Base de dados : MEDLINE
Pesquisa : A11.284.187 [Categoria DeCS]
Referências encontradas : 29799 [refinar]
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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


  2 / 29799 MEDLINE  
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[PMID]:28454565
[Au] Autor:Kominakis A; Hager-Theodorides AL; Zoidis E; Saridaki A; Antonakos G; Tsiamis G
[Ad] Endereço:Department of Animal Science and Aquaculture, Agricultural University of Athens, Iera Odos 75, 11855, Athens, Greece.
[Ti] Título:Combined GWAS and 'guilt by association'-based prioritization analysis identifies functional candidate genes for body size in sheep.
[So] Source:Genet Sel Evol;49(1):41, 2017 04 28.
[Is] ISSN:1297-9686
[Cp] País de publicação:France
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Body size in sheep is an important indicator of productivity, growth and health as well as of environmental adaptation. It is a composite quantitative trait that has been studied with high-throughput genomic methods, i.e. genome-wide association studies (GWAS) in various mammalian species. Several genomic markers have been associated with body size traits and genes have been identified as causative candidates in humans, dog and cattle. A limited number of related GWAS have been performed in various sheep breeds and have identified genomic regions and candidate genes that partly account for body size variability. Here, we conducted a GWAS in Frizarta dairy sheep with phenotypic data from 10 body size measurements and genotypic data (from Illumina ovineSNP50 BeadChip) for 459 ewes. RESULTS: The 10 body size measurements were subjected to principal component analysis and three independent principal components (PC) were constructed, interpretable as width, height and length dimensions, respectively. The GWAS performed for each PC identified 11 significant SNPs, at the chromosome level, one on each of the chromosomes 3, 8, 9, 10, 11, 12, 19, 20, 23 and two on chromosome 25. Nine out of the 11 SNPs were located on previously identified quantitative trait loci for sheep meat, production or reproduction. One hundred and ninety-seven positional candidate genes within a 1-Mb distance from each significant SNP were found. A guilt-by-association-based (GBA) prioritization analysis (PA) was performed to identify the most plausible functional candidate genes. GBA-based PA identified 39 genes that were significantly associated with gene networks relevant to body size traits. Prioritized genes were identified in the vicinity of all significant SNPs except for those on chromosomes 10 and 12. The top five ranking genes were TP53, BMPR1A, PIK3R5, RPL26 and PRKDC. CONCLUSIONS: The results of this GWAS provide evidence for 39 causative candidate genes across nine chromosomal regions for body size traits, some of which are novel and some are previously identified candidates from other studies (e.g. TP53, NTN1 and ZNF521). GBA-based PA has proved to be a useful tool to identify genes with increased biological relevance but it is subjected to certain limitations.
[Mh] Termos MeSH primário: Tamanho Corporal/genética
Locos de Características Quantitativas
Ovinos/genética
[Mh] Termos MeSH secundário: Animais
Cromossomos/genética
Feminino
Estudo de Associação Genômica Ampla
Polimorfismo de Nucleotídeo Único
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Em] Mês de entrada:1710
[Cu] Atualização por classe:180218
[Lr] Data última revisão:
180218
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170430
[St] Status:MEDLINE
[do] DOI:10.1186/s12711-017-0316-3


  3 / 29799 MEDLINE  
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[PMID]:29341686
[Au] Autor:Brackley CA; Johnson J; Michieletto D; Morozov AN; Nicodemi M; Cook PR; Marenduzzo D
[Ad] Endereço:SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom.
[Ti] Título:Nonequilibrium Chromosome Looping via Molecular Slip Links.
[So] Source:Phys Rev Lett;119(13):138101, 2017 Sep 29.
[Is] ISSN:1079-7114
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:We propose a model for the formation of chromatin loops based on the diffusive sliding of molecular slip links. These mimic the behavior of molecules like cohesin, which, along with the CTCF protein, stabilize loops which contribute to organizing the genome. By combining 3D Brownian dynamics simulations and 1D exactly solvable nonequilibrium models, we show that diffusive sliding is sufficient to account for the strong bias in favor of convergent CTCF-mediated chromosome loops observed experimentally. We also find that the diffusive motion of multiple slip links along chromatin is rectified by an intriguing ratchet effect that arises if slip links bind to the chromatin at a preferred "loading site." This emergent collective behavior favors the extrusion of loops which are much larger than the ones formed by single slip links.
[Mh] Termos MeSH primário: Fator de Ligação a CCCTC/química
Cromossomos/química
[Mh] Termos MeSH secundário: Proteínas de Ciclo Celular
Cromatina
Proteínas Cromossômicas não Histona
Difusão
Genoma
Modelos Moleculares
Conformação de Ácido Nucleico
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (CCCTC-Binding Factor); 0 (Cell Cycle Proteins); 0 (Chromatin); 0 (Chromosomal Proteins, Non-Histone); 0 (cohesins)
[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:180118
[St] Status:MEDLINE
[do] DOI:10.1103/PhysRevLett.119.138101


  4 / 29799 MEDLINE  
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[PMID]:29186505
[Au] Autor:Oudelaar AM; Davies JOJ; Downes DJ; Higgs DR; Hughes JR
[Ad] Endereço:Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
[Ti] Título:Robust detection of chromosomal interactions from small numbers of cells using low-input Capture-C.
[So] Source:Nucleic Acids Res;45(22):e184, 2017 Dec 15.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Chromosome conformation capture (3C) techniques are crucial to understanding tissue-specific regulation of gene expression, but current methods generally require large numbers of cells. This hampers the investigation of chromatin architecture in rare cell populations. We present a new low-input Capture-C approach that can generate high-quality 3C interaction profiles from 10 000-20 000 cells, depending on the resolution used for analysis. We also present a PCR-free, sequencing-free 3C technique based on NanoString technology called C-String. By comparing C-String and Capture-C interaction profiles we show that the latter are not skewed by PCR amplification. Furthermore, we demonstrate that chromatin interactions detected by Capture-C do not depend on the degree of cross-linking by performing experiments with varying formaldehyde concentrations.
[Mh] Termos MeSH primário: Cromatina/metabolismo
Cromossomos/metabolismo
Técnicas Genéticas
Nanotecnologia/métodos
[Mh] Termos MeSH secundário: Animais
Contagem de Células
Células Cultivadas
Cromatina/química
Cromatina/genética
Cromossomos/química
Cromossomos/genética
Feminino
Formaldeído/química
Regulação da Expressão Gênica
Camundongos Endogâmicos C57BL
Conformação Molecular
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Chromatin); 1HG84L3525 (Formaldehyde)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180115
[Lr] Data última revisão:
180115
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171130
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkx1194


  5 / 29799 MEDLINE  
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[PMID]:27770354
[Au] Autor:Grob S; Grossniklaus U
[Ad] Endereço:Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland. sgrob@botinst.uzh.ch.
[Ti] Título:Chromatin Conformation Capture-Based Analysis of Nuclear Architecture.
[So] Source:Methods Mol Biol;1456:15-32, 2017.
[Is] ISSN:1940-6029
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Nuclear organization and higher-order chromosome structure in interphase nuclei are thought to have important effects on fundamental biological processes, including chromosome condensation, replication, and transcription. Until recently, however, nuclear organization could only be analyzed microscopically. The development of chromatin conformation capture (3C)-based techniques now allows a detailed look at chromosomal architecture from the level of individual loci to the entire genome. Here we provide a robust Hi-C protocol, allowing the analysis of nuclear organization in nuclei from different wild-type and mutant plant tissues. This method is quantitative and provides a highly efficient and comprehensive way to study chromatin organization during plant development, in response to different environmental stimuli, and in mutants disrupting a variety of processes, including epigenetic pathways regulating gene expression.
[Mh] Termos MeSH primário: Núcleo Celular/química
Núcleo Celular/genética
Cromatina/química
Cromatina/genética
Conformação de Ácido Nucleico
[Mh] Termos MeSH secundário: Fracionamento Celular/métodos
Cromossomos/química
Cromossomos/genética
Sequenciamento de Nucleotídeos em Larga Escala
Plantas/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Chromatin)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180112
[Lr] Data última revisão:
180112
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161023
[St] Status:MEDLINE


  6 / 29799 MEDLINE  
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[PMID]:29217591
[Au] Autor:Wutz G; Várnai C; Nagasaka K; Cisneros DA; Stocsits RR; Tang W; Schoenfelder S; Jessberger G; Muhar M; Hossain MJ; Walther N; Koch B; Kueblbeck M; Ellenberg J; Zuber J; Fraser P; Peters JM
[Ad] Endereço:Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.
[Ti] Título:Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins.
[So] Source:EMBO J;36(24):3573-3599, 2017 12 15.
[Is] ISSN:1460-2075
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Mammalian genomes are spatially organized into compartments, topologically associating domains (TADs), and loops to facilitate gene regulation and other chromosomal functions. How compartments, TADs, and loops are generated is unknown. It has been proposed that cohesin forms TADs and loops by extruding chromatin loops until it encounters CTCF, but direct evidence for this hypothesis is missing. Here, we show that cohesin suppresses compartments but is required for TADs and loops, that CTCF defines their boundaries, and that the cohesin unloading factor WAPL and its PDS5 binding partners control the length of loops. In the absence of WAPL and PDS5 proteins, cohesin forms extended loops, presumably by passing CTCF sites, accumulates in axial chromosomal positions (vermicelli), and condenses chromosomes. Unexpectedly, PDS5 proteins are also required for boundary function. These results show that cohesin has an essential genome-wide function in mediating long-range chromatin interactions and support the hypothesis that cohesin creates these by loop extrusion, until it is delayed by CTCF in a manner dependent on PDS5 proteins, or until it is released from DNA by WAPL.
[Mh] Termos MeSH primário: Fator de Ligação a CCCTC/metabolismo
Proteínas de Transporte/metabolismo
Proteínas de Ciclo Celular/metabolismo
Cromatina/genética
Proteínas Cromossômicas não Histona/metabolismo
Proteínas de Ligação a DNA/metabolismo
Proteínas Nucleares/metabolismo
Proteínas Proto-Oncogênicas/metabolismo
Fatores de Transcrição/metabolismo
[Mh] Termos MeSH secundário: Fator de Ligação a CCCTC/genética
Proteínas de Transporte/genética
Proteínas de Ciclo Celular/genética
Proteínas Cromossômicas não Histona/genética
Cromossomos/genética
Proteínas de Ligação a DNA/genética
Genoma Humano/genética
Células HeLa
Seres Humanos
Proteínas Nucleares/genética
Proteínas Proto-Oncogênicas/genética
Fatores de Transcrição/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (CCCTC-Binding Factor); 0 (CTCF protein, human); 0 (Carrier Proteins); 0 (Cell Cycle Proteins); 0 (Chromatin); 0 (Chromosomal Proteins, Non-Histone); 0 (DNA-Binding Proteins); 0 (Nuclear Proteins); 0 (PDS5A protein, human); 0 (PDS5B protein, human); 0 (Proto-Oncogene Proteins); 0 (Transcription Factors); 0 (WAPAL protein, human); 0 (cohesins)
[Em] Mês de entrada:1712
[Cu] Atualização por classe:180106
[Lr] Data última revisão:
180106
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171209
[St] Status:MEDLINE
[do] DOI:10.15252/embj.201798004


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[PMID]:29217590
[Au] Autor:Gassler J; Brandão HB; Imakaev M; Flyamer IM; Ladstätter S; Bickmore WA; Peters JM; Mirny LA; Tachibana K
[Ad] Endereço:Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria.
[Ti] Título:A mechanism of cohesin-dependent loop extrusion organizes zygotic genome architecture.
[So] Source:EMBO J;36(24):3600-3618, 2017 12 15.
[Is] ISSN:1460-2075
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Fertilization triggers assembly of higher-order chromatin structure from a condensed maternal and a naïve paternal genome to generate a totipotent embryo. Chromatin loops and domains have been detected in mouse zygotes by single-nucleus Hi-C (snHi-C), but not bulk Hi-C. It is therefore unclear when and how embryonic chromatin conformations are assembled. Here, we investigated whether a mechanism of cohesin-dependent loop extrusion generates higher-order chromatin structures within the one-cell embryo. Using snHi-C of mouse knockout embryos, we demonstrate that the zygotic genome folds into loops and domains that critically depend on Scc1-cohesin and that are regulated in size and linear density by Wapl. Remarkably, we discovered distinct effects on maternal and paternal chromatin loop sizes, likely reflecting differences in loop extrusion dynamics and epigenetic reprogramming. Dynamic polymer models of chromosomes reproduce changes in snHi-C, suggesting a mechanism where cohesin locally compacts chromatin by active loop extrusion, whose processivity is controlled by Wapl. Our simulations and experimental data provide evidence that cohesin-dependent loop extrusion organizes mammalian genomes over multiple scales from the one-cell embryo onward.
[Mh] Termos MeSH primário: Proteínas de Transporte/metabolismo
Proteínas de Ciclo Celular/metabolismo
Cromatina/genética
Proteínas Cromossômicas não Histona/metabolismo
Genoma/genética
Proteínas Nucleares/metabolismo
Fosfoproteínas/metabolismo
Proteínas Proto-Oncogênicas/metabolismo
[Mh] Termos MeSH secundário: Animais
Proteínas de Transporte/genética
Proteínas de Ciclo Celular/genética
Proteínas Cromossômicas não Histona/genética
Cromossomos/genética
Epigenômica
Feminino
Técnicas de Inativação de Genes
Masculino
Camundongos
Camundongos Endogâmicos C57BL
Proteínas Nucleares/genética
Fosfoproteínas/genética
Proteínas Proto-Oncogênicas/genética
Zigoto
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Carrier Proteins); 0 (Cell Cycle Proteins); 0 (Chromatin); 0 (Chromosomal Proteins, Non-Histone); 0 (Nuclear Proteins); 0 (Phosphoproteins); 0 (Proto-Oncogene Proteins); 0 (RAD21 protein, human); 0 (WAPAL protein, human); 0 (cohesins)
[Em] Mês de entrada:1712
[Cu] Atualização por classe:180106
[Lr] Data última revisão:
180106
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171209
[St] Status:MEDLINE
[do] DOI:10.15252/embj.201798083


  8 / 29799 MEDLINE  
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[PMID]:28747439
[Au] Autor:Dewey EB; Johnston CA
[Ad] Endereço:Department of Biology, University of New Mexico, Albuquerque, NM 87131.
[Ti] Título:Diverse mitotic functions of the cytoskeletal cross-linking protein Shortstop suggest a role in Dynein/Dynactin activity.
[So] Source:Mol Biol Cell;28(19):2555-2568, 2017 Sep 15.
[Is] ISSN:1939-4586
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Proper assembly and orientation of the bipolar mitotic spindle is critical to the fidelity of cell division. Mitotic precision fundamentally contributes to cell fate specification, tissue development and homeostasis, and chromosome distribution within daughter cells. Defects in these events are thought to contribute to several human diseases. The underlying mechanisms that function in spindle morphogenesis and positioning remain incompletely defined, however. Here we describe diverse roles for the actin-microtubule cross-linker Shortstop (Shot) in mitotic spindle function in Shot localizes to mitotic spindle poles, and its knockdown results in an unfocused spindle pole morphology and a disruption of proper spindle orientation. Loss of Shot also leads to chromosome congression defects, cell cycle progression delay, and defective chromosome segregation during anaphase. These mitotic errors trigger apoptosis in epithelial tissue, and blocking this apoptotic response results in a marked induction of the epithelial-mesenchymal transition marker MMP-1. The actin-binding domain of Shot directly interacts with Actin-related protein-1 (Arp-1), a key component of the Dynein/Dynactin complex. Knockdown of Arp-1 phenocopies Shot loss universally, whereas chemical disruption of F-actin does so selectively. Our work highlights novel roles for Shot in mitosis and suggests a mechanism involving Dynein/Dynactin activation.
[Mh] Termos MeSH primário: Proteínas de Drosophila/metabolismo
Proteínas de Drosophila/fisiologia
Proteínas dos Microfilamentos/metabolismo
Proteínas dos Microfilamentos/fisiologia
[Mh] Termos MeSH secundário: Actinas/metabolismo
Anáfase
Animais
Ciclo Celular
Cromossomos/metabolismo
Citoesqueleto/patologia
Drosophila/metabolismo
Proteínas de Drosophila/genética
Complexo Dinactina/metabolismo
Dineínas/metabolismo
Proteínas dos Microfilamentos/genética
Proteínas Associadas aos Microtúbulos/metabolismo
Microtúbulos/metabolismo
Mitose/fisiologia
Ligação Proteica
Fuso Acromático/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Actins); 0 (Drosophila Proteins); 0 (Dynactin Complex); 0 (Microfilament Proteins); 0 (Microtubule-Associated Proteins); 0 (shot protein, Drosophila); EC 3.6.4.2 (Dyneins)
[Em] Mês de entrada:1711
[Cu] Atualização por classe:180106
[Lr] Data última revisão:
180106
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170728
[St] Status:MEDLINE
[do] DOI:10.1091/mbc.E17-04-0219


  9 / 29799 MEDLINE  
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[PMID]:29215640
[Au] Autor:Eeftens J; Dekker C
[Ad] Endereço:Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands.
[Ti] Título:Catching DNA with hoops-biophysical approaches to clarify the mechanism of SMC proteins.
[So] Source:Nat Struct Mol Biol;24(12):1012-1020, 2017 Dec 07.
[Is] ISSN:1545-9985
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Structural maintenance of chromosome (SMC) complexes are central regulators of chromosome architecture that are essential in all domains of life. For decades, the structural biology field has been debating how these conserved protein complexes use their intricate ring-like structures to structurally organize DNA. Here, we review the contributions of single-molecule biophysical approaches to resolving the molecular mechanism of SMC protein function.
[Mh] Termos MeSH primário: Proteínas Cromossômicas não Histona/metabolismo
Cromossomos/metabolismo
DNA/metabolismo
Conformação de Ácido Nucleico
[Mh] Termos MeSH secundário: Animais
Bactérias/genética
Proteínas de Bactérias/genética
Proteínas de Ciclo Celular/metabolismo
Proteínas de Ligação a DNA/metabolismo
Seres Humanos
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Nm] Nome de substância:
0 (Bacterial Proteins); 0 (Cell Cycle Proteins); 0 (Chromosomal Proteins, Non-Histone); 0 (DNA-Binding Proteins); 9007-49-2 (DNA)
[Em] Mês de entrada:1712
[Cu] Atualização por classe:171229
[Lr] Data última revisão:
171229
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171208
[St] Status:MEDLINE
[do] DOI:10.1038/nsmb.3507


  10 / 29799 MEDLINE  
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[PMID]:28450531
[Au] Autor:Lindblad KA; Bracht JR; Williams AE; Landweber LF
[Ad] Endereço:Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA.
[Ti] Título:Thousands of RNA-cached copies of whole chromosomes are present in the ciliate during development.
[So] Source:RNA;23(8):1200-1208, 2017 08.
[Is] ISSN:1469-9001
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The ciliate maintains two genomes: a germline genome that is active only during sexual conjugation and a transcriptionally active, somatic genome that derives from the germline via extensive sequence reduction and rearrangement. Previously, we found that long noncoding (lnc) RNA "templates"-telomere-containing, RNA-cached copies of mature chromosomes-provide the information to program the rearrangement process. Here we used a modified RNA-seq approach to conduct the first genome-wide search for endogenous, telomere-to-telomere RNA transcripts. We find that during development, produces long noncoding RNA copies for over 10,000 of its 16,000 somatic chromosomes, consistent with a model in which transmits an RNA-cached copy of its somatic genome to the sexual progeny. Both the primary sequence and expression profile of a somatic chromosome influence the temporal distribution and abundance of individual template RNAs. This suggests that may undergo multiple rounds of DNA rearrangement during development. These observations implicate a complex set of thousands of long RNA molecules in the wiring and maintenance of a highly elaborate somatic genome architecture.
[Mh] Termos MeSH primário: Cromossomos/genética
Genoma de Protozoário/genética
Oxytricha/genética
RNA Longo não Codificante/genética
RNA de Protozoário/genética
[Mh] Termos MeSH secundário: Animais
Variações do Número de Cópias de DNA
Sequenciamento de Nucleotídeos em Larga Escala/métodos
Oxytricha/crescimento & desenvolvimento
Telômero/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL
[Nm] Nome de substância:
0 (RNA, Long Noncoding); 0 (RNA, Protozoan)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:171223
[Lr] Data última revisão:
171223
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170429
[St] Status:MEDLINE
[do] DOI:10.1261/rna.058511.116



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