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  1 / 2544 MEDLINE  
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[PMID]:29212533
[Au] Autor:Gutiérrez G; Millán-Zambrano G; Medina DA; Jordán-Pla A; Pérez-Ortín JE; Peñate X; Chávez S
[Ad] Endereço:Departamento de Genética, Universidad de Sevilla, Seville, Spain.
[Ti] Título:Subtracting the sequence bias from partially digested MNase-seq data reveals a general contribution of TFIIS to nucleosome positioning.
[So] Source:Epigenetics Chromatin;10(1):58, 2017 12 07.
[Is] ISSN:1756-8935
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: TFIIS stimulates RNA cleavage by RNA polymerase II and promotes the resolution of backtracking events. TFIIS acts in the chromatin context, but its contribution to the chromatin landscape has not yet been investigated. Co-transcriptional chromatin alterations include subtle changes in nucleosome positioning, like those expected to be elicited by TFIIS, which are elusive to detect. The most popular method to map nucleosomes involves intensive chromatin digestion by micrococcal nuclease (MNase). Maps based on these exhaustively digested samples miss any MNase-sensitive nucleosomes caused by transcription. In contrast, partial digestion approaches preserve such nucleosomes, but introduce noise due to MNase sequence preferences. A systematic way of correcting this bias for massively parallel sequencing experiments is still missing. RESULTS: To investigate the contribution of TFIIS to the chromatin landscape, we developed a refined nucleosome-mapping method in Saccharomyces cerevisiae. Based on partial MNase digestion and a sequence-bias correction derived from naked DNA cleavage, the refined method efficiently mapped nucleosomes in promoter regions rich in MNase-sensitive structures. The naked DNA correction was also important for mapping gene body nucleosomes, particularly in those genes whose core promoters contain a canonical TATA element. With this improved method, we analyzed the global nucleosomal changes caused by lack of TFIIS. We detected a general increase in nucleosomal fuzziness and more restricted changes in nucleosome occupancy, which concentrated in some gene categories. The TATA-containing genes were preferentially associated with decreased occupancy in gene bodies, whereas the TATA-like genes did so with increased fuzziness. The detected chromatin alterations correlated with functional defects in nascent transcription, as revealed by genomic run-on experiments. CONCLUSIONS: The combination of partial MNase digestion and naked DNA correction of the sequence bias is a precise nucleosomal mapping method that does not exclude MNase-sensitive nucleosomes. This method is useful for detecting subtle alterations in nucleosome positioning produced by lack of TFIIS. Their analysis revealed that TFIIS generally contributed to nucleosome positioning in both gene promoters and bodies. The independent effect of lack of TFIIS on nucleosome occupancy and fuzziness supports the existence of alternative chromatin dynamics during transcription elongation.
[Mh] Termos MeSH primário: Nuclease do Micrococo/metabolismo
Nucleossomos/metabolismo
Fatores de Elongação da Transcrição/metabolismo
[Mh] Termos MeSH secundário: Sequenciamento de Nucleotídeos em Larga Escala
Reação em Cadeia da Polimerase em Tempo Real
Saccharomyces cerevisiae/metabolismo
Técnica de Subtração
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Nucleosomes); 0 (Transcriptional Elongation Factors); 0 (transcription factor S-II); EC 3.1.31.1 (Micrococcal Nuclease)
[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:171208
[St] Status:MEDLINE
[do] DOI:10.1186/s13072-017-0165-x


  2 / 2544 MEDLINE  
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[PMID]:29266956
[Au] Autor:Kougentakis CM; Grasso EM; Robinson AC; Caro JA; Schlessman JL; Majumdar A; García-Moreno E B
[Ti] Título:Anomalous Properties of Lys Residues Buried in the Hydrophobic Interior of a Protein Revealed with N-Detect NMR Spectroscopy.
[So] Source:J Phys Chem Lett;9(2):383-387, 2018 Jan 18.
[Is] ISSN:1948-7185
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Ionizable residues buried in hydrophobic environments in proteins are essential for many fundamental biochemical processes. These residues titrate with anomalous pK values that are challenging to reproduce with structure-based calculations owing to the conformational reorganization coupled to their ionization. Detailed characterization of this conformational reorganization is of interest; unfortunately, the properties of buried Lys residues are difficult to study experimentally. Here we demonstrate the utility of N NMR spectroscopy to gain insight into the protonation state, state of hydration and conformational dynamics of the Nζ amino group of buried Lys residues. The experiments were applied to five variants of staphylococcal nuclease, with internal Lys residues that titrate with pK values ranging from 6.2 to 8.1. Direct detection of buried Lys residues with these NMR spectroscopy methods will enable correlation between thermodynamic and structural data as well as unprecedented examination of how conformational transitions coupled to their ionization affect their pK values.
[Mh] Termos MeSH primário: Desoxirribonucleases/química
Espectroscopia de Ressonância Magnética
Nuclease do Micrococo/química
[Mh] Termos MeSH secundário: Interações Hidrofóbicas e Hidrofílicas
Conformação Proteica
Termodinâmica
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
EC 3.1.- (Deoxyribonucleases); EC 3.1.31.1 (Micrococcal Nuclease)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180205
[Lr] Data última revisão:
180205
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171222
[St] Status:MEDLINE
[do] DOI:10.1021/acs.jpclett.7b02668


  3 / 2544 MEDLINE  
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[PMID]:29073207
[Au] Autor:Fuse T; Katsumata K; Morohoshi K; Mukai Y; Ichikawa Y; Kurumizaka H; Yanagida A; Urano T; Kato H; Shimizu M
[Ad] Endereço:Department of Chemistry, Graduate School of Science and Engineering, Program in Chemistry and Life Science, School of Science and Engineering, Meisei University, Hino, Tokyo, Japan.
[Ti] Título:Parallel mapping with site-directed hydroxyl radicals and micrococcal nuclease reveals structural features of positioned nucleosomes in vivo.
[So] Source:PLoS One;12(10):e0186974, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Micrococcal nuclease (MNase) has been widely used for analyses of nucleosome locations in many organisms. However, due to its sequence preference, the interpretations of the positions and occupancies of nucleosomes using MNase have remained controversial. Next-generation sequencing (NGS) has also been utilized for analyses of MNase-digests, but some technical biases are commonly present in the NGS experiments. Here, we established a gel-based method to map nucleosome positions in Saccharomyces cerevisiae, using isolated nuclei as the substrate for the histone H4 S47C-site-directed chemical cleavage in parallel with MNase digestion. The parallel mapping allowed us to compare the chemically and enzymatically cleaved sites by indirect end-labeling and primer extension mapping, and thus we could determine the nucleosome positions and the sizes of the nucleosome-free regions (or nucleosome-depleted regions) more accurately, as compared to nucleosome mapping by MNase alone. The analysis also revealed that the structural features of the nucleosomes flanked by the nucleosome-free region were different from those within regularly arrayed nucleosomes, showing that the structures and dynamics of individual nucleosomes strongly depend on their locations. Moreover, we demonstrated that the parallel mapping results were generally consistent with the previous genome-wide chemical mapping and MNase-Seq results. Thus, the gel-based parallel mapping will be useful for the analysis of a specific locus under various conditions.
[Mh] Termos MeSH primário: Mapeamento Cromossômico/métodos
Radical Hidroxila/metabolismo
Nuclease do Micrococo/metabolismo
Nucleossomos/genética
Nucleossomos/metabolismo
[Mh] Termos MeSH secundário: Aldose-Cetose Isomerases/genética
DNA Fúngico/genética
Loci Gênicos/genética
Saccharomyces cerevisiae/citologia
Saccharomyces cerevisiae/genética
Proteínas de Saccharomyces cerevisiae/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Fungal); 0 (Nucleosomes); 0 (Saccharomyces cerevisiae Proteins); 3352-57-6 (Hydroxyl Radical); EC 3.1.31.1 (Micrococcal Nuclease); EC 5.3.1.- (Aldose-Ketose Isomerases); EC 5.3.1.24 (TRP1 protein, S cerevisiae)
[Em] Mês de entrada:1711
[Cu] Atualização por classe:171110
[Lr] Data última revisão:
171110
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171027
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0186974


  4 / 2544 MEDLINE  
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[PMID]:28952715
[Au] Autor:Peck MT; Ortega G; De Luca-Johnson JN; Schlessman JL; Robinson AC; García-Moreno E B
[Ad] Endereço:Department of Biophysics, Johns Hopkins University , Baltimore, Maryland 21218, United States.
[Ti] Título:Local Backbone Flexibility as a Determinant of the Apparent pK Values of Buried Ionizable Groups in Proteins.
[So] Source:Biochemistry;56(40):5338-5346, 2017 Oct 10.
[Is] ISSN:1520-4995
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Ionizable groups buried in the hydrophobic interior of proteins are essential for energy transduction. These groups can have highly anomalous pK values that reflect the incompatibility between charges and dehydrated environments. A systematic study of pK values of buried ionizable groups in staphylococcal nuclease (SNase) suggests that these pK values are determined in part by conformational reorganization of the protein. Lys-66 is one of the most deeply buried residues in SNase. We show that its apparent pK of 5.7 reflects the average of the pK values of Lys-66 in different conformational states of the protein. In the fully folded state, Lys-66 is deeply buried in the hydrophobic core of SNase and must titrate with a pK of ≪5.7. In other states, the side chain of Lys-66 is fully solvent-exposed and has a normal pK of ≈10.4. We show that the pK of Lys-66 can be shifted from 5.7 toward a more normal value of 7.1 via the insertion of flanking Gly residues at positions 64 and 67 to promote an "open" conformation of SNase. Crystal structures and nuclear magnetic resonance spectroscopy show that in these Gly-containing variants Lys-66 can access bulk water as a consequence of overwinding of the C-terminal end of helix 1. These data illustrate that the apparent pK values of buried groups in proteins are governed in part by the difference in free energy between different conformational states of the protein and by differences in the pK values of the buried groups in the different conformations.
[Mh] Termos MeSH primário: Nuclease do Micrococo/química
[Mh] Termos MeSH secundário: Cristalografia por Raios X
Concentração de Íons de Hidrogênio
Interações Hidrofóbicas e Hidrofílicas
Nuclease do Micrococo/metabolismo
Modelos Moleculares
Conformação Proteica
Termodinâmica
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
EC 3.1.31.1 (Micrococcal Nuclease)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171019
[Lr] Data última revisão:
171019
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170928
[St] Status:MEDLINE
[do] DOI:10.1021/acs.biochem.7b00678


  5 / 2544 MEDLINE  
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[PMID]:28902852
[Au] Autor:Pass DA; Sornay E; Marchbank A; Crawford MR; Paszkiewicz K; Kent NA; Murray JAH
[Ad] Endereço:Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom.
[Ti] Título:Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis.
[So] Source:PLoS Genet;13(9):e1006988, 2017 Sep.
[Is] ISSN:1553-7404
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:All eukaryotic genomes are packaged as chromatin, with DNA interlaced with both regularly patterned nucleosomes and sub-nucleosomal-sized protein structures such as mobile and labile transcription factors (TF) and initiation complexes, together forming a dynamic chromatin landscape. Whilst details of nucleosome position in Arabidopsis have been previously analysed, there is less understanding of their relationship to more dynamic sub-nucleosomal particles (subNSPs) defined as protected regions shorter than the ~150bp typical of nucleosomes. The genome-wide profile of these subNSPs has not been previously analysed in plants and this study investigates the relationship of dynamic bound particles with transcriptional control. Here we combine differential micrococcal nuclease (MNase) digestion and a modified paired-end sequencing protocol to reveal the chromatin structure landscape of Arabidopsis cells across a wide particle size range. Linking this data to RNAseq expression analysis provides detailed insight into the relationship of identified DNA-bound particles with transcriptional activity. The use of differential digestion reveals sensitive positions, including a labile -1 nucleosome positioned upstream of the transcription start site (TSS) of active genes. We investigated the response of the chromatin landscape to changes in environmental conditions using light and dark growth, given the large transcriptional changes resulting from this simple alteration. The resulting shifts in the suites of expressed and repressed genes show little correspondence to changes in nucleosome positioning, but led to significant alterations in the profile of subNSPs upstream of TSS both globally and locally. We examined previously mapped positions for the TFs PIF3, PIF4 and CCA1, which regulate light responses, and found that changes in subNSPs co-localized with these binding sites. This small particle structure is detected only under low levels of MNase digestion and is lost on more complete digestion of chromatin to nucleosomes. We conclude that wide-spectrum analysis of the Arabidopsis genome by differential MNase digestion allows detection of sensitive features hereto obscured, and the comparisons between genome-wide subNSP profiles reveals dynamic changes in their distribution, particularly at distinct genomic locations (i.e. 5'UTRs). The method here employed allows insight into the complex influence of genetic and extrinsic factors in modifying the sub-nucleosomal landscape in association with transcriptional changes.
[Mh] Termos MeSH primário: Arabidopsis/genética
Cromatina/genética
Genoma de Planta
Nucleossomos/genética
[Mh] Termos MeSH secundário: Montagem e Desmontagem da Cromatina
Mapeamento Cromossômico
Nuclease do Micrococo/genética
Nucleossomos/metabolismo
Regiões Promotoras Genéticas
Fatores de Transcrição/genética
Sítio de Iniciação de Transcrição
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Chromatin); 0 (Nucleosomes); 0 (Transcription Factors); EC 3.1.31.1 (Micrococcal Nuclease)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171009
[Lr] Data última revisão:
171009
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170914
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pgen.1006988


  6 / 2544 MEDLINE  
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[PMID]:28787030
[Au] Autor:Hu S; Chen X; Liao J; Chen Y; Zhao C; Zhang Y
[Ad] Endereço:Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Science and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai, China.
[Ti] Título:CAM: A quality control pipeline for MNase-seq data.
[So] Source:PLoS One;12(8):e0182771, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Nucleosome organization affects the accessibility of cis-elements to trans-acting factors. Micrococcal nuclease digestion followed by high-throughput sequencing (MNase-seq) is the most popular technology used to profile nucleosome organization on a genome-wide scale. Evaluating the data quality of MNase-seq data remains challenging, especially in mammalian. There is a strong need for a convenient and comprehensive approach to obtain dedicated quality control (QC) for MNase-seq data analysis. Here we developed CAM, which is a comprehensive QC pipeline for MNase-seq data. The CAM pipeline provides multiple informative QC measurements and nucleosome organization profiles on different potentially functional regions for given MNase-seq data. CAM also includes 268 historical MNase-seq datasets from human and mouse as a reference atlas for unbiased assessment. CAM is freely available at: http://www.tongji.edu.cn/~zhanglab/CAM.
[Mh] Termos MeSH primário: Sequenciamento de Nucleotídeos em Larga Escala/métodos
Nuclease do Micrococo/metabolismo
Análise de Sequência de DNA/métodos
[Mh] Termos MeSH secundário: Animais
Sequenciamento de Nucleotídeos em Larga Escala/normas
Seres Humanos
Camundongos
Nucleossomos/genética
Controle de Qualidade
Análise de Sequência de DNA/normas
Fatores de Tempo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Nucleosomes); EC 3.1.31.1 (Micrococcal Nuclease)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170929
[Lr] Data última revisão:
170929
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170809
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0182771


  7 / 2544 MEDLINE  
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[PMID]:28520421
[Au] Autor:Ford MC; Babaoglu K
[Ad] Endereço:Department of Modeling & Informatics, MRL, Merck & Co., Inc. , 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States.
[Ti] Título:Examining the Feasibility of Using Free Energy Perturbation (FEP+) in Predicting Protein Stability.
[So] Source:J Chem Inf Model;57(6):1276-1285, 2017 Jun 26.
[Is] ISSN:1549-960X
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The importance of engineering protein stability is well-known and has the potential to impact many fields ranging from pharmaceuticals to food sciences. Engineering proteins can be both a time-consuming and expensive experimental process. The use of computation is a potential solution to mitigating some of the time and expenses required to engineer a protein. This process has been previously hindered by inaccurate force fields or energy equations and slow computational processors; however, improved software and hardware have made this goal much more attainable. Here we find that Schrödinger's new FEP+, although still imperfect, proves more successful in predicting protein stability than other simpler methods of investigation. This increased accuracy comes at a cost of computational time and resources when compared to simpler methods. This work adds to the initial testing of FEP+ by offering options for more accurately predicting protein stability in an efficient manner.
[Mh] Termos MeSH primário: Biologia Computacional/métodos
Estabilidade Proteica
[Mh] Termos MeSH secundário: Estudos de Viabilidade
Nuclease do Micrococo/química
Nuclease do Micrococo/genética
Nuclease do Micrococo/metabolismo
Modelos Moleculares
Mutação
Conformação Proteica
Termodinâmica
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
EC 3.1.31.1 (Micrococcal Nuclease)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170921
[Lr] Data última revisão:
170921
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170519
[St] Status:MEDLINE
[do] DOI:10.1021/acs.jcim.7b00002


  8 / 2544 MEDLINE  
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[PMID]:28486547
[Au] Autor:Jha PK; Khan MI; Mishra A; Das P; Sinha KK
[Ad] Endereço:Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Hajipur, Bihar, India.
[Ti] Título:HAT2 mediates histone H4K4 acetylation and affects micrococcal nuclease sensitivity of chromatin in Leishmania donovani.
[So] Source:PLoS One;12(5):e0177372, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Histone post-translational modifications (PTMs) such as acetylation and methylation are known to affect chromatin higher order structures. Primary targets of these modifications include basic residues present at N-terminus tail region of core histones. Four histone acetyltransferase (HAT) genes have been identified in trypanosomatids. HAT1, HAT3 and HAT4 of Leishmania donovani have been partially characterized. However, there is no report about HAT2 of Leishmania donovani. Lysine residues present on the N-terminal tail of Leishmania donovani histone H4 are conserved in other trypanosomatids and humans. PTMs of lysines modulate various functions at chromatin level. The four histone acetyltransferases encoded in Leishmania genome were over-expressed to analyse their functional activity. All four HATs were found actively acetylating core histones H3/H4. Similar to L. donovani HAT3 and HAT4, HAT2 was found to be a member of MYST family protein and have SAS2 type domain. Over-expression of HAT2 significantly increases acetylation of H4K4. To analyse the effect of HAT2 over-expression on chromatin accessibility, micrococcal nuclease digestion assay was performed. MNase digestion resulted in a higher proportion of the mononucleosomes and dinucleosomes in HAT2 over-expressing cells as compared to WT L. donovani cells. Acetylation of lysine-4 neutralizes the amino terminal region of histone H4. This weakens its interaction with neighbouring nucleosomes and the linker DNA. HAT2 over-expression in L. donovani resulted in highly accessible chromatin suggesting chromatin decondensation. HAT2 may have an important role to play in global regulation of transcription in L. donovani. Better understanding of these epigenetic determinants of parasite would help in designing novel therapeutic strategies.
[Mh] Termos MeSH primário: Cromatina/metabolismo
Histonas/metabolismo
Leishmania donovani/metabolismo
Nuclease do Micrococo/metabolismo
Proteínas de Protozoários/metabolismo
[Mh] Termos MeSH secundário: Acetilação
Sequência de Aminoácidos
Animais
Histonas/química
Homologia de Sequência de Aminoácidos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Chromatin); 0 (Histones); 0 (Protozoan Proteins); EC 3.1.31.1 (Micrococcal Nuclease)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170926
[Lr] Data última revisão:
170926
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170510
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0177372


  9 / 2544 MEDLINE  
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[PMID]:28356342
[Au] Autor:Mueller B; Mieczkowski J; Kundu S; Wang P; Sadreyev R; Tolstorukov MY; Kingston RE
[Ad] Endereço:Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.
[Ti] Título:Widespread changes in nucleosome accessibility without changes in nucleosome occupancy during a rapid transcriptional induction.
[So] Source:Genes Dev;31(5):451-462, 2017 Mar 01.
[Is] ISSN:1549-5477
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Activation of transcription requires alteration of chromatin by complexes that increase the accessibility of nucleosomal DNA. Removing nucleosomes from regulatory sequences has been proposed to play a significant role in activation. We tested whether changes in nucleosome occupancy occurred on the set of genes that is activated by the unfolded protein response (UPR). We observed no decrease in occupancy on most promoters, gene bodies, and enhancers. Instead, there was an increase in the accessibility of nucleosomes, as measured by micrococcal nuclease (MNase) digestion and ATAC-seq (assay for transposase-accessible chromatin [ATAC] using sequencing), that did not result from removal of the nucleosome. Thus, changes in nucleosome accessibility predominate over changes in nucleosome occupancy during rapid transcriptional induction during the UPR.
[Mh] Termos MeSH primário: Regulação da Expressão Gênica
Nucleossomos/metabolismo
Resposta a Proteínas não Dobradas/fisiologia
[Mh] Termos MeSH secundário: Animais
Linhagem Celular
Cromatina/química
Cromatina/metabolismo
Mapeamento Cromossômico
Drosophila melanogaster/genética
Drosophila melanogaster/metabolismo
Elementos Facilitadores Genéticos/genética
Nuclease do Micrococo/metabolismo
Nucleossomos/química
Regiões Promotoras Genéticas/genética
Ligação Proteica
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Chromatin); 0 (Nucleosomes); EC 3.1.31.1 (Micrococcal Nuclease)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170912
[Lr] Data última revisão:
170912
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170331
[St] Status:MEDLINE
[do] DOI:10.1101/gad.293118.116


  10 / 2544 MEDLINE  
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[PMID]:28286326
[Au] Autor:Wedel C; Siegel TN
[Ad] Endereço:Research Center for Infectious Diseases (ZINF), University of Würzburg, Josef-Schneider-Straße 2 / Bau D15, 97080 Würzburg, Germany.
[Ti] Título:Genome-wide analysis of chromatin structures in Trypanosoma brucei using high-resolution MNase-ChIP-seq.
[So] Source:Exp Parasitol;180:2-12, 2017 Sep.
[Is] ISSN:1090-2449
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Specific DNA-protein interactions are the basis for many important cellular mechanisms like the regulation of gene expression or replication. Knowledge about the precise genomic locations of DNA-protein interactions is important because it provides insight into the regulation of these processes. Recently, we have adapted an approach that combines micrococcal nuclease (MNase) digestion of chromatin with chromatin immunoprecipitation in Trypanosoma brucei. Here, we describe in detail how this method can be used to map the genome-wide distribution of nucleosomes or other DNA-binding proteins at high resolution in T. brucei.
[Mh] Termos MeSH primário: Imunoprecipitação da Cromatina/métodos
Cromatina/genética
Nuclease do Micrococo/metabolismo
Trypanosoma brucei brucei/genética
[Mh] Termos MeSH secundário: Anticorpos Monoclonais/imunologia
Anticorpos Antiprotozoários/imunologia
Especificidade de Anticorpos
Cromatina/ultraestrutura
Imunoprecipitação da Cromatina/normas
Mapeamento Cromossômico/métodos
Fragmentação do DNA
Primers do DNA/química
DNA de Protozoário/química
DNA de Protozoário/isolamento & purificação
Proteínas de Ligação a DNA/metabolismo
Epitopos/imunologia
Estudo de Associação Genômica Ampla
Microscopia de Fluorescência
Nucleossomos/genética
Nucleossomos/ultraestrutura
Permeabilidade
Reação em Cadeia da Polimerase
Proteínas de Protozoários/genética
Proteínas de Protozoários/imunologia
Sonicação
Trypanosoma brucei brucei/imunologia
Trypanosoma brucei brucei/ultraestrutura
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Antibodies, Monoclonal); 0 (Antibodies, Protozoan); 0 (Chromatin); 0 (DNA Primers); 0 (DNA, Protozoan); 0 (DNA-Binding Proteins); 0 (Epitopes); 0 (Nucleosomes); 0 (Protozoan Proteins); EC 3.1.31.1 (Micrococcal Nuclease)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170808
[Lr] Data última revisão:
170808
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170314
[St] Status:MEDLINE



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