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  1 / 14174 MEDLINE  
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[PMID]:29267285
[Au] Autor:Colombo DF; Burger L; Baubec T; Schübeler D
[Ad] Endereço:Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
[Ti] Título:Binding of high mobility group A proteins to the mammalian genome occurs as a function of AT-content.
[So] Source:PLoS Genet;13(12):e1007102, 2017 12.
[Is] ISSN:1553-7404
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Genomic location can inform on potential function and recruitment signals for chromatin-associated proteins. High mobility group (Hmg) proteins are of similar size as histones with Hmga1 and Hmga2 being particularly abundant in replicating normal tissues and in cancerous cells. While several roles for Hmga proteins have been proposed we lack a comprehensive description of their genomic location as a function of chromatin, DNA sequence and functional domains. Here we report such a characterization in mouse embryonic stem cells in which we introduce biotin-tagged constructs of wild-type and DNA-binding domain mutants. Comparative analysis of the genome-wide distribution of Hmga proteins reveals pervasive binding, a feature that critically depends on a functional DNA-binding domain and which is shared by both Hmga proteins. Assessment of the underlying queues instructive for this binding modality identifies AT richness, defined as high frequency of A or T bases, as the major criterion for local binding. Additionally, we show that other chromatin states such as those linked to cis-regulatory regions have little impact on Hmga binding both in stem and differentiated cells. As a consequence, Hmga proteins are preferentially found at AT-rich regions such as constitutively heterochromatic regions but are absent from enhancers and promoters arguing for a limited role in regulating individual genes. In line with this model, we show that genetic deletion of Hmga proteins in stem cells causes limited transcriptional effects and that binding is conserved in neuronal progenitors. Overall our comparative study describing the in vivo binding modality of Hmga1 and Hmga2 identifies the proteins' preference for AT-rich DNA genome-wide and argues against a suggested function of Hmga at regulatory regions. Instead we discover pervasive binding with enrichment at regions of higher AT content irrespective of local variation in chromatin modifications.
[Mh] Termos MeSH primário: Sequência Rica em At
Proteínas de Grupo de Alta Mobilidade/genética
Proteínas de Grupo de Alta Mobilidade/metabolismo
[Mh] Termos MeSH secundário: Animais
Composição de Bases
Sequência de Bases
Cromatina/genética
Cromatina/metabolismo
DNA/química
DNA/genética
DNA/metabolismo
Proteínas de Ligação a DNA/genética
Proteínas de Ligação a DNA/metabolismo
Células-Tronco Embrionárias/metabolismo
Histonas/genética
Camundongos
Camundongos Endogâmicos C57BL
Regiões Promotoras Genéticas
Ligação Proteica
Sequências Reguladoras de Ácido Nucleico
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Chromatin); 0 (DNA-Binding Proteins); 0 (High Mobility Group Proteins); 0 (Histones); 9007-49-2 (DNA)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180227
[Lr] Data última revisão:
180227
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171222
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pgen.1007102


  2 / 14174 MEDLINE  
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[PMID]:28453430
[Au] Autor:Segala G; Picard D
[Ad] Endereço:a Département de Biologie Cellulaire , Université de Genève , Genève , Switzerland.
[Ti] Título:H2B monoubiquitination: t'ub or not t'ub for inducible enhancers.
[So] Source:Transcription;8(2):126-132, 2017 03 15.
[Is] ISSN:2154-1272
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Recently, we reported the unexpected finding that the monoubiquitination of histone H2B (H2Bub1) regulates inducible enhancers. Here, we propose a conceptual framework to reconcile the apparently discrepant roles of H2Bub1 in transcription initiation and elongation, and we discuss how H2Bub1 could regulate cellular processes linked to non-coding transcription.
[Mh] Termos MeSH primário: Histonas/metabolismo
Sequências Reguladoras de Ácido Nucleico
[Mh] Termos MeSH secundário: Animais
Metilação de DNA
Estradiol/farmacologia
Receptor alfa de Estrogênio/metabolismo
Histonas/genética
Seres Humanos
Células MCF-7
NF-kappa B/metabolismo
RNA/biossíntese
RNA Polimerase II/metabolismo
Sequências Reguladoras de Ácido Nucleico/efeitos dos fármacos
Elongação da Transcrição Genética
Iniciação da Transcrição Genética
Ubiquitinação/efeitos dos fármacos
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Estrogen Receptor alpha); 0 (Histones); 0 (NF-kappa B); 4TI98Z838E (Estradiol); 63231-63-0 (RNA); EC 2.7.7.- (RNA Polymerase II)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180228
[Lr] Data última revisão:
180228
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170429
[St] Status:MEDLINE
[do] DOI:10.1080/21541264.2017.1285852


  3 / 14174 MEDLINE  
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[PMID]:28451981
[Au] Autor:Abugessaisa I; Noguchi S; Carninci P; Kasukawa T
[Ad] Endereço:Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
[Ti] Título:The FANTOM5 Computation Ecosystem: Genomic Information Hub for Promoters and Active Enhancers.
[So] Source:Methods Mol Biol;1611:199-217, 2017.
[Is] ISSN:1940-6029
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The Functional Annotation of the Mammalian Genome 5 (FANTOM5) project conducted transcriptome analysis of various mammalian cell types and provided a comprehensive resource to understand transcriptome and transcriptional regulation in individual cellular states encoded in the genome.FANTOM5 used cap analysis of gene expression (CAGE) with single-molecule sequencing to map transcription start sites (TSS) and measured their expression in a diverse range of samples. The main results from FANTOM5 were published as a promoter-level mammalian expression atlas and an atlas of active enhancers across human cell types. The FANTOM5 dataset is composed of raw experimental data and the results of bioinformatics analyses. In this chapter, we give a detailed description of the content of the FANTOM5 dataset and elaborate on different computing applications developed to publish the data and enable reproducibility and discovery of new findings. We present use cases in which the FANTOM5 dataset has been reused, leading to new findings.
[Mh] Termos MeSH primário: Sítio de Iniciação de Transcrição
[Mh] Termos MeSH secundário: Animais
Biologia Computacional/métodos
Perfilação da Expressão Gênica/métodos
Genômica/métodos
Seres Humanos
Anotação de Sequência Molecular/métodos
Regiões Promotoras Genéticas/genética
Sequências Reguladoras de Ácido Nucleico/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180212
[Lr] Data última revisão:
180212
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170429
[St] Status:MEDLINE
[do] DOI:10.1007/978-1-4939-7015-5_15


  4 / 14174 MEDLINE  
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[PMID]:29298348
[Au] Autor:Bekiaris PS; Tekath T; Staiger D; Danisman S
[Ad] Endereço:RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany.
[Ti] Título:Computational exploration of cis-regulatory modules in rhythmic expression data using the "Exploration of Distinctive CREs and CRMs" (EDCC) and "CRM Network Generator" (CNG) programs.
[So] Source:PLoS One;13(1):e0190421, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Understanding the effect of cis-regulatory elements (CRE) and clusters of CREs, which are called cis-regulatory modules (CRM), in eukaryotic gene expression is a challenge of computational biology. We developed two programs that allow simple, fast and reliable analysis of candidate CREs and CRMs that may affect specific gene expression and that determine positional features between individual CREs within a CRM. The first program, "Exploration of Distinctive CREs and CRMs" (EDCC), correlates candidate CREs and CRMs with specific gene expression patterns. For pairs of CREs, EDCC also determines positional preferences of the single CREs in relation to each other and to the transcriptional start site. The second program, "CRM Network Generator" (CNG), prioritizes these positional preferences using a neural network and thus allows unbiased rating of the positional preferences that were determined by EDCC. We tested these programs with data from a microarray study of circadian gene expression in Arabidopsis thaliana. Analyzing more than 1.5 million pairwise CRE combinations, we found 22 candidate combinations, of which several contained known clock promoter elements together with elements that had not been identified as relevant to circadian gene expression before. CNG analysis further identified positional preferences of these CRE pairs, hinting at positional information that may be relevant for circadian gene expression. Future wet lab experiments will have to determine which of these combinations confer daytime specific circadian gene expression.
[Mh] Termos MeSH primário: Biologia Computacional
Regulação da Expressão Gênica de Plantas
Sequências Reguladoras de Ácido Nucleico
[Mh] Termos MeSH secundário: Arabidopsis/genética
Ritmo Circadiano
Genes de Plantas
Regiões Promotoras Genéticas
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180210
[Lr] Data última revisão:
180210
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180104
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0190421


  5 / 14174 MEDLINE  
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[PMID]:29293496
[Au] Autor:Bessière C; Taha M; Petitprez F; Vandel J; Marin JM; Bréhélin L; Lèbre S; Lecellier CH
[Ad] Endereço:IBC, Univ. Montpellier, CNRS, Montpellier, France.
[Ti] Título:Probing instructions for expression regulation in gene nucleotide compositions.
[So] Source:PLoS Comput Biol;14(1):e1005921, 2018 01.
[Is] ISSN:1553-7358
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Gene expression is orchestrated by distinct regulatory regions to ensure a wide variety of cell types and functions. A challenge is to identify which regulatory regions are active, what are their associated features and how they work together in each cell type. Several approaches have tackled this problem by modeling gene expression based on epigenetic marks, with the ultimate goal of identifying driving regions and associated genomic variations that are clinically relevant in particular in precision medicine. However, these models rely on experimental data, which are limited to specific samples (even often to cell lines) and cannot be generated for all regulators and all patients. In addition, we show here that, although these approaches are accurate in predicting gene expression, inference of TF combinations from this type of models is not straightforward. Furthermore these methods are not designed to capture regulation instructions present at the sequence level, before the binding of regulators or the opening of the chromatin. Here, we probe sequence-level instructions for gene expression and develop a method to explain mRNA levels based solely on nucleotide features. Our method positions nucleotide composition as a critical component of gene expression. Moreover, our approach, able to rank regulatory regions according to their contribution, unveils a strong influence of the gene body sequence, in particular introns. We further provide evidence that the contribution of nucleotide content can be linked to co-regulations associated with genome 3D architecture and to associations of genes within topologically associated domains.
[Mh] Termos MeSH primário: Composição de Bases
Regulação da Expressão Gênica
Sequências Reguladoras de Ácido Nucleico
[Mh] Termos MeSH secundário: Biologia Computacional
Variações do Número de Cópias de DNA
Elementos Facilitadores Genéticos
Genoma Humano
Seres Humanos
Modelos Genéticos
Neoplasias/genética
Neoplasias/metabolismo
Polimorfismo de Nucleotídeo Único
Regiões Promotoras Genéticas
Locos de Características Quantitativas
RNA Mensageiro/química
RNA Mensageiro/genética
RNA Mensageiro/metabolismo
Fatores de Transcrição/genética
Fatores de Transcrição/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T; VALIDATION STUDIES
[Nm] Nome de substância:
0 (RNA, Messenger); 0 (Transcription Factors)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180210
[Lr] Data última revisão:
180210
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180103
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pcbi.1005921


  6 / 14174 MEDLINE  
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[PMID]:29273679
[Au] Autor:Rodríguez-Carballo E; Lopez-Delisle L; Zhan Y; Fabre PJ; Beccari L; El-Idrissi I; Huynh THN; Ozadam H; Dekker J; Duboule D
[Ad] Endereço:Department of Genetics and Evolution, University of Geneva, 1205 Geneva, Switzerland.
[Ti] Título:The cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes.
[So] Source:Genes Dev;31(22):2264-2281, 2017 11 15.
[Is] ISSN:1549-5477
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The mammalian cluster lies between two topologically associating domains (TADs) matching distinct enhancer-rich regulatory landscapes. During limb development, the telomeric TAD controls the early transcription of genes in forearm cells, whereas the centromeric TAD subsequently regulates more posterior genes in digit cells. Therefore, the TAD boundary prevents the terminal gene from responding to forearm enhancers, thereby allowing proper limb patterning. To assess the nature and function of this CTCF-rich DNA region in embryos we compared chromatin interaction profiles between proximal and distal limb bud cells isolated from mutant stocks where various parts of this boundary region were removed. The resulting progressive release in boundary effect triggered inter-TAD contacts, favored by the activity of the newly accessed enhancers. However, the boundary was highly resilient, and only a 400-kb deletion, including the whole-gene cluster, was eventually able to merge the neighboring TADs into a single structure. In this unified TAD, both proximal and distal limb enhancers nevertheless continued to work independently over a targeted transgenic reporter construct. We propose that the whole cluster is a dynamic TAD border and that the exact boundary position varies depending on both the transcriptional status and the developmental context.
[Mh] Termos MeSH primário: Genes Homeobox
Família Multigênica
Sequências Reguladoras de Ácido Nucleico
[Mh] Termos MeSH secundário: Animais
Fator de Ligação a CCCTC/metabolismo
Proteínas de Ciclo Celular/metabolismo
Proteínas Cromossômicas não Histona/metabolismo
Elementos Facilitadores Genéticos
Botões de Extremidades/metabolismo
Camundongos
Deleção de Sequência
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 (Cell Cycle Proteins); 0 (Chromosomal Proteins, Non-Histone); 0 (Ctcf protein, mouse); 0 (cohesins)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180202
[Lr] Data última revisão:
180202
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171224
[St] Status:MEDLINE
[do] DOI:10.1101/gad.307769.117


  7 / 14174 MEDLINE  
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[PMID]:27779464
[Au] Autor:Keefe MD; Bonkowsky JL
[Ad] Endereço:Department of Pediatrics, Department of Neurobiology and Anatomy, University of Utah School of Medicine , Salt Lake City, Utah.
[Ti] Título:Transvection Arising from Transgene Interactions in Zebrafish.
[So] Source:Zebrafish;14(1):8-9, 2017 02.
[Is] ISSN:1557-8542
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:There has been a rapid expansion in use of transgenic technologies in zebrafish. We report a novel example of transinteractions of genetic elements, or transvection. This interaction led to a novel expression pattern and illustrates a precautionary example regarding use of transgenes in zebrafish.
[Mh] Termos MeSH primário: Animais Geneticamente Modificados/genética
Epistasia Genética
Proteínas de Fluorescência Verde/metabolismo
Sequências Reguladoras de Ácido Nucleico
Transgenes
Peixe-Zebra/genética
[Mh] Termos MeSH secundário: Animais
Animais Geneticamente Modificados/crescimento & desenvolvimento
Animais Geneticamente Modificados/metabolismo
Regulação da Expressão Gênica
Proteínas de Fluorescência Verde/genética
Seres Humanos
Canais de Potássio Corretores do Fluxo de Internalização/genética
Canais de Potássio Corretores do Fluxo de Internalização/metabolismo
Regiões Promotoras Genéticas
Peixe-Zebra/crescimento & desenvolvimento
Peixe-Zebra/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (KCNJ2 protein, human); 0 (Potassium Channels, Inwardly Rectifying); 147336-22-9 (Green Fluorescent Proteins)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:180201
[Lr] Data última revisão:
180201
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161026
[St] Status:MEDLINE
[do] DOI:10.1089/zeb.2016.1312


  8 / 14174 MEDLINE  
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[PMID]:28455377
[Au] Autor:Haro E; Watson BA; Feenstra JM; Tegeler L; Pira CU; Mohan S; Oberg KC
[Ad] Endereço:Department of Pathology and Human Anatomy, Loma Linda University, Loma Linda, CA 92354, USA.
[Ti] Título:Lmx1b-targeted -regulatory modules involved in limb dorsalization.
[So] Source:Development;144(11):2009-2020, 2017 06 01.
[Is] ISSN:1477-9129
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Lmx1b is a homeodomain transcription factor responsible for limb dorsalization. Despite striking double-ventral (loss-of-function) and double-dorsal (gain-of-function) limb phenotypes, no direct gene targets in the limb have been confirmed. To determine direct targets, we performed a chromatin immunoprecipitation against Lmx1b in mouse limbs at embryonic day 12.5 followed by next-generation sequencing (ChIP-seq). Nearly 84% ( =617) of the Lmx1b-bound genomic intervals (LBIs) identified overlap with chromatin regulatory marks indicative of potential -regulatory modules (PCRMs). In addition, 73 LBIs mapped to CRMs that are known to be active during limb development. We compared Lmx1b-bound PCRMs with genes regulated by Lmx1b and found 292 PCRMs within 1 Mb of 254 Lmx1b-regulated genes. Gene ontological analysis suggests that Lmx1b targets extracellular matrix production, bone/joint formation, axonal guidance, vascular development, cell proliferation and cell movement. We validated the functional activity of a PCRM associated with joint-related that provides a mechanism for Lmx1b-mediated joint modification and a PCRM associated with that suggests a role in autoregulation. This is the first report to describe genome-wide Lmx1b binding during limb development, directly linking Lmx1b to targets that accomplish limb dorsalization.
[Mh] Termos MeSH primário: Padronização Corporal/genética
Extremidades/embriologia
Proteínas com Homeodomínio LIM/metabolismo
Sequências Reguladoras de Ácido Nucleico/genética
Fatores de Transcrição/metabolismo
[Mh] Termos MeSH secundário: Animais
Galinhas
Imunoprecipitação da Cromatina
Sequência Conservada/genética
Elementos Facilitadores Genéticos/genética
Regulação da Expressão Gênica no Desenvolvimento
Genoma
Fator 5 de Diferenciação de Crescimento/genética
Fator 5 de Diferenciação de Crescimento/metabolismo
Proteínas com Homeodomínio LIM/genética
Camundongos Endogâmicos C57BL
Modelos Biológicos
Reprodutibilidade dos Testes
Análise de Sequência de RNA
Fatores de Transcrição/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Gdf5 protein, mouse); 0 (Growth Differentiation Factor 5); 0 (LIM homeobox transcription factor 1 beta); 0 (LIM-Homeodomain Proteins); 0 (Transcription Factors)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:171126
[Lr] Data última revisão:
171126
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170430
[St] Status:MEDLINE
[do] DOI:10.1242/dev.146332


  9 / 14174 MEDLINE  
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[PMID]:29049320
[Au] Autor:Kakumanu A; Velasco S; Mazzoni E; Mahony S
[Ad] Endereço:Center for Eukaryotic Gene Regulation, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America.
[Ti] Título:Deconvolving sequence features that discriminate between overlapping regulatory annotations.
[So] Source:PLoS Comput Biol;13(10):e1005795, 2017 Oct.
[Is] ISSN:1553-7358
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Genomic loci with regulatory potential can be annotated with various properties. For example, genomic sites bound by a given transcription factor (TF) can be divided according to whether they are proximal or distal to known promoters. Sites can be further labeled according to the cell types and conditions in which they are active. Given such a collection of labeled sites, it is natural to ask what sequence features are associated with each annotation label. However, discovering such label-specific sequence features is often confounded by overlaps between the labels; e.g. if regulatory sites specific to a given cell type are also more likely to be promoter-proximal, it is difficult to assess whether motifs identified in that set of sites are associated with the cell type or associated with promoters. In order to meet this challenge, we developed SeqUnwinder, a principled approach to deconvolving interpretable discriminative sequence features associated with overlapping annotation labels. We demonstrate the novel analysis abilities of SeqUnwinder using three examples. Firstly, SeqUnwinder is able to unravel sequence features associated with the dynamic binding behavior of TFs during motor neuron programming from features associated with chromatin state in the initial embryonic stem cells. Secondly, we characterize distinct sequence properties of multi-condition and cell-specific TF binding sites after controlling for uneven associations with promoter proximity. Finally, we demonstrate the scalability of SeqUnwinder to discover cell-specific sequence features from over one hundred thousand genomic loci that display DNase I hypersensitivity in one or more ENCODE cell lines.
[Mh] Termos MeSH primário: Anotação de Sequência Molecular
Sequências Reguladoras de Ácido Nucleico/genética
Software
Fatores de Transcrição/metabolismo
[Mh] Termos MeSH secundário: Sítios de Ligação
Linhagem Celular
Linhagem da Célula/genética
Cromatina/genética
Cromatina/metabolismo
Biologia Computacional/métodos
Desoxirribonuclease I/genética
Desoxirribonuclease I/metabolismo
Células-Tronco Embrionárias/citologia
Células-Tronco Embrionárias/metabolismo
Regulação da Expressão Gênica
Loci Gênicos
Sequenciamento de Nucleotídeos em Larga Escala
Seres Humanos
Regiões Promotoras Genéticas
Fatores de Transcrição/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Chromatin); 0 (Transcription Factors); EC 3.1.21.1 (Deoxyribonuclease I)
[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:171020
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pcbi.1005795


  10 / 14174 MEDLINE  
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[PMID]:29028826
[Au] Autor:Pérez-Zamorano B; Rosas-Madrigal S; Lozano OAM; Castillo Méndez M; Valverde-Garduño V
[Ad] Endereço:Departamento de Infección e Inmunidad, Centro de Investigaciones Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México.
[Ti] Título:Identification of cis-regulatory sequences reveals potential participation of lola and Deaf1 transcription factors in Anopheles gambiae innate immune response.
[So] Source:PLoS One;12(10):e0186435, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The innate immune response of Anopheles gambiae involves the transcriptional upregulation of effector genes. Therefore, the cis-regulatory sequences and their cognate binding factors play essential roles in the mosquito's immune response. However, the genetic control of the mosquito's innate immune response is not yet fully understood. To gain further insight on the elements, the factors and the potential mechanisms involved, an open chromatin profiling was carried out on A. gambiae-derived immune-responsive cells. Here, we report the identification of cis-regulatory sites, immunity-related transcription factor binding sites, and cis-regulatory modules. A de novo motif discovery carried out on this set of cis-regulatory sequences identified immunity-related motifs and cis-regulatory modules. These modules contain motifs that are similar to binding sites for REL-, STAT-, lola- and Deaf1-type transcription factors. Sequence motifs similar to the binding sites for GAGA were found within a cis-regulatory module, together with immunity-related transcription factor binding sites. The presence of Deaf1- and lola-type binding sites, along with REL- and STAT-type binding sites, suggests that the immunity function of these two factors could have been conserved both in Drosophila and Anopheles gambiae.
[Mh] Termos MeSH primário: Anopheles/genética
Anopheles/imunologia
Imunidade Inata/genética
Proteínas de Insetos/metabolismo
Sequências Reguladoras de Ácido Nucleico/genética
Fatores de Transcrição/metabolismo
[Mh] Termos MeSH secundário: Animais
Anopheles/metabolismo
Cromatina/genética
Genômica
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Chromatin); 0 (Insect Proteins); 0 (Transcription Factors)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171116
[Lr] Data última revisão:
171116
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171014
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0186435



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