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  1 / 1046 MEDLINE  
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[PMID]:28741379
[Au] Autor:Choi JW; Um JH; Cho JH; Lee HJ
[Ad] Endereço:1 Department of Microbiology and Immunology, Kyungpook National University School of Dentistry, Daegu 41940, Korea.
[Ti] Título:Tiny RNAs and their voyage via extracellular vesicles: Secretion of bacterial small RNA and eukaryotic microRNA.
[So] Source:Exp Biol Med (Maywood);242(15):1475-1481, 2017 09.
[Is] ISSN:1535-3699
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:MicroRNAs are small non-coding RNAs that bind to the 3'-untranslated region of target mRNAs and have transcriptional or translational inhibitory function in eukaryotes. Before microRNAs were widely known, bacterial non-coding small RNAs around 50-200 nt in length were discovered whose mechanism of action resembled that of microRNAs. Recently, RNAs that are of similar size to or smaller than microRNAs have been discovered in bacteria and indeed, this class of small RNAs have been found throughout all domains of life. Moreover, recent findings suggest that these tiny RNAs can be released via extracellular vesicles (such as exosomes in eukaryotes and outer membrane vesicles in bacteria), which in turn heralds a new field of research, interkingdom communication. This review discusses two similar classes of small RNAs in evolutionarily distinct eukaryotes and bacteria. In addition to their biogenesis and regulation, we discuss small RNA vehicles and their secretion. Impact statement The possible endogenous functions of small RNAs such as regulatory small RNAs in bacteria and microRNAs in eukaryotes have been extensively studied since they were first discovered. However, their powerful functions should not be seen as limited to their cells of origin. Recently, several papers have demonstrated that small RNAs function as signaling molecules between cells. This is possible because small RNAs can be shuttled around after being incorporated into environmentally protective extracellular vesicles. It is now clearly plausible that secreted small RNAs can regulate other types of cells through biofluids. Given their "common molecule" status, the role of small RNAs in mediating bacteria-human crosstalk is an emerging and competitive area of genetic research. This review provides insight into the function of small RNAs in intercellular and even interkingdom communication.
[Mh] Termos MeSH primário: Vesículas Extracelulares/metabolismo
Pequeno RNA não Traduzido/secreção
[Mh] Termos MeSH secundário: Bactérias/metabolismo
Eucariotos/metabolismo
RNA Bacteriano/secreção
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (RNA, Bacterial); 0 (RNA, Small Untranslated)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:180301
[Lr] Data última revisão:
180301
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170726
[St] Status:MEDLINE
[do] DOI:10.1177/1535370217723166


  2 / 1046 MEDLINE  
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[PMID]:28463242
[Au] Autor:Short AK; Yeshurun S; Powell R; Perreau VM; Fox A; Kim JH; Pang TY; Hannan AJ
[Ad] Endereço:Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, University of Melbourne, Parkville, VIC, Australia.
[Ti] Título:Exercise alters mouse sperm small noncoding RNAs and induces a transgenerational modification of male offspring conditioned fear and anxiety.
[So] Source:Transl Psychiatry;7(5):e1114, 2017 May 02.
[Is] ISSN:2158-3188
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:There is growing evidence that the preconceptual lifestyle and other environmental exposures of a father can significantly alter the physiological and behavioral phenotypes of their children. We and others have shown that paternal preconception stress, regardless of whether the stress was experienced during early-life or adulthood, results in offspring with altered anxiety and depression-related behaviors, attributed to hypothalamic-pituitary-adrenal axis dysregulation. The transgenerational response to paternal preconceptual stress is believed to be mediated by sperm-borne small noncoding RNAs, specifically microRNAs. As physical activity confers physical and mental health benefits for the individual, we used a model of voluntary wheel-running and investigated the transgenerational response to paternal exercise. We found that male offspring of runners had suppressed reinstatement of juvenile fear memory, and reduced anxiety in the light-dark apparatus during adulthood. No changes in these affective behaviors were observed in female offspring. We were surprised to find that running had a limited impact on sperm-borne microRNAs. The levels of three unique microRNAs (miR-19b, miR-455 and miR-133a) were found to be altered in the sperm of runners. In addition, we discovered that the levels of two species of tRNA-derived RNAs (tDRs)-tRNA-Gly and tRNA-Pro-were also altered by running. Taken together, we believe this is the first evidence that paternal exercise is associated with an anxiolytic behavioral phenotype of male offspring and altered levels of small noncoding RNAs in sperm. These small noncoding RNAs are known to have an impact on post-transcriptional gene regulation and can thus change the developmental trajectory of offspring brains and associated affective behaviors.
[Mh] Termos MeSH primário: Ansiedade/genética
Medo/psicologia
Transmissão Vertical de Doença Infecciosa/veterinária
MicroRNAs/genética
Condicionamento Físico Animal/efeitos adversos
Espermatozoides/metabolismo
[Mh] Termos MeSH secundário: Animais
Ansiedade/psicologia
Depressão/genética
Depressão/psicologia
Exposição Ambiental/efeitos adversos
Feminino
Regulação da Expressão Gênica
Sistema Hipotálamo-Hipofisário/fisiopatologia
Masculino
Camundongos
Camundongos Endogâmicos C57BL
Fenótipo
Sistema Hipófise-Suprarrenal/fisiopatologia
Pequeno RNA não Traduzido
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (MicroRNAs); 0 (RNA, Small Untranslated)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180220
[Lr] Data última revisão:
180220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170503
[St] Status:MEDLINE
[do] DOI:10.1038/tp.2017.82


  3 / 1046 MEDLINE  
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[PMID]:28456960
[Au] Autor:García-López J; Larriba E; Del Mazo J
[Ad] Endereço:Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, Madrid 28040, Spain.
[Ti] Título:Detection and Characterization of Small Noncoding RNAs in Mouse Gametes and Embryos Prior to Zygotic Genome Activation.
[So] Source:Methods Mol Biol;1605:105-120, 2017.
[Is] ISSN:1940-6029
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Small noncoding RNAs (ncRNAs) are regulatory elements of gene expression in all cell types and tissues. An ever-increasing number of studies have implicated ncRNAs in differentiation and developmental processes. In mammals, as a consequence of fertilization, the content of ncRNAs in the zygote is mostly the result of the maternal material included on oocytes and the potential sperm-borne paternal contributions. The genetic identity program of any individual is the reprogramming of each parental contribution to the zygotic genome activation. In mouse, this activation occurs at 2-cell stage. In this program of early development the small ncRNAs can play important roles. Here, we describe protocols for collection of oocytes, spermatozoa, and zygotes in mouse, followed by RNA purification to analyze the different types of small ncRNA by next-generation sequencing approaches (NGS). Bioinformatics protocols also describe the methodology able to characterize microRNAs (miRNAs) as the most well-known and widespread regulatory small ncRNA. The comparative analysis allows identifying the changes and background previous to zygotic genome activation.
[Mh] Termos MeSH primário: Oócitos/química
Pequeno RNA não Traduzido/análise
Espermatozoides/química
Zigoto/química
[Mh] Termos MeSH secundário: Animais
Feminino
Regulação da Expressão Gênica no Desenvolvimento
Sequenciamento de Nucleotídeos em Larga Escala
Masculino
Camundongos
Análise de Sequência de RNA
Ativação Transcricional
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (RNA, Small Untranslated)
[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:170501
[St] Status:MEDLINE
[do] DOI:10.1007/978-1-4939-6988-3_7


  4 / 1046 MEDLINE  
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[PMID]:27770368
[Au] Autor:Ilnytskyy S; Bilichak A
[Ad] Endereço:Department of Biological Sciences, University of Lethbridge, 4401 University Drive, Lethbridge, AB, Canada, T1K 3M4. slava.ilyntskyy@uleth.ca.
[Ti] Título:Bioinformatics Analysis of Small RNA Transcriptomes: The Detailed Workflow.
[So] Source:Methods Mol Biol;1456:197-224, 2017.
[Is] ISSN:1940-6029
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Next-generation sequencing became a method of choice for the investigation of small RNA transcriptomes in plants and animals. Although a technical side of sequencing itself is becoming routine, and experimental costs are affordable, data analysis still remains a challenge, especially for researchers with limited computational experience. Here, we present a detailed description of a computational workflow designed to take raw sequencing reads as input, to obtain small RNA predictions, and to detect the differentially expressed microRNAs as a result. The exact commands and pieces of code are provided and hopefully can be adapted and used by other researchers to facilitate the study of small RNA regulation.
[Mh] Termos MeSH primário: Biologia Computacional/métodos
Perfilação da Expressão Gênica
Pequeno RNA não Traduzido/genética
Transcriptoma
[Mh] Termos MeSH secundário: Brassica/genética
Biblioteca Gênica
Genômica/métodos
MicroRNAs/genética
Controle de Qualidade
RNA Interferente Pequeno/genética
Análise de Sequência de RNA
Software
Navegador
Fluxo de Trabalho
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (MicroRNAs); 0 (RNA, Small Interfering); 0 (RNA, Small Untranslated)
[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


  5 / 1046 MEDLINE  
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[PMID]:27770366
[Au] Autor:Tsuzuki M; Watanabe Y
[Ad] Endereço:Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Komaba 3-8-1, Meguro, Tokyo, 153-8902, Japan.
[Ti] Título:Profiling New Small RNA Sequences.
[So] Source:Methods Mol Biol;1456:177-188, 2017.
[Is] ISSN:1940-6029
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Small RNAs are key molecules in RNA silencing pathways that exert the sequence-specific regulation of gene expression and chromatin modifications in many eukaryotes. In plants, endogenous small RNAs, including microRNAs (miRNAs), trans-acting short interfering RNAs (tasiRNAs), and heterochromatic siRNAs (hc-siRNAs), play an important role in switching or orchestrating biological processes during the development and at the onset of stress responses. These endogenous and exogenous small RNAs are mainly 20-24 nucleotides in length. In addition, viral genome-derived siRNAs of similar lengths are produced during viral infection, and they exhibit anti-viral defense activity in RNA silencing pathway.Here, we introduce a method to isolate and characterize small RNA molecules possibly applicable to a wide range of plant resources and tissues. After purification from total RNAs, small RNAs were subjected to Illumina sequencing analysis using compatible reagents kits. Following the sample preparation protocol, small RNAs are ligated first at the 3'- and then at the 5'-end to the respective RNA adapters followed by reverse transcription with a set of primers to produce cDNAs with Index sequences at ends. After PCR amplification, cDNAs are subjected (after gel purification) to RNA-seq analysis. This method could be applied to isolate small RNAs from different sources and characterize small RNA profiles to compare different sets of samples, e.g., wild-type and mutant plants, plants under different stress environments, and virus-infected plants because the starting RNA material is free of contaminated starch or similar material which would block further analysis.
[Mh] Termos MeSH primário: Perfilação da Expressão Gênica
Pequeno RNA não Traduzido/genética
Transcriptoma
[Mh] Termos MeSH secundário: Arabidopsis/genética
Biologia Computacional/métodos
Sequenciamento de Nucleotídeos em Larga Escala
Marchantia/genética
MicroRNAs/genética
RNA de Plantas
RNA Interferente Pequeno/genética
Pequeno RNA não Traduzido/isolamento & purificação
RNA Viral/genética
Reação em Cadeia da Polimerase Via Transcriptase Reversa
Software
Navegador
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (MicroRNAs); 0 (RNA, Plant); 0 (RNA, Small Interfering); 0 (RNA, Small Untranslated); 0 (RNA, Viral)
[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 / 1046 MEDLINE  
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[PMID]:27770367
[Au] Autor:Bilichak A; Golubov A; Kovalchuk I
[Ad] Endereço:Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada.
[Ti] Título:Small RNA Library Preparation and Illumina Sequencing in Plants.
[So] Source:Methods Mol Biol;1456:189-196, 2017.
[Is] ISSN:1940-6029
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The discovery of small RNAs in plants and animals almost two decades ago attracted a significant interest towards epigenetic regulation of gene expression and the practical implementation of the gained knowledge in applied studies. New and sometimes unexpected functions have been ascribed to sRNAs almost every couple of years since their discovery, hence indicating that the complete role of sRNAs in plant and animal physiology is still barely understood. Next-generation sequencing technologies allow to generate high-resolution profiles of sRNAs for the consequent analysis and possibly to discover novel functions of sRNAs. In this chapter, we provide brief guidelines for sRNA library preparation in plants and a practical approach that can be implemented to overcome possible difficulties with sequencing library generation.
[Mh] Termos MeSH primário: Biblioteca Gênica
Sequenciamento de Nucleotídeos em Larga Escala
RNA de Plantas
Pequeno RNA não Traduzido/genética
[Mh] Termos MeSH secundário: Plantas/genética
Análise de Sequência de RNA
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (RNA, Plant); 0 (RNA, Small Untranslated)
[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


  7 / 1046 MEDLINE  
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[PMID]:27770364
[Au] Autor:Blevins T
[Ad] Endereço:Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS) UPR2357, 12 rue du Général Zimmer, Strasbourg Cedex, 67084, USA. todd.blevins@ibmp-cnrs.unistra.fr.
[Ti] Título:Northern Blotting Techniques for Small RNAs.
[So] Source:Methods Mol Biol;1456:141-162, 2017.
[Is] ISSN:1940-6029
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Cells have evolved intricate RNA-directed mechanisms that destroy viruses, silence transposons, and regulate gene expression. These nucleic acid surveillance and gene silencing mechanisms rely upon the selective base-pairing of ~19-25 nt small RNAs to complementary RNA targets. This chapter describes northern blot hybridization techniques for the detection of such small RNAs. Blots spiked with synthetic standards are used to illustrate the detection specificity and sensitivity of DNA oligonucleotide probes. Known endogenous small RNAs are then analyzed in samples prepared from several model plants, including Arabidopsis thaliana, Nicotiana benthamiana, Oryza sativa, Zea mays, and Physcomitrella patens, as well as from the animals Drosophila melanogaster and Mus musculus. Finally, the value of northern blotting for dissecting small RNA biogenesis is shown using an example of virus infection in A. thaliana.
[Mh] Termos MeSH primário: Northern Blotting
Pequeno RNA não Traduzido
[Mh] Termos MeSH secundário: Northern Blotting/métodos
Inativação Gênica
MicroRNAs/genética
Hibridização de Ácido Nucleico/métodos
Interferência de RNA
RNA Interferente Pequeno/genética
Pequeno RNA não Traduzido/isolamento & purificação
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (MicroRNAs); 0 (RNA, Small Interfering); 0 (RNA, Small Untranslated)
[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


  8 / 1046 MEDLINE  
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[PMID]:27770363
[Au] Autor:Boccara M; Sarazin A; Billoud B; Bulski A; Chapell L; Baulcombe D; Colot V
[Ad] Endereço:PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, Ecole NormaleSupérieure, 46 rue d'Ulm, Paris, F75005, France. martine.boccara@upmc.fr.
[Ti] Título:Analysis of Small RNA Populations Using Hybridization to DNA Tiling Arrays.
[So] Source:Methods Mol Biol;1456:127-139, 2017.
[Is] ISSN:1940-6029
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Epigenetic response to stress in plants involves changes in DNA methylation, histone modifications, and expression of small noncoding RNAs (sRNA). Here we present the method of analysis of differential expression of sRNA populations using DNA tiling arrays. sRNA extracted from Arabidopsis thaliana plants exposed to pathogen elicitor or control plants were reverse-transcribed into cDNAs, and subsequently hybridized after labeling to a custom-made DNA tiling array covering Arabidopsis chromosome 4. We first designed a control experiment with eight cDNA clones corresponding to sequences located on chromosome 4 and obtained robust and specific hybridization signals. Furthermore, hybridization signals along chromosome 4 were in good agreement with sRNA abundance as previously determined by massive parallel sequence signature (MPSS) in the case of untreated plants, but differed substantially after stress treatment. These results demonstrate the utility of hybridization to DNA tiling arrays to detect major changes in sRNA abundance.
[Mh] Termos MeSH primário: Perfilação da Expressão Gênica/métodos
Hibridização de Ácido Nucleico/métodos
Análise de Sequência com Séries de Oligonucleotídeos/métodos
Pequeno RNA não Traduzido/genética
[Mh] Termos MeSH secundário: Arabidopsis/genética
Biblioteca Gênica
Reprodutibilidade dos Testes
Estresse Fisiológico/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (RNA, Small Untranslated)
[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


  9 / 1046 MEDLINE  
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[PMID]:29215635
[Au] Autor:Melamed S; Faigenbaum-Romm R; Peer A; Reiss N; Shechter O; Bar A; Altuvia Y; Argaman L; Margalit H
[Ad] Endereço:Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
[Ti] Título:Mapping the small RNA interactome in bacteria using RIL-seq.
[So] Source:Nat Protoc;13(1):1-33, 2018 Jan.
[Is] ISSN:1750-2799
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Small RNAs (sRNAs) are major post-transcriptional regulators of gene expression in bacteria. To enable transcriptome-wide mapping of bacterial sRNA-target pairs, we developed RIL-seq (RNA interaction by ligation and sequencing). RIL-seq is an experimental-computational methodology for capturing sRNA-target interactions in vivo that takes advantage of the mutual binding of the sRNA and target RNA molecules to the RNA chaperone protein Hfq. The experimental part of the protocol involves co-immunoprecipitation of Hfq and bound RNAs, ligation of RNAs, library preparation and sequencing. The computational pipeline maps the sequenced fragments to the genome, reveals chimeric fragments (fragments comprising two ligated independent fragments) and determines statistically significant overrepresented chimeric fragments as interacting RNAs. The statistical filter is aimed at reducing the number of spurious interactions resulting from ligation of random neighboring RNA fragments, thus increasing the reliability of the determined sRNA-target pairs. A major advantage of RIL-seq is that it does not require overexpression of sRNAs; instead, it simultaneously captures the in vivo targets of all sRNAs in the native state of the cell. Application of RIL-seq to bacteria grown under different conditions provides distinctive snapshots of the sRNA interactome and sheds light on the dynamics and rewiring of the post-transcriptional regulatory network. As RIL-seq needs no prior information about the sRNA and target sequences, it can identify novel sRNAs, along with their targets. It can be adapted to detect protein-mediated RNA-RNA interactions in any bacterium with a sequenced genome. The experimental part of the RIL-seq protocol takes 7-9 d and the computational analysis takes ∼2 d.
[Mh] Termos MeSH primário: Mapeamento Cromossômico/métodos
Sequenciamento de Nucleotídeos em Larga Escala/métodos
RNA Bacteriano/genética
Pequeno RNA não Traduzido/genética
Análise de Sequência de RNA/métodos
Transcriptoma/genética
[Mh] Termos MeSH secundário: Genoma Bacteriano
Genômica
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (RNA, Bacterial); 0 (RNA, Small Untranslated)
[Em] Mês de entrada:1712
[Cu] Atualização por classe:171220
[Lr] Data última revisão:
171220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171208
[St] Status:MEDLINE
[do] DOI:10.1038/nprot.2017.115


  10 / 1046 MEDLINE  
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[PMID]:29184180
[Au] Autor:Storici F; Tichon AE
[Ad] Endereço:School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.
[Ti] Título:RNA takes over control of DNA break repair.
[So] Source:Nat Cell Biol;19(12):1382-1384, 2017 Nov 29.
[Is] ISSN:1476-4679
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Small RNAs generated at DNA break sites are implicated in mammalian DNA repair. Now, a study shows that following the formation of DNA double-strand breaks, bidirectional transcription events adjacent to the break generate small RNAs that trigger the DNA damage response by local RNA:RNA interactions.
[Mh] Termos MeSH primário: Quebras de DNA de Cadeia Dupla
Reparo do DNA
RNA/genética
RNA/metabolismo
[Mh] Termos MeSH secundário: Animais
Modelos Biológicos
RNA Polimerase II/metabolismo
RNA Longo não Codificante/genética
RNA Longo não Codificante/metabolismo
Pequeno RNA não Traduzido/genética
Pequeno RNA não Traduzido/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (RNA, Long Noncoding); 0 (RNA, Small Untranslated); 63231-63-0 (RNA); EC 2.7.7.- (RNA Polymerase II)
[Em] Mês de entrada:1712
[Cu] Atualização por classe:171219
[Lr] Data última revisão:
171219
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171130
[St] Status:MEDLINE
[do] DOI:10.1038/ncb3645



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