TL; Gulbahce HE; Downs-Kelly E; Geiersbach KB
[Ad] Endereço:From the ARUP Laboratories, Salt Lake City, UT.
[Ti] Título:Inconsistent Results With Different Secondary Reflex Assays for Resolving HER2 Status.
[So] Source:Am J Clin Pathol;146(5):618-626, 2016 Nov 01.
[Is] ISSN:1943-7722
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Objectives: Guidelines suggest that secondary reflex testing may be useful for resolving HER2 status in breast cancers with equivocal results by both immunohistochemistry (IHC) and in situ hybridization (ISH). We compared two reflex ISH assays and a polymerase chain reaction (PCR) assay for this application. Methods: Twenty-nine breast cancers with equivocal IHC and ISH results were retested two ways: (1) ISH using differentially labeled probes targeting ERBB2 ( HER2 , 17q12) and either RAI1 (17p11.2) or ORC4 (2q22.3-2q23.1) in two separate assays and (2) real-time quantitative PCR amplification of ERBB2 and a control locus ( EIF5B , 2q11.2). Results: Results of the HER2 / RAI1 and HER2 / ORC4 ISH assays were concordant for 21 (72%) cases, and results of all three secondary reflex assays were concordant for only 18 (62%) cases. Result discrepancies between the two ISH readers were observed for cases close to the cutoff threshold. Conclusions: Use of different control loci for ISH is associated with discordant results, and PCR is more likely to classify cases as nonamplified, possibly due to contamination with nontumor cells. While resolution of HER2 -equivocal results is desirable from a clinical perspective, different secondary reflex assays yield different results, and the correlation of these results with clinical outcomes is unknown.
[Mh] Termos MeSH primário: Biomarcadores Tumorais/metabolismo
Neoplasias da Mama/metabolismo
Receptor ErbB-2/metabolismo
[Mh] Termos MeSH secundário: Neoplasias da Mama/diagnóstico
Neoplasias da Mama/patologia
Proteínas de Ciclo Celular/genética
Proteínas de Ciclo Celular/metabolismo
Feminino
Seres Humanos
Imuno-Histoquímica
Hibridização In Situ
Complexo de Reconhecimento de Origem/genética
Complexo de Reconhecimento de Origem/metabolismo
Reação em Cadeia da Polimerase em Tempo Real
Receptor ErbB-2/genética
Reflexo
Fatores de Transcrição/genética
Fatores de Transcrição/metabolismo
[Pt] Tipo de publicação:COMPARATIVE STUDY; JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Biomarkers, Tumor); 0 (Cell Cycle Proteins); 0 (ORC4 protein, human); 0 (Origin Recognition Complex); 0 (RAI1 protein, human); 0 (Transcription Factors); EC 2.7.10.1 (ERBB2 protein, human); EC 2.7.10.1 (Receptor, ErbB-2)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:AIM; IM
[Da] Data de entrada para processamento:161025
[St] Status:MEDLINE
[do] DOI:10.1093/ajcp/aqw177


  7 / 150967 MEDLINE  
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[PMID]:29237530
[Au] Autor:Zhu XH; Li QG; Wang J; Hu GZ; Liu ZQ; Hu QH; Wu G
[Ad] Endereço:School of Medicine, Nanchang University, Nanchang 330006, China. nclqg2017@163.com.
[Ti] Título:[Mechanism of action of BET bromodomain inhibitor JQ1 in treating airway remodeling in asthmatic mice].
[So] Source:Zhongguo Dang Dai Er Ke Za Zhi;19(12):1278-1284, 2017 Dec.
[Is] ISSN:1008-8830
[Cp] País de publicação:China
[La] Idioma:chi
[Ab] Resumo:OBJECTIVE: To investigate the molecular mechanism of action of BET bromodomain inhibitor JQ1 in treating airway remodeling in asthmatic mice. METHODS: A total of 24 mice were randomly divided into control group, ovalbumin (OVA)-induced asthma group (OVA group), and JQ1 intervention group (JQ1+OVA group), with 8 mice in each group. OVA sensitization/challenge was performed to establish a mouse model of asthma. At 1 hour before challenge, the mice in the JQ1+OVA group were given intraperitoneal injection of JQ1 solution (50 µg/g). Bronchoalveolar lavage fluid (BALF) and lung tissue samples were collected at 24 hours after the last challenge, and the total number of cells and percentage of eosinophils in BALF were calculated. Pathological staining was performed to observe histopathological changes in lung tissue. RT-PCR and Western blot were used to measure the mRNA and protein expression of E-cadherin and vimentin during epithelial-mesenchymal transition (EMT). RESULTS: Compared with the control group, the OVA group had marked infiltration of inflammatory cells in the airway, thickening of the airway wall, increased secretion of mucus, and increases in the total number of cells and percentage of eosinophils in BALF (P<0.01). Compared with the OVA group, the JQ1+OVA group had significantly alleviated airway inflammatory response and significant reductions in the total number of cells and percentage of eosinophils in BALF (P<0.01). Compared with the control group, the OVA group had significant reductions in the mRNA and protein expression of E-cadherin and significant increases in the mRNA and protein expression of vimentin (P<0.01); compared with the OVA group, the JQ1+OVA group had significant increases in the mRNA and protein expression of E-cadherin and significant reductions in the mRNA and protein expression of vimentin (P<0.01); there were no significant differences in these indices between the JQ1+OVA group and the control group (P>0.05). CONCLUSIONS: Mice with OVA-induced asthma have airway remodeling during EMT. BET bromodomain inhibitor JQ1 can reduce airway inflammation, inhibit EMT, and alleviate airway remodeling, which provides a new direction for the treatment of asthma.
[Mh] Termos MeSH primário: Remodelação das Vias Aéreas/efeitos dos fármacos
Asma/tratamento farmacológico
Azepinas/farmacologia
Triazóis/farmacologia
[Mh] Termos MeSH secundário: Animais
Caderinas/análise
Caderinas/genética
Transição Epitelial-Mesenquimal
Feminino
Camundongos
Proteínas Nucleares/antagonistas & inibidores
Ovalbumina/imunologia
RNA Mensageiro/análise
Fatores de Transcrição/antagonistas & inibidores
Vimentina/análise
Vimentina/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 ((+)-JQ1 compound); 0 (Azepines); 0 (Brd4 protein, mouse); 0 (Cadherins); 0 (E-cadherin protein, mouse); 0 (Nuclear Proteins); 0 (RNA, Messenger); 0 (Transcription Factors); 0 (Triazoles); 0 (Vimentin); 9006-59-1 (Ovalbumin)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180306
[Lr] Data última revisão:
180306
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171215
[St] Status:MEDLINE


  8 / 150967 MEDLINE  
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[PMID]:29187152
[Au] Autor:Spadafore M; Najarian K; Boyle AP
[Ad] Endereço:University of Michigan Medical School, 1301 Catherine, Ann Arbor, 48109-5624, USA. maxspad@umich.edu.
[Ti] Título:A proximity-based graph clustering method for the identification and application of transcription factor clusters.
[So] Source:BMC Bioinformatics;18(1):530, 2017 Nov 29.
[Is] ISSN:1471-2105
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Transcription factors (TFs) form a complex regulatory network within the cell that is crucial to cell functioning and human health. While methods to establish where a TF binds to DNA are well established, these methods provide no information describing how TFs interact with one another when they do bind. TFs tend to bind the genome in clusters, and current methods to identify these clusters are either limited in scope, unable to detect relationships beyond motif similarity, or not applied to TF-TF interactions. METHODS: Here, we present a proximity-based graph clustering approach to identify TF clusters using either ChIP-seq or motif search data. We use TF co-occurrence to construct a filtered, normalized adjacency matrix and use the Markov Clustering Algorithm to partition the graph while maintaining TF-cluster and cluster-cluster interactions. We then apply our graph structure beyond clustering, using it to increase the accuracy of motif-based TFBS searching for an example TF. RESULTS: We show that our method produces small, manageable clusters that encapsulate many known, experimentally validated transcription factor interactions and that our method is capable of capturing interactions that motif similarity methods might miss. Our graph structure is able to significantly increase the accuracy of motif TFBS searching, demonstrating that the TF-TF connections within the graph correlate with biological TF-TF interactions. CONCLUSION: The interactions identified by our method correspond to biological reality and allow for fast exploration of TF clustering and regulatory dynamics.
[Mh] Termos MeSH primário: Algoritmos
Fatores de Transcrição/metabolismo
[Mh] Termos MeSH secundário: Imunoprecipitação da Cromatina
Análise por Conglomerados
DNA/química
DNA/isolamento & purificação
DNA/metabolismo
Redes Reguladoras de Genes
Seres Humanos
Células K562
Cadeias de Markov
Mapas de Interação de Proteínas/genética
Análise de Sequência de DNA
Fatores de Transcrição/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Transcription Factors); 9007-49-2 (DNA)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180306
[Lr] Data última revisão:
180306
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171201
[St] Status:MEDLINE
[do] DOI:10.1186/s12859-017-1935-y


  9 / 150967 MEDLINE  
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[PMID]:29178831
[Au] Autor:Myschyshyn M; Farren-Dai M; Chuang TJ; Vocadlo D
[Ad] Endereço:Department of Molecular Biology and Biochemistry, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada. mmyschyshyn@gmail.com.
[Ti] Título:Software for rapid time dependent ChIP-sequencing analysis (TDCA).
[So] Source:BMC Bioinformatics;18(1):521, 2017 Nov 25.
[Is] ISSN:1471-2105
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) and associated methods are widely used to define the genome wide distribution of chromatin associated proteins, post-translational epigenetic marks, and modifications found on DNA bases. An area of emerging interest is to study time dependent changes in the distribution of such proteins and marks by using serial ChIP-seq experiments performed in a time resolved manner. Despite such time resolved studies becoming increasingly common, software to facilitate analysis of such data in a robust automated manner is limited. RESULTS: We have designed software called Time-Dependent ChIP-Sequencing Analyser (TDCA), which is the first program to automate analysis of time-dependent ChIP-seq data by fitting to sigmoidal curves. We provide users with guidance for experimental design of TDCA for modeling of time course (TC) ChIP-seq data using two simulated data sets. Furthermore, we demonstrate that this fitting strategy is widely applicable by showing that automated analysis of three previously published TC data sets accurately recapitulates key findings reported in these studies. Using each of these data sets, we highlight how biologically relevant findings can be readily obtained by exploiting TDCA to yield intuitive parameters that describe behavior at either a single locus or sets of loci. TDCA enables customizable analysis of user input aligned DNA sequencing data, coupled with graphical outputs in the form of publication-ready figures that describe behavior at either individual loci or sets of loci sharing common traits defined by the user. TDCA accepts sequencing data as standard binary alignment map (BAM) files and loci of interest in browser extensible data (BED) file format. CONCLUSIONS: TDCA accurately models the number of sequencing reads, or coverage, at loci from TC ChIP-seq studies or conceptually related TC sequencing experiments. TC experiments are reduced to intuitive parametric values that facilitate biologically relevant data analysis, and the uncovering of variations in the time-dependent behavior of chromatin. TDCA automates the analysis of TC ChIP-seq experiments, permitting researchers to easily obtain raw and modeled data for specific loci or groups of loci with similar behavior while also enhancing consistency of data analysis of TC data within the genomics field.
[Mh] Termos MeSH primário: Imunoprecipitação da Cromatina/métodos
Sequenciamento de Nucleotídeos em Larga Escala/métodos
Software
[Mh] Termos MeSH secundário: Algoritmos
Animais
Linhagem Celular
Cromossomos/química
Cromossomos/metabolismo
DNA/química
DNA/isolamento & purificação
DNA/metabolismo
Proteínas de Ligação a DNA/química
Proteínas de Ligação a DNA/genética
Proteínas de Ligação a DNA/metabolismo
Histonas/química
Histonas/genética
Histonas/metabolismo
Seres Humanos
Saccharomyces cerevisiae/metabolismo
Proteínas de Saccharomyces cerevisiae/química
Proteínas de Saccharomyces cerevisiae/genética
Proteínas de Saccharomyces cerevisiae/metabolismo
Análise de Sequência de DNA
Fatores de Transcrição/química
Fatores de Transcrição/genética
Fatores de Transcrição/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (ABF1 protein, S cerevisiae); 0 (DNA-Binding Proteins); 0 (Histones); 0 (Saccharomyces cerevisiae Proteins); 0 (Transcription Factors); 9007-49-2 (DNA)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180306
[Lr] Data última revisão:
180306
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171128
[St] Status:MEDLINE
[do] DOI:10.1186/s12859-017-1936-x


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[PMID]:28461451
[Au] Autor:Li L; Jiang W; Lu Y
[Ad] Endereço:Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
[Ti] Título:A Novel Two-Component System, GluR-GluK, Involved in Glutamate Sensing and Uptake in Streptomyces coelicolor.
[So] Source:J Bacteriol;199(18), 2017 09 15.
[Is] ISSN:1098-5530
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Two-component systems (TCSs), the predominant signal transduction pathways employed by bacteria, play important roles in physiological metabolism in Here, a novel TCS, GluR-GluK (encoded by ), which is located divergently from the operon encoding a glutamate uptake system, was identified as being involved in glutamate sensing and uptake as well as antibiotic biosynthesis in Under the condition of minimal medium (MM) supplemented with different concentrations of glutamate, deletion of the operon ( ) resulted in enhanced actinorhodin (ACT) but reduced undecylprodigiosin (RED) and yellow type I polyketide (yCPK) production, suggesting that GluR-GluK plays a differential role in antibiotic biosynthesis. Furthermore, we found that the response regulator GluR directly promotes the expression of under the culture condition of MM with a high concentration of glutamate (75 mM). Using the biolayer interferometry assay, we demonstrated that glutamate acts as the direct signal of the histidine kinase GluK. It was therefore suggested that upon sensing high concentrations of glutamate, GluR-GluK would be activated and thereby facilitate glutamate uptake by increasing expression. Finally, we demonstrated that the role of GluR-GluK in antibiotic biosynthesis is independent of its function in glutamate uptake. Considering the wide distribution of the glutamate-sensing (GluR-GluK) and uptake (GluABCD) module in actinobacteria, it could be concluded that the GluR-GluK signal transduction pathway involved in secondary metabolism and glutamate uptake should be highly conserved in this bacterial phylum. In this study, a novel two-component system (TCS), GluR-GluK, was identified to be involved in glutamate sensing and uptake as well as antibiotic biosynthesis in A possible GluR-GluK working model was proposed. Upon sensing high glutamate concentrations (such as 75 mM), activated GluR-GluK could regulate both glutamate uptake and antibiotic biosynthesis. However, under a culture condition of MM supplemented with low concentrations of glutamate (such as 10 mM), although GluR-GluK is activated, its activity is sufficient only for the regulation of antibiotic biosynthesis. To the best of our knowledge, this is the first report describing a TCS signal transduction pathway for glutamate sensing and uptake in actinobacteria.
[Mh] Termos MeSH primário: Ácido Glutâmico/metabolismo
Histidina Quinase/metabolismo
Transdução de Sinais
Streptomyces coelicolor/metabolismo
Fatores de Transcrição/metabolismo
[Mh] Termos MeSH secundário: Transporte Biológico
Meios de Cultura/química
Deleção de Genes
Regulação da Expressão Gênica
Histidina Quinase/genética
Proteínas de Membrana Transportadoras/genética
Proteínas de Membrana Transportadoras/metabolismo
Óperon
Streptomyces coelicolor/genética
Fatores de Transcrição/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Culture Media); 0 (Membrane Transport Proteins); 0 (Transcription Factors); 3KX376GY7L (Glutamic Acid); EC 2.7.13.1 (Histidine Kinase)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:180306
[Lr] Data última revisão:
180306
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170503
[St] Status:MEDLINE



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