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[PMID]:28460090
[Au] Autor:Liu Q; Wang J; Zhao Y; Li CI; Stengel KR; Acharya P; Johnston G; Hiebert SW; Shyr Y
[Ad] Endereço:Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
[Ti] Título:Identification of active miRNA promoters from nuclear run-on RNA sequencing.
[So] Source:Nucleic Acids Res;45(13):e121, 2017 Jul 27.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:The genome-wide identification of microRNA transcription start sites (miRNA TSSs) is essential for understanding how miRNAs are regulated in development and disease. In this study, we developed mirSTP (mirna transcription Start sites Tracking Program), a probabilistic model for identifying active miRNA TSSs from nascent transcriptomes generated by global run-on sequencing (GRO-seq) and precision run-on sequencing (PRO-seq). MirSTP takes advantage of characteristic bidirectional transcription signatures at active TSSs in GRO/PRO-seq data, and provides accurate TSS prediction for human intergenic miRNAs at a high resolution. MirSTP performed better than existing generalized and experiment specific methods, in terms of the enrichment of various promoter-associated marks. MirSTP analysis of 27 human cell lines in 183 GRO-seq and 28 PRO-seq experiments identified TSSs for 480 intergenic miRNAs, indicating a wide usage of alternative TSSs. By integrating predicted miRNA TSSs with matched ENCODE transcription factor (TF) ChIP-seq data, we connected miRNAs into the transcriptional circuitry, which provides a valuable source for understanding the complex interplay between TF and miRNA. With mirSTP, we not only predicted TSSs for 72 miRNAs, but also identified 12 primary miRNAs with significant RNA polymerase pausing alterations after JQ1 treatment; each miRNA was further validated through BRD4 binding to its predicted promoter. MirSTP is available at http://bioinfo.vanderbilt.edu/mirSTP/.
[Mh] Termos MeSH primário: MicroRNAs/genética
Regiões Promotoras Genéticas
Análise de Sequência de RNA/métodos
[Mh] Termos MeSH secundário: Algoritmos
Linhagem Celular
DNA Intergênico/genética
Sequenciamento de Nucleotídeos em Larga Escala/métodos
Sequenciamento de Nucleotídeos em Larga Escala/estatística & dados numéricos
Seres Humanos
MicroRNAs/metabolismo
Modelos Estatísticos
RNA Nuclear/genética
RNA Nuclear/metabolismo
Análise de Sequência de RNA/estatística & dados numéricos
Software
Sítio de Iniciação de Transcrição
[Pt] Tipo de publicação:COMPARATIVE STUDY; JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Intergenic); 0 (MicroRNAs); 0 (RNA, Nuclear)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:180228
[Lr] Data última revisão:
180228
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170502
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkx318


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[PMID]:28886202
[Au] Autor:Mootha VV; Hansen B; Rong Z; Mammen PP; Zhou Z; Xing C; Gong X
[Ad] Endereço:Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, Texas, United States.
[Ti] Título:Fuchs' Endothelial Corneal Dystrophy and RNA Foci in Patients With Myotonic Dystrophy.
[So] Source:Invest Ophthalmol Vis Sci;58(11):4579-4585, 2017 Sep 01.
[Is] ISSN:1552-5783
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Purpose: The most common cause of Fuchs' endothelial corneal dystrophy (FECD) is an intronic CTG repeat expansion in TCF4. Expanded CUG repeat RNA colocalize with splicing factor, muscleblind-like 1 (MBNL1), in nuclear foci in endothelium as a molecular hallmark. Myotonic dystrophy type 1 (DM1) is a neuromuscular disorder caused by a CTG repeat expansion in the 3'-untranslated region (UTR) of DMPK. In this study, we examine for RNA-MBNL1 foci in endothelial cells of FECD subjects with DM1, test the hypothesis that DM1 patients are at risk for FECD, and determine prevalence of TCF4 and DMPK expansions in a FECD cohort. Methods: Using FISH, we examined for nuclear RNA-MBNL1 foci in endothelial cells from FECD subjects with DM1. We examined 13 consecutive unrelated DM1 patients for FECD using slit-lamp and specular microscopy. We genotyped TCF4 and DMPK repeat polymorphisms in a FECD cohort of 317 probands using short-tandem repeat and triplet repeat-primed PCR assays. Results: We detected abundant nuclear RNA foci colocalizing with MBNL1 in endothelial cells of FECD subjects with DM1. Six of thirteen DM1 patients (46%) had slit-lamp and specular microscopic findings of FECD, compared to 4% disease prevalence (P = 5.5 × 10-6). As expected, 222 out of 317 (70%) FECD probands harbored TCF4 expansion, while one subject harbored DMPK expansion without prior diagnosis of DM1. Conclusions: Our work suggests that DM1 patients are at risk for FECD. DMPK mutations contribute to the genetic burden of FECD but are uncommon. We establish a connection between two repeat expansion disorders converging upon RNA-MBNL1 foci and FECD.
[Mh] Termos MeSH primário: Fatores de Transcrição de Zíper de Leucina e Hélice-Alça-Hélix Básicos/genética
Distrofia Endotelial de Fuchs/genética
Distrofia Miotônica/genética
Miotonina Proteína Quinase/genética
RNA Nuclear
Proteínas de Ligação a RNA/genética
Fatores de Transcrição/genética
[Mh] Termos MeSH secundário: Adulto
Idoso
Epitélio Posterior/metabolismo
Epitélio Posterior/patologia
Feminino
Distrofia Endotelial de Fuchs/patologia
Técnicas de Genotipagem
Seres Humanos
Hibridização in Situ Fluorescente
Masculino
Meia-Idade
Distrofia Miotônica/patologia
Reação em Cadeia da Polimerase
Processamento de RNA
Lâmpada de Fenda
Fator de Transcrição 4
Expansão das Repetições de Trinucleotídeos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Basic Helix-Loop-Helix Leucine Zipper Transcription Factors); 0 (DMPK protein, human); 0 (MBNL1 protein, human); 0 (RNA, Nuclear); 0 (RNA-Binding Proteins); 0 (TCF4 protein, human); 0 (Transcription Factor 4); 0 (Transcription Factors); EC 2.7.11.1 (Myotonin-Protein Kinase)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:171116
[Lr] Data última revisão:
171116
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170909
[St] Status:MEDLINE
[do] DOI:10.1167/iovs.17-22350


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[PMID]:28801509
[Au] Autor:Fan J; Kuai B; Wu G; Wu X; Chi B; Wang L; Wang K; Shi Z; Zhang H; Chen S; He Z; Wang S; Zhou Z; Li G; Cheng H
[Ad] Endereço:State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
[Ti] Título:Exosome cofactor hMTR4 competes with export adaptor ALYREF to ensure balanced nuclear RNA pools for degradation and export.
[So] Source:EMBO J;36(19):2870-2886, 2017 Oct 02.
[Is] ISSN:1460-2075
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:The exosome is a key RNA machine that functions in the degradation of unwanted RNAs. Here, we found that significant fractions of precursors and mature forms of mRNAs and long noncoding RNAs are degraded by the nuclear exosome in normal human cells. Exosome-mediated degradation of these RNAs requires its cofactor hMTR4. Significantly, hMTR4 plays a key role in specifically recruiting the exosome to its targets. Furthermore, we provide several lines of evidence indicating that hMTR4 executes this role by directly competing with the mRNA export adaptor ALYREF for associating with ARS2, a component of the cap-binding complex (CBC), and this competition is critical for determining whether an RNA is degraded or exported to the cytoplasm. Together, our results indicate that the competition between hMTR4 and ALYREF determines exosome recruitment and functions in creating balanced nuclear RNA pools for degradation and export.
[Mh] Termos MeSH primário: Proteínas Nucleares/metabolismo
RNA Helicases/metabolismo
Estabilidade de RNA
Transporte de RNA/genética
RNA Nuclear/metabolismo
Proteínas de Ligação a RNA/metabolismo
Fatores de Transcrição/metabolismo
[Mh] Termos MeSH secundário: Transporte Ativo do Núcleo Celular/genética
Complexo Multienzimático de Ribonucleases do Exossomo/genética
Complexo Multienzimático de Ribonucleases do Exossomo/metabolismo
Exossomos/genética
Exossomos/metabolismo
Técnicas de Silenciamento de Genes
Células HEK293
Células HeLa
Seres Humanos
Proteínas Nucleares/genética
Ligação Proteica
RNA Helicases/genética
Estabilidade de RNA/genética
RNA Longo não Codificante/metabolismo
RNA Mensageiro/metabolismo
Proteínas de Ligação a RNA/genética
Fatores de Transcrição/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (ALYREF protein, human); 0 (Nuclear Proteins); 0 (RNA, Long Noncoding); 0 (RNA, Messenger); 0 (RNA, Nuclear); 0 (RNA-Binding Proteins); 0 (Transcription Factors); EC 3.1.- (Exosome Multienzyme Ribonuclease Complex); EC 3.6.1.- (SKIV2L2 protein, human); EC 3.6.4.13 (RNA Helicases)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171013
[Lr] Data última revisão:
171013
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170813
[St] Status:MEDLINE
[do] DOI:10.15252/embj.201696139


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[PMID]:28383682
[Au] Autor:Sztuba-Solinska J; Rausch JW; Smith R; Miller JT; Whitby D; Le Grice SFJ
[Ad] Endereço:Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
[Ti] Título:Kaposi's sarcoma-associated herpesvirus polyadenylated nuclear RNA: a structural scaffold for nuclear, cytoplasmic and viral proteins.
[So] Source:Nucleic Acids Res;45(11):6805-6821, 2017 Jun 20.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Kaposi's sarcoma-associated herpes virus (KSHV) polyadenylated nuclear (PAN) RNA facilitates lytic infection, modulating the cellular immune response by interacting with viral and cellular proteins and DNA. Although a number nucleoprotein interactions involving PAN have been implicated, our understanding of binding partners and PAN RNA binding motifs remains incomplete. Herein, we used SHAPE-mutational profiling (SHAPE-MaP) to probe PAN in its nuclear, cytoplasmic or viral environments or following cell/virion lysis and removal of proteins. We thus characterized and put into context discrete RNA structural elements, including the cis-acting Mta responsive element and expression and nuclear retention element (1,2). By comparing mutational profiles in different biological contexts, we identified sites on PAN either protected from chemical modification by protein binding or characterized by a loss of structure. While some protein binding sites were selectively localized, others were occupied in all three biological contexts. Individual binding sites of select KSHV gene products on PAN RNA were also identified in in vitro experiments. This work constitutes the most extensive structural characterization of a viral lncRNA and interactions with its protein partners in discrete biological contexts, providing a broad framework for understanding the roles of PAN RNA in KSHV infection.
[Mh] Termos MeSH primário: Herpesvirus Humano 8/genética
RNA Mensageiro/metabolismo
RNA Nuclear/metabolismo
RNA Viral/metabolismo
[Mh] Termos MeSH secundário: Sítios de Ligação
Núcleo Celular/metabolismo
Núcleo Celular/virologia
Citoplasma/metabolismo
Citoplasma/virologia
Herpesvirus Humano 8/metabolismo
Seres Humanos
Sequências Repetidas Invertidas
Proteínas Nucleares/metabolismo
Conformação de Ácido Nucleico
Fases de Leitura Aberta
Polimorfismo de Nucleotídeo Único
Ligação Proteica
RNA Mensageiro/genética
RNA Nuclear/genética
RNA Viral/genética
Células Tumorais Cultivadas
Proteínas Virais/genética
Proteínas Virais/metabolismo
Replicação Viral
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Nuclear Proteins); 0 (RNA, Messenger); 0 (RNA, Nuclear); 0 (RNA, Viral); 0 (Viral Proteins)
[Em] Mês de entrada:1711
[Cu] Atualização por classe:171107
[Lr] Data última revisão:
171107
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170407
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkx241


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[PMID]:28190770
[Au] Autor:Bresson S; Tuck A; Staneva D; Tollervey D
[Ad] Endereço:Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, King's Buildings, Edinburgh EH9 3BF, Scotland.
[Ti] Título:Nuclear RNA Decay Pathways Aid Rapid Remodeling of Gene Expression in Yeast.
[So] Source:Mol Cell;65(5):787-800.e5, 2017 Mar 02.
[Is] ISSN:1097-4164
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:In budding yeast, the nuclear RNA surveillance system is active on all pre-mRNA transcripts and modulated by nutrient availability. To test the role of nuclear surveillance in reprogramming gene expression, we identified transcriptome-wide binding sites for RNA polymerase II and the exosome cofactors Mtr4 (TRAMP complex) and Nab3 (NNS complex) by UV crosslinking immediately following glucose withdrawal (0, 4, and 8 min). In glucose, mRNA binding by Nab3 and Mtr4 was mainly restricted to promoter-proximal sites, reflecting early transcription termination. Following glucose withdrawal, many growth-related mRNAs showed reduced transcription but increased Nab3 binding, accompanied by downstream recruitment of Mtr4, and oligo(A) tailing. We conclude that transcription termination is followed by TRAMP-mediated RNA decay. Upregulated transcripts evaded increased surveillance factor binding following glucose withdrawal. Some upregulated genes showed use of alternative transcription starts to bypass strong NNS binding sites. We conclude that nuclear surveillance pathways regulate both positive and negative responses to glucose availability.
[Mh] Termos MeSH primário: Núcleo Celular/metabolismo
Regulação Fúngica da Expressão Gênica
Processamento Pós-Transcricional do RNA
Estabilidade de RNA
RNA Fúngico/metabolismo
RNA Mensageiro/metabolismo
RNA Nuclear/metabolismo
Saccharomyces cerevisiae/metabolismo
Transcrição Genética
[Mh] Termos MeSH secundário: Adaptação Fisiológica
Sítios de Ligação
RNA Helicases DEAD-box/genética
RNA Helicases DEAD-box/metabolismo
Glucose/deficiência
Glucose/metabolismo
Proteínas Nucleares/genética
Proteínas Nucleares/metabolismo
Ligação Proteica
RNA Polimerase II/genética
RNA Polimerase II/metabolismo
RNA Fúngico/genética
RNA Mensageiro/genética
RNA Nuclear/genética
Proteínas de Ligação a RNA/genética
Proteínas de Ligação a RNA/metabolismo
Saccharomyces cerevisiae/genética
Proteínas de Saccharomyces cerevisiae/genética
Proteínas de Saccharomyces cerevisiae/metabolismo
Fatores de Tempo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (NAB3 protein, S cerevisiae); 0 (Nuclear Proteins); 0 (RNA, Fungal); 0 (RNA, Messenger); 0 (RNA, Nuclear); 0 (RNA-Binding Proteins); 0 (Saccharomyces cerevisiae Proteins); EC 2.7.7.- (RNA Polymerase II); EC 3.6.1.- (MTR4 protein, S cerevisiae); EC 3.6.4.13 (DEAD-box RNA Helicases); IY9XDZ35W2 (Glucose)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170906
[Lr] Data última revisão:
170906
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170214
[St] Status:MEDLINE


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[PMID]:28127559
[Au] Autor:Savelyeva AV; Kuligina EV; Bariakin DN; Kozlov VV; Ryabchikova EI; Richter VA; Semenov DV
[Ad] Endereço:Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentiev Avenue 8, Novosibirsk 630090, Russia.
[Ti] Título:Variety of RNAs in Peripheral Blood Cells, Plasma, and Plasma Fractions.
[So] Source:Biomed Res Int;2017:7404912, 2017.
[Is] ISSN:2314-6141
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Human peripheral blood contains RNA in cells and in extracellular membrane vesicles, microvesicles and exosomes, as well as in cell-free ribonucleoproteins. Circulating mRNAs and noncoding RNAs, being internalized, possess the ability to modulate vital processes in recipient cells. In this study, with SOLiD sequencing technology, we performed identification, classification, and quantification of RNAs from blood fractions: cells, plasma, plasma vesicles pelleted at 16,000 and 160,000 , and vesicle-depleted plasma supernatant of healthy donors and non-small cell lung cancer (NSCLC) patients. It was determined that 16,000 blood plasma vesicles were enriched with cell-free mitochondria and with a set of mitochondrial RNAs. The variable RNA set of blood plasma 160,000 pellets reflected the prominent contribution of U1, U5, and U6 small nuclear RNAs' fragments and at the same time was characterized by a remarkable depletion of small nucleolar RNAs. Besides microRNAs, the variety of fragments of mRNAs and snoRNAs dominated in the set of circulating RNAs differentially expressed in blood fractions of NSCLC patients. Taken together, our data emphasize that not only extracellular microRNAs but also circulating fragments of messenger and small nuclear/nucleolar RNAs represent prominent classes of circulating regulatory ncRNAs as well as promising circulating biomarkers for the development of disease diagnostic approaches.
[Mh] Termos MeSH primário: RNA/sangue
[Mh] Termos MeSH secundário: Adenocarcinoma/sangue
Adenocarcinoma/genética
Células Sanguíneas/metabolismo
Carcinoma Pulmonar de Células não Pequenas/sangue
Carcinoma Pulmonar de Células não Pequenas/genética
Carcinoma de Células Escamosas/sangue
Carcinoma de Células Escamosas/genética
Estudos de Casos e Controles
Seres Humanos
Neoplasias Pulmonares/sangue
Neoplasias Pulmonares/genética
Masculino
MicroRNAs/sangue
MicroRNAs/genética
Meia-Idade
Plasma/metabolismo
RNA/classificação
RNA/genética
RNA Mensageiro/sangue
RNA Mensageiro/genética
RNA Nuclear/sangue
RNA Nuclear/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (MicroRNAs); 0 (RNA, Messenger); 0 (RNA, Nuclear); 0 (RNA, mitochondrial); 63231-63-0 (RNA)
[Em] Mês de entrada:1702
[Cu] Atualização por classe:170224
[Lr] Data última revisão:
170224
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170128
[St] Status:MEDLINE
[do] DOI:10.1155/2017/7404912


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[PMID]:27897007
[Au] Autor:Aevermann B; McCorrison J; Venepally P; Hodge R; Bakken T; Miller J; Novotny M; Tran DN; Diezfuertes F; Christiansen L; Zhang F; Steemers F; Lasken RS; Lein ED; Schork N; Scheuermann RH
[Ad] Endereço:J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USA#Contributed equally to this work.
[Ti] Título:PRODUCTION OF A PRELIMINARY QUALITY CONTROL PIPELINE FOR SINGLE NUCLEI RNA-SEQ AND ITS APPLICATION IN THE ANALYSIS OF CELL TYPE DIVERSITY OF POST-MORTEM HUMAN BRAIN NEOCORTEX.
[So] Source:Pac Symp Biocomput;22:564-575, 2017.
[Is] ISSN:2335-6936
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Next generation sequencing of the RNA content of single cells or single nuclei (sc/nRNA-seq) has become a powerful approach to understand the cellular complexity and diversity of multicellular organisms and environmental ecosystems. However, the fact that the procedure begins with a relatively small amount of starting material, thereby pushing the limits of the laboratory procedures required, dictates that careful approaches for sample quality control (QC) are essential to reduce the impact of technical noise and sample bias in downstream analysis applications. Here we present a preliminary framework for sample level quality control that is based on the collection of a series of quantitative laboratory and data metrics that are used as features for the construction of QC classification models using random forest machine learning approaches. We've applied this initial framework to a dataset comprised of 2272 single nuclei RNA-seq results and determined that ~79% of samples were of high quality. Removal of the poor quality samples from downstream analysis was found to improve the cell type clustering results. In addition, this approach identified quantitative features related to the proportion of unique or duplicate reads and the proportion of reads remaining after quality trimming as useful features for pass/fail classification. The construction and use of classification models for the identification of poor quality samples provides for an objective and scalable approach to sc/nRNA-seq quality control.
[Mh] Termos MeSH primário: Sequenciamento de Nucleotídeos em Larga Escala/estatística & dados numéricos
Neocórtex/citologia
Neocórtex/metabolismo
RNA Nuclear/genética
Análise de Sequência de RNA/estatística & dados numéricos
[Mh] Termos MeSH secundário: Autopsia
Viés
Núcleo Celular/genética
Biologia Computacional
Bases de Dados de Ácidos Nucleicos
Árvores de Decisões
Sequenciamento de Nucleotídeos em Larga Escala/normas
Seres Humanos
Aprendizado de Máquina
Controle de Qualidade
Análise de Sequência de RNA/normas
Análise de Célula Única
Software
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (RNA, Nuclear)
[Em] Mês de entrada:1703
[Cu] Atualização por classe:171116
[Lr] Data última revisão:
171116
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161130
[St] Status:MEDLINE
[do] DOI:10.1142/9789813207813_0052


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[PMID]:27113499
[Au] Autor:Reddy AS; O'Brien D; Pisat N; Weichselbaum CT; Sakers K; Lisci M; Dalal JS; Dougherty JD
[Ad] Endereço:Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri.
[Ti] Título:A Comprehensive Analysis of Cell Type-Specific Nuclear RNA From Neurons and Glia of the Brain.
[So] Source:Biol Psychiatry;81(3):252-264, 2017 Feb 01.
[Is] ISSN:1873-2402
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Studies in psychiatric genetics have identified >100 loci associated with disease risk, yet many of these loci are distant from protein coding genes. Recent characterization of the transcriptional landscape of cell lines and whole tissues has suggested widespread transcription in both coding and noncoding regions of the genome, including differential expression from loci that produce regulatory noncoding RNAs that function within the nucleus; however, the nuclear transcriptome of specific cell types in the brain has not been previously investigated. METHODS: We defined the nuclear transcriptional landscape of the three major cellular divisions of the nervous system using flow sorting of genetically labeled nuclei from bacTRAP mouse lines. Next, we characterized the unique expression of coding, noncoding, and intergenic RNAs in the mature mouse brain with RNA-Seq and validation with independent methods. RESULTS: We found diverse expression across the cell types of all classes of RNAs, including long noncoding RNAs, several of which were confirmed as highly enriched in the nuclei of specific cell types using anatomic methods. We also discovered several examples of cell type-specific expression of tandem gene fusions, and we report the first cell type-specific expression of circular RNAs-a neuron-specific and nuclear-enriched RNA arising from the gene Hnrnpu. CONCLUSIONS: These data provide an important resource for studies evaluating the function of various noncoding RNAs in the brain, including noncoding RNAs that may play a role in psychiatric disease.
[Mh] Termos MeSH primário: Encéfalo/metabolismo
Neuroglia/metabolismo
Neurônios/metabolismo
RNA Nuclear/metabolismo
Transcriptoma
[Mh] Termos MeSH secundário: Animais
Feminino
Ribonucleoproteínas Nucleares Heterogêneas Grupo U/metabolismo
Masculino
Camundongos
Oligodendroglia/metabolismo
RNA Longo não Codificante/metabolismo
Análise de Sequência de RNA
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Heterogeneous-Nuclear Ribonucleoprotein U); 0 (RNA, Long Noncoding); 0 (RNA, Nuclear)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170809
[Lr] Data última revisão:
170809
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160427
[St] Status:MEDLINE


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[PMID]:26861021
[Au] Autor:Eckwahl MJ; Telesnitsky A; Wolin SL
[Ad] Endereço:Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut, USA.
[Ti] Título:Host RNA Packaging by Retroviruses: A Newly Synthesized Story.
[So] Source:MBio;7(1):e02025-15, 2016 Feb 09.
[Is] ISSN:2150-7511
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:A fascinating aspect of retroviruses is their tendency to nonrandomly incorporate host cell RNAs into virions. In addition to the specific tRNAs that prime reverse transcription, all examined retroviruses selectively package multiple host cell noncoding RNAs (ncRNAs). Many of these ncRNAs appear to be encapsidated shortly after synthesis, before assembling with their normal protein partners. Remarkably, although some packaged ncRNAs, such as pre-tRNAs and the spliceosomal U6 small nuclear RNA (snRNA), were believed to reside exclusively within mammalian nuclei, it was demonstrated recently that the model retrovirus murine leukemia virus (MLV) packages these ncRNAs from a novel pathway in which unneeded nascent ncRNAs are exported to the cytoplasm for degradation. The finding that retroviruses package forms of ncRNAs that are rare in cells suggests several hypotheses for how these RNAs could assist retrovirus assembly and infectivity. Moreover, recent experiments in several laboratories have identified additional ways in which cellular ncRNAs may contribute to the retrovirus life cycle. This review focuses on the ncRNAs that are packaged by retroviruses and the ways in which both encapsidated ncRNAs and other cellular ncRNAs may contribute to retrovirus replication.
[Mh] Termos MeSH primário: RNA Nuclear/metabolismo
RNA não Traduzido/metabolismo
Retroviridae/fisiologia
Replicação Viral
[Mh] Termos MeSH secundário: Animais
Núcleo Celular/metabolismo
Citoplasma/metabolismo
Seres Humanos
Vírus da Leucemia Murina/genética
Vírus da Leucemia Murina/fisiologia
Camundongos
Retroviridae/genética
Retroviridae/crescimento & desenvolvimento
Vírion/genética
Vírion/fisiologia
Montagem de Vírus/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; REVIEW
[Nm] Nome de substância:
0 (RNA, Nuclear); 0 (RNA, Untranslated)
[Em] Mês de entrada:1612
[Cu] Atualização por classe:161230
[Lr] Data última revisão:
161230
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160211
[St] Status:MEDLINE


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[PMID]:26721484
[Au] Autor:Dhaliwal NK; Mitchell JA
[Ad] Endereço:Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, Canada, M5S 3G5.
[Ti] Título:Nuclear RNA Isolation and Sequencing.
[So] Source:Methods Mol Biol;1402:63-71, 2016.
[Is] ISSN:1940-6029
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Most transcriptome studies involve sequencing and quantification of steady-state mRNA by isolating and sequencing poly (A) RNA. Although this type of sequencing data is informative to determine steady-state mRNA levels it does not provide information on transcriptional output and thus may not always reflect changes in transcriptional regulation of gene expression. Furthermore, sequencing poly (A) RNA may miss transcribed regions of the genome not usually modified by polyadenylation which includes many long noncoding RNAs. Here, we describe nuclear-RNA sequencing (nucRNA-seq) which investigates the transcriptional landscape through sequencing and quantification of nuclear RNAs which are both unspliced and spliced transcripts for protein-coding genes and nuclear-retained long noncoding RNAs.
[Mh] Termos MeSH primário: Perfilação da Expressão Gênica/métodos
RNA Nuclear/genética
RNA Nuclear/isolamento & purificação
Análise de Sequência de RNA/métodos
Transcriptoma
[Mh] Termos MeSH secundário: Animais
Fracionamento Celular/métodos
Sequenciamento de Nucleotídeos em Larga Escala/métodos
Seres Humanos
Poliadenilação
RNA Longo não Codificante/genética
RNA Longo não Codificante/isolamento & purificação
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (RNA, Long Noncoding); 0 (RNA, Nuclear)
[Em] Mês de entrada:1610
[Cu] Atualização por classe:170518
[Lr] Data última revisão:
170518
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160102
[St] Status:MEDLINE
[do] DOI:10.1007/978-1-4939-3378-5_7



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