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  1 / 38807 MEDLINE  
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[PMID]:29309426
[Au] Autor:McDonald JS; McDonald RJ; Ekins JB; Tin AS; Costes S; Hudson TM; Schroeder DJ; Kallmes K; Kaufmann SH; Young PM; Lu A; Kadirvel R; Kallmes DF
[Ad] Endereço:Department of Radiology, College of Medicine, Mayo Clinic, Rochester, MN, United States of America.
[Ti] Título:Gadolinium-enhanced cardiac MR exams of human subjects are associated with significant increases in the DNA repair marker 53BP1, but not the damage marker γH2AX.
[So] Source:PLoS One;13(1):e0190890, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Magnetic resonance imaging is considered low risk, yet recent studies have raised a concern of potential damage to DNA in peripheral blood leukocytes. This prospective Institutional Review Board-approved study examined potential double-strand DNA damage by analyzing changes in the DNA damage and repair markers γH2AX and 53BP1 in patients who underwent a 1.5 T gadolinium-enhanced cardiac magnetic resonance (MR) exam. Sixty patients were enrolled (median age 55 years, 39 males). Patients with history of malignancy or who were receiving chemotherapy, radiation therapy, or steroids were excluded. MR sequence data were recorded and blood samples obtained immediately before and after MR exposure. An automated immunofluorescence assay quantified γH2AX or 53BP1 foci number in isolated peripheral blood mononuclear cells. Changes in foci number were analyzed using the Wilcoxon signed-rank test. Clinical and MR procedural characteristics were compared between patients who had a >10% increase in γH2AX or 53BP1 foci numbers and patients who did not. The number of γH2AX foci did not significantly change following cardiac MR (median foci per cell pre-MR = 0.11, post-MR = 0.11, p = .90), but the number of 53BP1 foci significantly increased following MR (median foci per cell pre-MR = 0.46, post-MR = 0.54, p = .0140). Clinical and MR characteristics did not differ significantly between patients who had at least a 10% increase in foci per cell and those who did not. We conclude that MR exposure leads to a small (median 25%) increase in 53BP1 foci, however the clinical relevance of this increase is unknown and may be attributable to normal variation instead of MR exposure.
[Mh] Termos MeSH primário: Biomarcadores/metabolismo
Dano ao DNA
Reparo do DNA
Gadolínio/administração & dosagem
Coração/diagnóstico por imagem
Histonas/metabolismo
Imagem por Ressonância Magnética/métodos
Proteína 1 de Ligação à Proteína Supressora de Tumor p53/metabolismo
[Mh] Termos MeSH secundário: Adulto
Idoso
Feminino
Seres Humanos
Masculino
Meia-Idade
Estudos Prospectivos
Estudos Retrospectivos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Biomarkers); 0 (H2AFX protein, human); 0 (Histones); 0 (TP53BP1 protein, human); 0 (Tumor Suppressor p53-Binding Protein 1); AU0V1LM3JT (Gadolinium)
[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:180109
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0190890


  2 / 38807 MEDLINE  
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[PMID]:29191233
[Au] Autor:Posukh OV; Maksimov DA; Laktionov PP; Koryakov DE; Belyakin SN
[Ad] Endereço:Genomics Lab, Institute of Molecular and Cellular Biology SB RAS, Lavrentyev ave. 8/2, Novosibirsk, Russia, 630090.
[Ti] Título:Functional dissection of Drosophila melanogaster SUUR protein influence on H3K27me3 profile.
[So] Source:Epigenetics Chromatin;10(1):56, 2017 12 01.
[Is] ISSN:1756-8935
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: In eukaryotes, heterochromatin replicates late in S phase of the cell cycle and contains specific covalent modifications of histones. SuUR mutation found in Drosophila makes heterochromatin replicate earlier than in wild type and reduces the level of repressive histone modifications. SUUR protein was shown to be associated with moving replication forks, apparently through the interaction with PCNA. The biological process underlying the effects of SUUR on replication and composition of heterochromatin remains unknown. RESULTS: Here we performed a functional dissection of SUUR protein effects on H3K27me3 level. Using hidden Markow model-based algorithm we revealed SuUR-sensitive chromosomal regions that demonstrated unusual characteristics: They do not contain Polycomb and require SUUR function to sustain H3K27me3 level. We tested the role of SUUR protein in the mechanisms that could affect H3K27me3 histone levels in these regions. We found that SUUR does not affect the initial H3K27me3 pattern formation in embryogenesis or Polycomb distribution in the chromosomes. We also ruled out the possible effect of SUUR on histone genes expression and its involvement in DSB repair. CONCLUSIONS: Obtained results support the idea that SUUR protein contributes to the heterochromatin maintenance during the chromosome replication. A model that explains major SUUR-associated phenotypes is proposed.
[Mh] Termos MeSH primário: Proteínas de Drosophila/metabolismo
Drosophila melanogaster/metabolismo
Histonas/genética
[Mh] Termos MeSH secundário: Algoritmos
Animais
Proteínas de Drosophila/genética
Heterocromatina/metabolismo
Mutação
Proteínas do Grupo Polycomb/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Drosophila Proteins); 0 (Heterochromatin); 0 (Histones); 0 (Polycomb-Group Proteins)
[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:171202
[St] Status:MEDLINE
[do] DOI:10.1186/s13072-017-0163-z


  3 / 38807 MEDLINE  
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[PMID]:29179736
[Au] Autor:Erives AJ
[Ad] Endereço:Department of Biology, University of Iowa, Iowa City, IA, 52242-1324, USA. albert-erives@uiowa.edu.
[Ti] Título:Phylogenetic analysis of the core histone doublet and DNA topo II genes of Marseilleviridae: evidence of proto-eukaryotic provenance.
[So] Source:Epigenetics Chromatin;10(1):55, 2017 11 28.
[Is] ISSN:1756-8935
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: While the genomes of eukaryotes and Archaea both encode the histone-fold domain, only eukaryotes encode the core histone paralogs H2A, H2B, H3, and H4. With DNA, these core histones assemble into the nucleosomal octamer underlying eukaryotic chromatin. Importantly, core histones for H2A and H3 are maintained as neofunctionalized paralogs adapted for general bulk chromatin (canonical H2 and H3) or specialized chromatin (H2A.Z enriched at gene promoters and cenH3s enriched at centromeres). In this context, the identification of core histone-like "doublets" in the cytoplasmic replication factories of the Marseilleviridae (MV) is a novel finding with possible relevance to understanding the origin of eukaryotic chromatin. Here, we analyze and compare the core histone doublet genes from all known MV genomes as well as other MV genes relevant to the origin of the eukaryotic replisome. RESULTS: Using different phylogenetic approaches, we show that MV histone domains encode obligate H2B-H2A and H4-H3 dimers of possible proto-eukaryotic origin. MV core histone moieties form sister clades to each of the four eukaryotic clades of canonical and variant core histones. This suggests that MV core histone moieties diverged prior to eukaryotic neofunctionalizations associated with paired linear chromosomes and variant histone octamer assembly. We also show that MV genomes encode a proto-eukaryotic DNA topoisomerase II enzyme that forms a sister clade to eukaryotes. This is a relevant finding given that DNA topo II influences histone deposition and chromatin compaction and is the second most abundant nuclear protein after histones. CONCLUSIONS: The combined domain architecture and phylogenomic analyses presented here suggest that a primitive origin for MV histone genes is a more parsimonious explanation than horizontal gene transfers + gene fusions + sufficient divergence to eliminate relatedness to eukaryotic neofunctionalizations within the H2A and H3 clades without loss of relatedness to each of the four core histone clades. We thus suggest MV histone doublet genes and their DNA topo II gene possibly were acquired from an organism with a chromatinized replisome that diverged prior to the origin of eukaryotic core histone variants for H2/H2A.Z and H3/cenH3. These results also imply that core histones were utilized ancestrally in viral DNA compaction and/or protection from host endonucleases.
[Mh] Termos MeSH primário: DNA Topoisomerases Tipo II/genética
Vírus de DNA/genética
Histonas/genética
Filogenia
[Mh] Termos MeSH secundário: Vírus de DNA/classificação
Genes Virais
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Histones); EC 5.99.1.3 (DNA Topoisomerases, Type II)
[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:171129
[St] Status:MEDLINE
[do] DOI:10.1186/s13072-017-0162-0


  4 / 38807 MEDLINE  
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[PMID]:27777629
[Au] Autor:Lau AC; Zhu KP; Brouhard EA; Davis MB; Csankovszki G
[Ad] Endereço:Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N. University Ave., Ann Arbor, MI 48109-1048 USA ; Genome Technologies, The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA.
[Ti] Título:An H4K16 histone acetyltransferase mediates decondensation of the X chromosome in males.
[So] Source:Epigenetics Chromatin;9:44, 2016.
[Is] ISSN:1756-8935
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: In , in order to equalize gene expression between the sexes and balance X and autosomal expression, two steps are believed to be required. First, an unknown mechanism is hypothesized to upregulate the X chromosome in both sexes. This mechanism balances the X to autosomal expression in males, but creates X overexpression in hermaphrodites. Therefore, to restore the balance, hermaphrodites downregulate gene expression twofold on both X chromosomes. While many studies have focused on X chromosome downregulation, the mechanism of X upregulation is not known. RESULTS: To gain more insight into X upregulation, we studied the effects of chromatin condensation and histone acetylation on gene expression levels in male . We have found that the H4K16 histone acetyltransferase MYS-1/Tip60 mediates dramatic decondensation of the male X chromosome as measured by FISH. However, RNA-seq analysis revealed that MYS-1 contributes only slightly to upregulation of gene expression on the X chromosome. These results suggest that the level of chromosome decondensation does not necessarily correlate with the degree of gene expression change in vivo. Furthermore, the X chromosome is more sensitive to MYS-1-mediated decondensation than the autosomes, despite similar levels of H4K16ac on all chromosomes, as measured by ChIP-seq. H4K16ac levels weakly correlate with gene expression levels on both the X and the autosomes, but highly expressed genes on the X chromosome do not contain exceptionally high levels of H4K16ac. CONCLUSION: These results indicate that H4K16ac and chromosome decondensation influence regulation of the male X chromosome; however, they do not fully account for the high levels of gene expression observed on the X chromosomes.
[Mh] Termos MeSH primário: Proteínas de Caenorhabditis elegans/metabolismo
Caenorhabditis elegans/metabolismo
Histona Acetiltransferases/metabolismo
Cromossomo X/metabolismo
[Mh] Termos MeSH secundário: Acetilação
Animais
Caenorhabditis elegans/genética
Proteínas de Caenorhabditis elegans/genética
Cromatina/metabolismo
Montagem e Desmontagem da Cromatina
Imunoprecipitação da Cromatina
Compensação de Dosagem (Genética)
Expressão Gênica
Histona Acetiltransferases/genética
Histonas/metabolismo
Hibridização in Situ Fluorescente
Masculino
Análise de Sequência de DNA
Cromossomo X/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL
[Nm] Nome de substância:
0 (Caenorhabditis elegans Proteins); 0 (Chromatin); 0 (Histones); EC 2.3.1.48 (Histone Acetyltransferases); EC 2.3.1.48 (MYS-1 protein, C elegans)
[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


  5 / 38807 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


  6 / 38807 MEDLINE  
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[PMID]:28463415
[Au] Autor:McCullough SD; On DM; Bowers EC
[Ad] Endereço:National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina.
[Ti] Título:Using Chromatin Immunoprecipitation in Toxicology: A Step-by-Step Guide to Increasing Efficiency, Reducing Variability, and Expanding Applications.
[So] Source:Curr Protoc Toxicol;72:3.14.1-3.14.28, 2017 May 02.
[Is] ISSN:1934-9262
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Histone modifications work in concert with DNA methylation to regulate cellular structure, function, and response to environmental stimuli. More than 130 unique histone modifications have been described to date, and chromatin immunoprecipitation (ChIP) allows for the exploration of their associations with the regulatory regions of target genes and other DNA/chromatin-associated proteins across the genome. Many variations of ChIP have been developed in the 30 years since its earliest version came into use, which makes it challenging for users to integrate the procedure into their research programs. Furthermore, the differences in ChIP protocols can confound efforts to increase reproducibility across studies. The streamlined ChIP procedure presented here can be readily applied to samples from a wide range of in vitro studies (cell lines and primary cells) and clinical samples (peripheral leukocytes) in toxicology. We also provide detailed guidance on the optimization of critical protocol parameters, such as chromatin fixation, fragmentation, and immunoprecipitation, to increase efficiency and improve reproducibility. Expanding toxicoepigenetic studies to more readily include histone modifications will facilitate a more comprehensive understanding of the role of the epigenome in environmental exposure effects and the integration of epigenetic data in mechanistic toxicology, adverse outcome pathways, and risk assessment. © 2017 by John Wiley & Sons, Inc.
[Mh] Termos MeSH primário: Imunoprecipitação da Cromatina/métodos
Toxicologia/métodos
[Mh] Termos MeSH secundário: Linhagem Celular
DNA/isolamento & purificação
Epigênese Genética
Redes Reguladoras de Genes
Marcação de Genes
Histonas/metabolismo
Seres Humanos
Leucócitos/química
Peptídeo Hidrolases/química
Reação em Cadeia da Polimerase
Cultura Primária de Células
Reprodutibilidade dos Testes
Sonicação
Toxicologia/normas
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Histones); 9007-49-2 (DNA); EC 3.4.- (Peptide Hydrolases)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170503
[St] Status:MEDLINE
[do] DOI:10.1002/cptx.22


  7 / 38807 MEDLINE  
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[PMID]:29434199
[Au] Autor:Hayashi T; Ozaki H; Sasagawa Y; Umeda M; Danno H; Nikaido I
[Ad] Endereço:Bioinformatics Research Unit, Advanced Center for Computing and Communication, RIKEN, 2-1 Hirosawa Wako, Saitama, 351-0198, Japan.
[Ti] Título:Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs.
[So] Source:Nat Commun;9(1):619, 2018 02 12.
[Is] ISSN:2041-1723
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Total RNA sequencing has been used to reveal poly(A) and non-poly(A) RNA expression, RNA processing and enhancer activity. To date, no method for full-length total RNA sequencing of single cells has been developed despite the potential of this technology for single-cell biology. Here we describe random displacement amplification sequencing (RamDA-seq), the first full-length total RNA-sequencing method for single cells. Compared with other methods, RamDA-seq shows high sensitivity to non-poly(A) RNA and near-complete full-length transcript coverage. Using RamDA-seq with differentiation time course samples of mouse embryonic stem cells, we reveal hundreds of dynamically regulated non-poly(A) transcripts, including histone transcripts and long noncoding RNA Neat1. Moreover, RamDA-seq profiles recursive splicing in >300-kb introns. RamDA-seq also detects enhancer RNAs and their cell type-specific activity in single cells. Taken together, we demonstrate that RamDA-seq could help investigate the dynamics of gene expression, RNA-processing events and transcriptional regulation in single cells.
[Mh] Termos MeSH primário: Sequenciamento de Nucleotídeos em Larga Escala/métodos
Células-Tronco Embrionárias Murinas/metabolismo
Processamento de RNA
RNA Longo não Codificante/genética
RNA Mensageiro/genética
Análise de Célula Única/métodos
[Mh] Termos MeSH secundário: Animais
Sequência de Bases
Diferenciação Celular
Elementos Facilitadores Genéticos
Éxons
Histonas/genética
Histonas/metabolismo
Íntrons
Camundongos
Células-Tronco Embrionárias Murinas/citologia
RNA Longo não Codificante/metabolismo
RNA Mensageiro/metabolismo
Análise de Sequência de RNA
Transcrição Genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Histones); 0 (NEAT1 long non-coding RNA, mouse); 0 (RNA, Long Noncoding); 0 (RNA, Messenger)
[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:180214
[St] Status:MEDLINE
[do] DOI:10.1038/s41467-018-02866-0


  8 / 38807 MEDLINE  
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[PMID]:28460084
[Au] Autor:van der Meulen PM; Barendregt AM; Cuadrado E; Magro-Checa C; Steup-Beekman GM; Schonenberg-Meinema D; Van den Berg JM; Li QZ; Baars PA; Wouters D; Voskuyl AE; Ten Berge IRJM; Huizinga TWJ; Kuijpers TW
[Ad] Endereço:Department of Pediatric Hematology, Immunology and Infectious Diseases, Emma Children's Hospital Academic Medical Center.
[Ti] Título:Protein array autoantibody profiles to determine diagnostic markers for neuropsychiatric systemic lupus erythematosus.
[So] Source:Rheumatology (Oxford);56(8):1407-1416, 2017 Aug 01.
[Is] ISSN:1462-0332
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Objective: The aim was to investigate the association between autoantibodies (autoAbs) and neuropsychiatric (NP) involvement in patients with SLE and to evaluate whether any autoAb or a combination of these autoAbs could indicate the underlying pathogenic process. Methods: Using a multiplexed protein array for 94 antigens, we compared the serum autoAb profiles of 69 NPSLE patients, 203 SLE patients without NP involvement (non-NPSLE) and 51 healthy controls. Furthermore, we compared the profiles of NPSLE patients with clinical inflammatory (n = 38) and ischaemic (n = 31) NP involvement. Results: In total, 75 IgG and 47 IgM autoAbs were associated with SLE patients in comparison with healthy controls. Comparing NPSLE with non-NPSLE and healthy control sera, 9 IgG (amyloid, cardiolipin, glycoprotein 2, glycoprotein 210, heparin, heparan sulphate, histone H2A, prothrombin protein and vimentin) and 12 IgM (amyloid, cardiolipin, centromere protein A, collagen II, histones H2A and H2B, heparan sulphate, heparin, mitochondrial 2, nuclear Mi-2, nucleoporin 62 and vimentin) autoAbs were present at significantly different levels in NPSLE. The combination of IgG autoAbs against heparan sulphate, histone H2B and vimentin could differentiate NPSLE from non-NPSLE (area under the curve 0.845, 99.97% CI: 0.756, 0.933; P < 0.0001). Compared with non-NPSLE, four IgG and seven IgM autoAbs were significantly associated with inflammatory NPSLE. In ischaemic NPSLE, three IgG and three IgM autoAbs were significantly different from non-NPSLE patients. Conclusion: In our cohort, the presence of high levels of anti-heparan sulphate and anti-histone H2B combined with low levels of anti-vimentin IgG autoAbs is highly suggestive of NPSLE. These results need to be validated in external cohorts.
[Mh] Termos MeSH primário: Autoanticorpos/sangue
Vasculite Associada ao Lúpus do Sistema Nervoso Central/diagnóstico
[Mh] Termos MeSH secundário: Adulto
Autoanticorpos/imunologia
Biomarcadores/sangue
Estudos de Casos e Controles
Feminino
Heparitina Sulfato/imunologia
Histonas/imunologia
Seres Humanos
Imunoglobulina G/imunologia
Vasculite Associada ao Lúpus do Sistema Nervoso Central/imunologia
Masculino
Meia-Idade
Análise Serial de Proteínas
Vimentina/imunologia
[Pt] Tipo de publicação:EVALUATION STUDIES; JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Autoantibodies); 0 (Biomarkers); 0 (Histones); 0 (Immunoglobulin G); 0 (Vimentin); 9050-30-0 (Heparitin Sulfate)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:AIM; IM
[Da] Data de entrada para processamento:170502
[St] Status:MEDLINE
[do] DOI:10.1093/rheumatology/kex073


  9 / 38807 MEDLINE  
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[PMID]:29254924
[Au] Autor:Cui TT; Xing TY; Chu YK; Li H; Wang N
[Ad] Endereço:1. Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin 150030, China; 2. Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China; 3. Key Laboratory of Animal Cells and Genetic Engineering of Heilon
[Ti] Título:Genetic and epigenetic regulation of PPARγ during adipogenesis.
[So] Source:Yi Chuan;39(11):1066-1077, 2017 Nov 20.
[Is] ISSN:0253-9772
[Cp] País de publicação:China
[La] Idioma:eng
[Ab] Resumo:Peroxisome proliferator-activated receptor gamma (PPARγ) is the master regulator of adipogenesis and adipose tissue development. It also plays crucial roles in many other biological processes, including lipid and glucose metabolism and energy homeostasis. Recently, evidence has been accumulating that the PPARγ gene is not only genetically regulated, but also epigenetically regulated by DNA methylation, histone modification, non-coding RNA and chromosome remodeling. In this review, we summarize the advances in the genetic and epigenetic regulation of the PPARγ gene during adipogenesis, and discuss future research directions and trends for the study of its regulation.
[Mh] Termos MeSH primário: Adipogenia
Metilação de DNA
PPAR gama/genética
[Mh] Termos MeSH secundário: Animais
Montagem e Desmontagem da Cromatina
Histonas/metabolismo
Seres Humanos
Polimorfismo de Nucleotídeo Único
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Nm] Nome de substância:
0 (Histones); 0 (PPAR gamma)
[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:171220
[St] Status:MEDLINE
[do] DOI:10.16288/j.yczz.17-121


  10 / 38807 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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