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Pesquisa : D13.444.735.544.875 [Categoria DeCS]
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[PMID]:27775231
[Au] Autor:Wang SX; Xu YP
[Ad] Endereço:Key Laboratory of Shenzhen for Histocompatibility and Immunogenetics, Shenzhen Blood Center, Shenzhen, P. R. China.
[Ti] Título:Genomic full-length sequence of two HLA-A alleles, A*24:08 and A*24:10, identified by cloning and sequencing.
[So] Source:HLA;88(6):300-302, 2016 12.
[Is] ISSN:2059-2310
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Genomic full-length sequences of HLA-A*24:08 and A*24:10, were identified by cloning and sequencing.
[Mh] Termos MeSH primário: Alelos
Éxons
Antígeno HLA-A24/genética
Polimorfismo de Nucleotídeo Único
Doadores de Tecidos
Regiões não Traduzidas
[Mh] Termos MeSH secundário: Sequência de Bases
Clonagem Molecular
Códon/química
Expressão Gênica
Genótipo
Antígeno HLA-A24/imunologia
Transplante de Células-Tronco Hematopoéticas
Teste de Histocompatibilidade
Seres Humanos
Íntrons
Reação em Cadeia da Polimerase
Alinhamento de Sequência
Análise de Sequência de DNA
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Codon); 0 (HLA-A24 Antigen); 0 (Untranslated Regions)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180127
[Lr] Data última revisão:
180127
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161025
[St] Status:MEDLINE
[do] DOI:10.1111/tan.12916


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[PMID]:28941403
[Au] Autor:Hyodo K; Nagai H; Okuno T
[Ad] Endereço:Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan. Electronic address: khyodo@okayama-u.ac.jp.
[Ti] Título:Dual function of a cis-acting RNA element that acts as a replication enhancer and a translation repressor in a plant positive-stranded RNA virus.
[So] Source:Virology;512:74-82, 2017 Dec.
[Is] ISSN:1096-0341
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The genome of red clover necrotic mosaic virus is divided into two positive-stranded RNA molecules of RNA1 and RNA2, which have no 5' cap structure and no 3' poly(A) tail. Previously, we showed that any mutations in the cis-acting RNA replication elements of RNA2 abolished its cap-independent translational activity, suggesting a strong link between RNA replication and translation. Here, we investigated the functions of the 5' untranslated region (UTR) of RNA2 and revealed that the basal stem-structure (5'BS) predicted in the 5' UTR is essential for robust RNA replication. Interestingly, RNA2 mutants with substitution or deletion in the right side of the 5'BS showed strong translational activity, despite their impaired replication competency. Furthermore, nucleotide sequences other than the 5'BS of the 5' UTR were essential to facilitate the replication-associated translation. Overall, these cis-acting RNA elements seem to coordinately regulate the balance between RNA replication and replication-associated translation.
[Mh] Termos MeSH primário: Regulação Viral da Expressão Gênica/fisiologia
Tombusviridae/genética
Tombusviridae/fisiologia
Replicação Viral/fisiologia
[Mh] Termos MeSH secundário: Biossíntese de Proteínas
Protoplastos
RNA Viral/genética
Tabaco
Regiões não Traduzidas/genética
Regiões não Traduzidas/fisiologia
Proteínas Virais
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (RNA, Viral); 0 (Untranslated Regions); 0 (Viral Proteins)
[Em] Mês de entrada:1711
[Cu] Atualização por classe:171109
[Lr] Data última revisão:
171109
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170924
[St] Status:MEDLINE


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[PMID]:28939196
[Au] Autor:Zhang H; Shi Y; He M
[Ad] Endereço:CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China.
[Ti] Título:Molecular identification of an insulin growth factor binding protein (IGFBP) and its potential role in an insulin-like peptide system of the pearl oyster, Pinctada fucata.
[So] Source:Comp Biochem Physiol B Biochem Mol Biol;214:27-35, 2017 Dec.
[Is] ISSN:1879-1107
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Insulin-like growth factors (IGFs) play critical roles in regulating metabolism, growth, and reproduction in invertebrates. IGF binding proteins (IGFBPs) serve as major regulators of IGF activity and regulate endocrine system. In the present study, the full-length cDNA of an igfbp was identified from the pearl oyster, Pinctada fucata, using expressed sequence tag (EST) sequence. The 1124bp Pfigfbp cDNA contains a 465bp open reading frame (ORF) encoding a putative protein of 154 amino acids, a 5'-untranslated region (UTR) of 238bp, and a 3'-UTR of 394bp (not including polyA+). Multiple sequence alignment of the deduced IB domain sequences revealed that twelve conserved Cys and ILP binding site in PfIGFBP were well aligned with human IGFBPs1-7, Mizuhopecten yessoensis IGFBP5 and Eriocheir sinensis IGFBP7. Gene expression analysis indicated that Pfigfbp mRNA was expressed in all the tissues and developmental stages examined, with a higher level in the foot than in other tissues and a higher level in the polar body stage and 32-cell stage than in the other stages. Pfigfbp and PfILP (insulin-like peptide) mRNA levels significantly increased in the digestive gland after feeding, while levels were dramatically reduced during a week of food deprivation and increased upon refeeding. In vitro experiments indicated that Pfigfbp mRNA expression in mantle cells was affected by insulin/IGFs (IGF-I, IGF-II). Our data suggests that Pfigfbp may be involved in endocrine signaling in P. fucata via the regulation of insulin-like peptide signaling.
[Mh] Termos MeSH primário: Regulação da Expressão Gênica no Desenvolvimento
Proteínas de Ligação a Fator de Crescimento Semelhante a Insulina/genética
Insulina/genética
Fases de Leitura Aberta
Pinctada/genética
Somatomedinas/genética
[Mh] Termos MeSH secundário: Sequência de Aminoácidos
Animais
Sítios de Ligação
Clonagem Molecular
Ingestão de Alimentos/genética
Escherichia coli/genética
Escherichia coli/metabolismo
Etiquetas de Sequências Expressas/química
Seres Humanos
Insulina/metabolismo
Proteínas de Ligação a Fator de Crescimento Semelhante a Insulina/metabolismo
Especificidade de Órgãos
Pectinidae
Filogenia
Pinctada/classificação
Pinctada/crescimento & desenvolvimento
Pinctada/metabolismo
Ligação Proteica
Domínios e Motivos de Interação entre Proteínas
Proteínas Recombinantes/genética
Proteínas Recombinantes/metabolismo
Alinhamento de Sequência
Homologia de Sequência de Aminoácidos
Transdução de Sinais
Somatomedinas/metabolismo
Inanição/genética
Inanição/metabolismo
Regiões não Traduzidas
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Insulin); 0 (Insulin-Like Growth Factor Binding Proteins); 0 (Recombinant Proteins); 0 (Somatomedins); 0 (Untranslated Regions)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171030
[Lr] Data última revisão:
171030
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170924
[St] Status:MEDLINE


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[PMID]:28886105
[Au] Autor:Fernández-Pérez J; Nantón A; Ruiz-Ruano FJ; Camacho JPM; Méndez J
[Ad] Endereço:Grupo Xenomar, Departamento de Bioloxía, Facultade de Ciencias and CICA (Centro de Investigacións Científicas Avanzadas), Universidade da Coruña, Campus de A Zapateira, A Coruña, Spain.
[Ti] Título:First complete female mitochondrial genome in four bivalve species genus Donax and their phylogenetic relationships within the Veneroida order.
[So] Source:PLoS One;12(9):e0184464, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Four species of the genus Donax (D. semistriatus, D. trunculus, D. variegatus and D. vittatus) are common on Iberian Peninsula coasts. Nevertheless, despite their economic importance and overexploitation, scarce genetic resources are available. In this work, we newly determined the complete mitochondrial genomes of these four representatives of the family Donacidae, with the aim of contributing to unveil phylogenetic relationships within the Veneroida order, and of developing genetic markers being useful in wedge clam identification and authentication, and aquaculture stock management. PRINCIPAL FINDINGS: The complete female mitochondrial genomes of the four species vary in size from 17,044 to 17,365 bp, and encode 13 protein-coding genes (including the atp8 gene), 2 rRNAs and 22 tRNAs, all located on the same strand. A long non-coding region was identified in each of the four Donax species between cob and cox2 genes, presumably corresponding to the Control Region. The Bayesian and Maximum Likelihood phylogenetic analysis of the Veneroida order indicate that all four species of Donax form a single clade as a sister group of other bivalves within the Tellinoidea superfamily. However, although Tellinoidea is actually monophyletic, none of its families are monophyletic. CONCLUSIONS: Sequencing of complete mitochondrial genomes provides highly valuable information to establish the phylogenetic relationships within the Veneroida order. Furthermore, we provide here significant genetic resources for further research and conservation of this commercially important fishing resource.
[Mh] Termos MeSH primário: Bivalves/classificação
Bivalves/genética
Genoma Mitocondrial
Filogenia
[Mh] Termos MeSH secundário: Animais
Biologia Computacional/métodos
Feminino
Ordem dos Genes
Genômica/métodos
Sequenciamento de Nucleotídeos em Larga Escala
Anotação de Sequência Molecular
Fases de Leitura Aberta
RNA Ribossômico/genética
RNA de Transferência/genética
Regiões não Traduzidas
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (RNA, Ribosomal); 0 (Untranslated Regions); 9014-25-9 (RNA, Transfer)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171018
[Lr] Data última revisão:
171018
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170909
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0184464


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[PMID]:28229978
[Au] Autor:Rao SJ; Chatterjee S; Pal JK
[Ad] Endereço:Cell and Molecular Biology Laboratory, Department of Biotechnology, Savitribai Phule Pune University, Pune 411 007, India.
[Ti] Título:Untranslated regions of mRNA and their role in regulation of gene expression in protozoan parasites.
[So] Source:J Biosci;42(1):189-207, 2017 Mar.
[Is] ISSN:0973-7138
[Cp] País de publicação:India
[La] Idioma:eng
[Ab] Resumo:Protozoan parasites are one of the oldest living entities in this world that throughout their existence have shown excellent resilience to the odds of survival and have adapted beautifully to ever changing rigors of the environment. In view of the dynamic environment encountered by them throughout their life cycle, and in establishing pathogenesis, it is unsurprising that modulation of gene expression plays a fundamental role in their survival. In higher eukaryotes, untranslated regions (UTRs) of transcripts are one of the crucial regulators of gene expression (influencing mRNA stability and translation efficiency). Parasitic protozoan genome studies have led to the characterization (in silico, in vitro and in vivo) of a large number of their genes. Comparison of higher eukaryotic UTRs with parasitic protozoan UTRs reveals the existence of several similar and dissimilar facets of the UTRs. This review focuses on the elements of UTRs of medically important protozoan parasites and their regulatory role in gene expression. Such information may be useful to researchers in designing gene targeting strategies linked with perturbation of host-parasite relationships leading to control of specific parasites.
[Mh] Termos MeSH primário: Eucariotos/genética
Biossíntese de Proteínas/genética
Proteínas de Protozoários/biossíntese
Regiões não Traduzidas/genética
[Mh] Termos MeSH secundário: Animais
Regulação da Expressão Gênica/genética
Interações Hospedeiro-Parasita/genética
Parasitos/genética
Parasitos/patogenicidade
Proteínas de Protozoários/genética
Estabilidade de RNA
RNA Mensageiro/biossíntese
RNA Mensageiro/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Nm] Nome de substância:
0 (Protozoan Proteins); 0 (RNA, Messenger); 0 (Untranslated Regions)
[Em] Mês de entrada:1703
[Cu] Atualização por classe:171108
[Lr] Data última revisão:
171108
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170224
[St] Status:MEDLINE


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[PMID]:28143396
[Au] Autor:Zafrir Z; Tuller T
[Ad] Endereço:Department of Biomedical Engineering, Tel Aviv University, P.O. Box 39040, Tel Aviv, 6997801, Israel.
[Ti] Título:Unsupervised detection of regulatory gene expression information in different genomic regions enables gene expression ranking.
[So] Source:BMC Bioinformatics;18(1):77, 2017 Feb 01.
[Is] ISSN:1471-2105
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: The regulation of all gene expression steps (e.g., Transcription, RNA processing, Translation, and mRNA Degradation) is known to be primarily encoded in different parts of genes and in genomic regions in proximity to genes (e.g., promoters, untranslated regions, coding regions, introns, etc.). However, the entire gene expression codes and the genomic regions where they are encoded are still unknown. RESULTS: Here, we employ an unsupervised approach to estimate the concentration of gene expression codes in different non-coding parts of genes and transcripts, such as introns and untranslated regions, focusing on three model organisms (Escherichia coli, Saccharomyces cerevisiae, and Schizosaccharomyces pombe). Our analyses support the conjecture that regions adjacent to the beginning and end of ORFs and the beginning and end of introns tend to include higher concentration of gene expression information relatively to regions further away. In addition, we report the exact regions with elevated concentration of gene expression codes. Furthermore, we demonstrate that the concentration of these codes in different genetic regions is correlated with the expression levels of the corresponding genes, and with splicing efficiency measurements and meiotic stage gene expression measurements in S. cerevisiae. CONCLUSION: We suggest that these discoveries improve our understanding of gene expression regulation and evolution; they can also be used for developing improved models of genome/gene evolution and for engineering gene expression in various biotechnological and synthetic biology applications.
[Mh] Termos MeSH primário: Algoritmos
Escherichia coli/genética
Regulação da Expressão Gênica
Saccharomyces cerevisiae/genética
Schizosaccharomyces/genética
[Mh] Termos MeSH secundário: Íntrons
Fases de Leitura Aberta/genética
RNA Mensageiro/genética
RNA Mensageiro/metabolismo
Regiões não Traduzidas
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (RNA, Messenger); 0 (Untranslated Regions)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170823
[Lr] Data última revisão:
170823
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170202
[St] Status:MEDLINE
[do] DOI:10.1186/s12859-017-1497-z


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[PMID]:28100260
[Au] Autor:Liang S; Tippens ND; Zhou Y; Mort M; Stenson PD; Cooper DN; Yu H
[Ad] Endereço:Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, 14853, USA.
[Ti] Título:iRegNet3D: three-dimensional integrated regulatory network for the genomic analysis of coding and non-coding disease mutations.
[So] Source:Genome Biol;18(1):10, 2017 Jan 18.
[Is] ISSN:1474-760X
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:The mechanistic details of most disease-causing mutations remain poorly explored within the context of regulatory networks. We present a high-resolution three-dimensional integrated regulatory network (iRegNet3D) in the form of a web tool, where we resolve the interfaces of all known transcription factor (TF)-TF, TF-DNA and chromatin-chromatin interactions for the analysis of both coding and non-coding disease-associated mutations to obtain mechanistic insights into their functional impact. Using iRegNet3D, we find that disease-associated mutations may perturb the regulatory network through diverse mechanisms including chromatin looping. iRegNet3D promises to be an indispensable tool in large-scale sequencing and disease association studies.
[Mh] Termos MeSH primário: Redes Reguladoras de Genes
Predisposição Genética para Doença
Estudo de Associação Genômica Ampla/métodos
Genômica/métodos
Modelos Moleculares
Mutação
Relação Quantitativa Estrutura-Atividade
[Mh] Termos MeSH secundário: Sítios de Ligação
Cromatina/genética
Cromatina/metabolismo
DNA/química
DNA/metabolismo
Proteínas de Ligação a DNA/química
Proteínas de Ligação a DNA/metabolismo
Epistasia Genética
Regulação da Expressão Gênica
Seres Humanos
Motivos de Nucleotídeos
Fases de Leitura Aberta
Fatores de Transcrição/química
Fatores de Transcrição/metabolismo
Regiões não Traduzidas
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Chromatin); 0 (DNA-Binding Proteins); 0 (Transcription Factors); 0 (Untranslated Regions); 9007-49-2 (DNA)
[Em] Mês de entrada:1707
[Cu] Atualização por classe:170707
[Lr] Data última revisão:
170707
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170120
[St] Status:MEDLINE
[do] DOI:10.1186/s13059-016-1138-2


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[PMID]:28082390
[Au] Autor:Le Rhun A; Lécrivain AL; Reimegård J; Proux-Wéra E; Broglia L; Della Beffa C; Charpentier E
[Ad] Endereço:The Laboratory for Molecular Infection Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, S-90187 Umeå, Sweden.
[Ti] Título:Identification of endoribonuclease specific cleavage positions reveals novel targets of RNase III in Streptococcus pyogenes.
[So] Source:Nucleic Acids Res;45(5):2329-2340, 2017 Mar 17.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:A better understanding of transcriptional and post-transcriptional regulation of gene expression in bacteria relies on studying their transcriptome. RNA sequencing methods are used not only to assess RNA abundance but also the exact boundaries of primary and processed transcripts. Here, we developed a method, called identification of specific cleavage position (ISCP), which enables the identification of direct endoribonuclease targets in vivo by comparing the 5΄ and 3΄ ends of processed transcripts between wild type and RNase deficient strains. To demonstrate the ISCP method, we used as a model the double-stranded specific RNase III in the human pathogen Streptococcus pyogenes. We mapped 92 specific cleavage positions (SCPs) among which, 48 were previously described and 44 are new, with the characteristic 2 nucleotides 3΄ overhang of RNase III. Most SCPs were located in untranslated regions of RNAs. We screened for RNase III targets using transcriptomic differential expression analysis (DEA) and compared those with the RNase III targets identified using the ISCP method. Our study shows that in S. pyogenes, under standard growth conditions, RNase III has a limited impact both on antisense transcripts and on global gene expression with the expression of most of the affected genes being downregulated in an RNase III deletion mutant.
[Mh] Termos MeSH primário: Regulação Bacteriana da Expressão Gênica
RNA Antissenso/genética
RNA Bacteriano/genética
Ribonuclease III/genética
Streptococcus pyogenes/genética
[Mh] Termos MeSH secundário: Proteínas de Bactérias
Pareamento de Bases
Sequência de Bases
Deleção de Genes
Conformação de Ácido Nucleico
Clivagem do RNA
RNA Antissenso/metabolismo
RNA Mensageiro/genética
RNA Mensageiro/metabolismo
Ribonuclease III/deficiência
Streptococcus pyogenes/metabolismo
Transcriptoma
Regiões não Traduzidas
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Bacterial Proteins); 0 (RNA, Antisense); 0 (RNA, Bacterial); 0 (RNA, Messenger); 0 (Untranslated Regions); EC 3.1.26.3 (Ribonuclease III)
[Em] Mês de entrada:1707
[Cu] Atualização por classe:170718
[Lr] Data última revisão:
170718
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170114
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkw1316


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[PMID]:28077174
[Au] Autor:Geuens T; De Winter V; Rajan N; Achsel T; Mateiu L; Almeida-Souza L; Asselbergh B; Bouhy D; Auer-Grumbach M; Bagni C; Timmerman V
[Ad] Endereço:Peripheral Neuropathy Group, Department of Molecular Genetics, VIB, Institute Born Bunge and University of Antwerp, Antwerpen, Belgium.
[Ti] Título:Mutant HSPB1 causes loss of translational repression by binding to PCBP1, an RNA binding protein with a possible role in neurodegenerative disease.
[So] Source:Acta Neuropathol Commun;5(1):5, 2017 Jan 11.
[Is] ISSN:2051-5960
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:The small heat shock protein HSPB1 (Hsp27) is an ubiquitously expressed molecular chaperone able to regulate various cellular functions like actin dynamics, oxidative stress regulation and anti-apoptosis. So far disease causing mutations in HSPB1 have been associated with neurodegenerative diseases such as distal hereditary motor neuropathy, Charcot-Marie-Tooth disease and amyotrophic lateral sclerosis. Most mutations in HSPB1 target its highly conserved α-crystallin domain, while other mutations affect the C- or N-terminal regions or its promotor. Mutations inside the α-crystallin domain have been shown to enhance the chaperone activity of HSPB1 and increase the binding to client proteins. However, the HSPB1-P182L mutation, located outside and downstream of the α-crystallin domain, behaves differently. This specific HSPB1 mutation results in a severe neuropathy phenotype affecting exclusively the motor neurons of the peripheral nervous system. We identified that the HSPB1-P182L mutant protein has a specifically increased interaction with the RNA binding protein poly(C)binding protein 1 (PCBP1) and results in a reduction of its translational repressive activity. RNA immunoprecipitation followed by RNA sequencing on mouse brain lead to the identification of PCBP1 mRNA targets. These targets contain larger 3'- and 5'-UTRs than average and are enriched in an RNA motif consisting of the CTCCTCCTCCTCC consensus sequence. Interestingly, next to the clear presence of neuronal transcripts among the identified PCBP1 targets we identified known genes associated with hereditary peripheral neuropathies and hereditary spastic paraplegias. We therefore conclude that HSPB1 can mediate translational repression through interaction with an RNA binding protein further supporting its role in neurodegenerative disease.
[Mh] Termos MeSH primário: Proteínas de Transporte/metabolismo
Proteínas de Choque Térmico HSP27/metabolismo
Proteínas de Choque Térmico/metabolismo
Ribonucleoproteínas Nucleares Heterogêneas/metabolismo
Proteínas de Neoplasias/metabolismo
[Mh] Termos MeSH secundário: Animais
Encéfalo/metabolismo
Proteínas de Transporte/genética
Doença de Charcot-Marie-Tooth/genética
Doença de Charcot-Marie-Tooth/metabolismo
Sequência Consenso
Fibroblastos/metabolismo
Regulação da Expressão Gênica/fisiologia
Células HEK293
Proteínas de Choque Térmico HSP27/genética
Células HeLa
Proteínas de Choque Térmico/genética
Ribonucleoproteínas Nucleares Heterogêneas/genética
Seres Humanos
Camundongos
Proteínas Mutantes/genética
Proteínas Mutantes/metabolismo
Mutação
Proteínas de Neoplasias/genética
Ligação Proteica
Biossíntese de Proteínas/fisiologia
RNA Mensageiro/genética
RNA Mensageiro/metabolismo
Regiões não Traduzidas
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Carrier Proteins); 0 (HSP27 Heat-Shock Proteins); 0 (HSPB1 protein, human); 0 (Heat-Shock Proteins); 0 (Heterogeneous-Nuclear Ribonucleoproteins); 0 (Hspb1 protein, mouse); 0 (Mutant Proteins); 0 (Neoplasm Proteins); 0 (PCBP1 protein, human); 0 (Pcbp1 protein, mouse); 0 (RNA, Messenger); 0 (Untranslated Regions)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171025
[Lr] Data última revisão:
171025
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170113
[St] Status:MEDLINE
[do] DOI:10.1186/s40478-016-0407-3


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[PMID]:28056774
[Au] Autor:Piraino SW; Furney SJ
[Ad] Endereço:School of Biomolecular and Biomedical Science, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.
[Ti] Título:Identification of coding and non-coding mutational hotspots in cancer genomes.
[So] Source:BMC Genomics;18(1):17, 2017 01 05.
[Is] ISSN:1471-2164
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: The identification of mutations that play a causal role in tumour development, so called "driver" mutations, is of critical importance for understanding how cancers form and how they might be treated. Several large cancer sequencing projects have identified genes that are recurrently mutated in cancer patients, suggesting a role in tumourigenesis. While the landscape of coding drivers has been extensively studied and many of the most prominent driver genes are well characterised, comparatively less is known about the role of mutations in the non-coding regions of the genome in cancer development. The continuing fall in genome sequencing costs has resulted in a concomitant increase in the number of cancer whole genome sequences being produced, facilitating systematic interrogation of both the coding and non-coding regions of cancer genomes. RESULTS: To examine the mutational landscapes of tumour genomes we have developed a novel method to identify mutational hotspots in tumour genomes using both mutational data and information on evolutionary conservation. We have applied our methodology to over 1300 whole cancer genomes and show that it identifies prominent coding and non-coding regions that are known or highly suspected to play a role in cancer. Importantly, we applied our method to the entire genome, rather than relying on predefined annotations (e.g. promoter regions) and we highlight recurrently mutated regions that may have resulted from increased exposure to mutational processes rather than selection, some of which have been identified previously as targets of selection. Finally, we implicate several pan-cancer and cancer-specific candidate non-coding regions, which could be involved in tumourigenesis. CONCLUSIONS: We have developed a framework to identify mutational hotspots in cancer genomes, which is applicable to the entire genome. This framework identifies known and novel coding and non-coding mutional hotspots and can be used to differentiate candidate driver regions from likely passenger regions susceptible to somatic mutation.
[Mh] Termos MeSH primário: Genoma Humano
Genômica
Mutação
Neoplasias/genética
Fases de Leitura Aberta
Regiões não Traduzidas
[Mh] Termos MeSH secundário: Sítios de Ligação
Fator de Ligação a CCCTC
Análise Mutacional de DNA
Genômica/métodos
Seres Humanos
Neoplasias/metabolismo
Proteínas Repressoras/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (CCCTC-Binding Factor); 0 (CTCF protein, human); 0 (Repressor Proteins); 0 (Untranslated Regions)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:171120
[Lr] Data última revisão:
171120
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170107
[St] Status:MEDLINE
[do] DOI:10.1186/s12864-016-3420-9



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