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1.
Gene ; 720: 144099, 2019 Dec 15.
Artigo em Inglês | MEDLINE | ID: mdl-31479715

RESUMO

Emerging evidence demonstrates that circular RNA (circRNA) is a novel class of non-coding RNA that plays a pivotal role in cancer. Recently, circ-PRMT5 was identified as an oncogene in bladder cancer. Nevertheless, its contribution to non-small cell lung cancer (NSCLC) is unknown. Herein, we aimed to clarify the biological role of circ-PRMT5 in NSCLC. High circ-PRMT5 expression was identified in NSCLC tissues and cell lines and positively correlated with larger tumor size, advanced clinic stage, lymph node metastasis as well as worse prognosis. Stable knockdown of circ-PRMT5 dramatically weakened the proliferative capacities of NSCLC cells both in vitro and in vivo. Mechanically, circ-PRMT5 could simultaneously effectively sponge three miRNAs (miR-377, miR-382 and miR-498) and alleviate their repression on the well-known oncogenic EZH2, resulting in increased EZH2 expression, thereby facilitating NSCLC progression. Importantly, a strong positive correlation between circ-PRMT5 and EZH2 expression was observed in NSCLC tissues. Overall, our data indicate that circ-PRMT5 is an oncogenic circRNA in NSCLC that can promote the growth of NSCLC via regulation of miR-377/382/498-EZH2 axis.


Assuntos
Carcinoma Pulmonar de Células não Pequenas/secundário , Proteína Potenciadora do Homólogo 2 de Zeste/metabolismo , MicroRNAs/genética , Proteína-Arginina N-Metiltransferases/genética , RNA/genética , Animais , Apoptose , Biomarcadores Tumorais/análise , Carcinogênese , Carcinoma Pulmonar de Células não Pequenas/genética , Carcinoma Pulmonar de Células não Pequenas/metabolismo , Proliferação de Células , Progressão da Doença , Proteína Potenciadora do Homólogo 2 de Zeste/genética , Feminino , Regulação Neoplásica da Expressão Gênica , Humanos , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/metabolismo , Neoplasias Pulmonares/patologia , Metástase Linfática , Masculino , Camundongos , Camundongos Nus , Pessoa de Meia-Idade , Prognóstico , Células Tumorais Cultivadas , Ensaios Antitumorais Modelo de Xenoenxerto
2.
BMC Plant Biol ; 19(1): 340, 2019 Aug 05.
Artigo em Inglês | MEDLINE | ID: mdl-31382873

RESUMO

BACKGROUND: Circular RNAs (circRNAs) are known to play an important role in the regulation of gene expression in eukaryotes. Photo-thermosensitive genic male sterile (PTGMS) is a very important germplasm resource in two-line hybrid rice breeding. Although many circRNAs have been identified in rice (Oryza sativa L.), little is known about the biological roles of circRNAs in the fertility transition of the PTGMS rice line. RESULTS: In the present study, RNA-sequencing libraries were constructed from the young panicles of the Wuxiang S sterile line rice (WXS (S)) and its fertile line rice (WXS (F)) at three development stages with three biological replicates. A total of 9994 circRNAs were obtained in WXS rice based on high-throughput strand-specific RNA sequencing and bioinformatic approaches, of which 5305 were known circRNAs and 4689 were novel in rice. And 14 of 16 randomly selected circRNAs were experimentally validated with divergent primers. Our results showed that 186 circRNAs were significantly differentially expressed in WXS (F) compared with WXS (S), of which 97, 87 and 60 circRNAs were differentially expressed at the pollen mother cell (PMC) formation stage (P2), the meiosis stage (P3) and the microspore formation stage (P4), respectively. Fertility specific expression patterns of eight circRNAs were analysis by qRT-PCR. Gene ontology (GO) and KEGG pathway analysis of the parental genes of differentially expressed circRNAs (DECs) revealed that they mainly participated in various biological processes such as development, response to stimulation, hormonal regulation, and reproduction. Furthermore, 15 DECs were found to act as putative miRNA sponges to involved in fertility transition in PTGMS rice line. CONCLUSION: In the present study, the abundance and characteristics of circRNAs were investigated in the PTGMS rice line using bioinformatic approaches. Moreover, the expression patterns of circRNAs were different between WXS (F) and WXS (S). Our findings primarily revealed that circRNAs might be endogenous noncoding regulators of flower and pollen development, and were involved in the fertility transition in the PTGMS rice line, and guide the production and application of two-line hybrid rice.


Assuntos
Oryza/genética , RNA/genética , Fertilidade/genética , Fertilidade/fisiologia , Flores/crescimento & desenvolvimento , Genes de Plantas/genética , Genes de Plantas/fisiologia , Resposta ao Choque Térmico , Sequenciamento de Nucleotídeos em Larga Escala , Oryza/fisiologia , Pólen/crescimento & desenvolvimento , RNA/fisiologia
4.
BMC Bioinformatics ; 20(1): 414, 2019 Aug 06.
Artigo em Inglês | MEDLINE | ID: mdl-31387525

RESUMO

BACKGROUND: R-loops are three-stranded nucleic acid structures that usually form during transcription and that may lead to gene regulation or genome instability. DRIP (DNA:RNA Immunoprecipitation)-seq techniques are widely used to map R-loops genome-wide providing insights into R-loop biology. However, annotation of DRIP-seq peaks to genes can be a tricky step, due to the lack of strand information when using the common basic DRIP technique. RESULTS: Here, we introduce DRIP-seq Optimized Peak Annotator (DROPA), a new tool for gene annotation of R-loop peaks based on gene expression information. DROPA allows a full customization of annotation options, ranging from the choice of reference datasets to gene feature definitions. DROPA allows to assign R-loop peaks to the DNA template strand in gene body with a false positive rate of less than 7%. A comparison of DROPA performance with three widely used annotation tools show that it identifies less false positive annotations than the others. CONCLUSIONS: DROPA is a fully customizable peak-annotation tool optimized for co-transcriptional DRIP-seq peaks, which allows a finest gene annotation based on gene expression information. Its output can easily be integrated into pipelines to perform downstream analyses, while useful and informative summary plots and statistical enrichment tests can be produced.


Assuntos
DNA/metabolismo , Imunoprecipitação , Anotação de Sequência Molecular , RNA/metabolismo , Software , Sequência de Bases , DNA/genética , Regulação da Expressão Gênica , RNA/genética
5.
Sheng Li Xue Bao ; 71(4): 613-624, 2019 Aug 25.
Artigo em Chinês | MEDLINE | ID: mdl-31440759

RESUMO

Circular RNAs (circRNAs) are a class of endogenous, covalently closed, single-stranded RNA without 3'-poly(A) and 5'-cap structures. CircRNAs are characterized by universality, diversity, stability and conservation, and have been found to regulate mammalian transcription and be translated into proteins. In this review, we summarized the biogenesis, classification, expression, distribution, biological functions and regulation of circRNAs. In addition, we discussed the association of circRNAs with diseases and the methods for identification and characterization of circRNAs. Finally, we speculated the application prospect and research direction of circRNAs.


Assuntos
RNA/genética , Animais , Pesquisa/tendências
6.
Medicine (Baltimore) ; 98(34): e16922, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31441876

RESUMO

BACKGROUND: Circular RNAs (circRNAs) have displayed dysregulated expression in several types of cancer. Nevertheless, their function and underlying mechanisms in cervical cancer remains largely unknown. This study aimed to describe the regulatory mechanisms in cervical cancer. METHODS: We downloaded the circRNAs expression profiles from Gene Expression Omnibus database, and RNAs expression profiles from The Cancer Genome Atlas database. We established a circRNA-miRNA-mRNA and circRNA-miRNA-hubgene network. The interactions between proteins were analyzed using the STRING database and hubgenes were identified using MCODE plugin. Then, we conducted a circRNA-miRNA-hubgenes regulatory module. Functional and pathway enrichment analyses were conducted using R packages "Clusterprofile". RESULTS: Six circRNAs, 15 miRNAs, and 158 mRNAs were identified to construct the ceRNA network of cervical cancer. PPI (protein-protein interaction) network and module analysis identified 7 hubgenes. Then, a circRNA-miRNA-hubgene subnetwork was constructed based on the 1 DEcircRNAs, 3 DEmiRNAs, and 3 DEmRNAs. The KEGG pathway analysis indicated DEmRNAs are involved in progesterone-mediated oocyte maturation, cell cycle, and oocyte meiosis. CONCLUSION: These ceRNAs are critical in the pathogenesis of cervical and may serve as future therapeutic biomarkers.


Assuntos
Regulação Neoplásica da Expressão Gênica/genética , Redes Reguladoras de Genes/genética , RNA/genética , Neoplasias do Colo do Útero/genética , Biomarcadores Tumorais/genética , Feminino , Humanos , Mapas de Interação de Proteínas , RNA/metabolismo
7.
Graefes Arch Clin Exp Ophthalmol ; 257(9): 1897-1913, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31327036

RESUMO

PURPOSE: Putative roles of long non-coding RNAs (lncRNAs) as indicators for diabetic retinopathy (DR) and associated complications are beginning to emerge. We aimed to evaluate a panel of circulating hyperglycemia-related lncRNAs: RNCR2, NEAT2, CDKN2B-AS1, and PVT1 in type 2 diabetes patients with/without DR and to correlate their levels with the clinical characteristics and response to aflibercept intravitreal injection in terms of visual acuity (VA) improvement, central macular thickness (CMT) decline, and macular edema resolution after 4 weeks of the initial injection. METHODS: Pre-treatment plasma relative expression levels of the specified lncRNAs were quantified in 130 consecutive patients with diabetes (75 and 55 with/without DR, respectively) and 108 controls using quantitative real-time PCR. RESULTS: One month after aflibercept injection, significant reductions in CMT and VA were observed in DR cohorts. The four lncRNAs were over-expressed in DM compared with those in controls. However, downregulated baseline plasma levels of RNCR2 and NEAT2 were observed in glycemic-controlled DR patients. None of the lncRNAs showed a correlation with the severity of retinopathy or drug response. CONCLUSION: Though circulating levels of the analyzed lncRNAs did not show an association with DR progression or aflibercept therapy response, the expression pattern demonstrated good diagnostic performance in differentiating DM from controls and DR.


Assuntos
Retinopatia Diabética/sangue , RNA Longo não Codificante/sangue , Receptores de Fatores de Crescimento do Endotélio Vascular/administração & dosagem , Proteínas Recombinantes de Fusão/administração & dosagem , Retinopatia Diabética/tratamento farmacológico , Retinopatia Diabética/genética , Progressão da Doença , Feminino , Regulação da Expressão Gênica , Humanos , Injeções Intravítreas , Masculino , Pessoa de Meia-Idade , Reação em Cadeia da Polimerase , RNA/genética , RNA Longo não Codificante/genética , Receptores de Fatores de Crescimento do Endotélio Vascular/antagonistas & inibidores , Retina/patologia , Estudos Retrospectivos , Tomografia de Coerência Óptica , Resultado do Tratamento , Acuidade Visual
8.
Yi Chuan ; 41(6): 469-485, 2019 Jun 20.
Artigo em Chinês | MEDLINE | ID: mdl-31257196

RESUMO

The field of circular non-coding RNAs have been gradually attracted wide attention with the developments of high-throughput sequencing. In this review, we systematically summarize three driving models for circRNAs biogenesis: intron-pairing-driven, RNA binding protein-driven and lariat-driven. In addition, we also briefly introduce the current research methods of circRNAs, which include high-throughput library construction methods, identification through bioinformatics and common experimental verification. Here, we also systematically summarize the functions of circRNAs, including microRNA (miRNA) or protein sponges, regulating the alternative splicing (AS) and expression of host genes, and extensive translation. Finally, we provide a systematic characterization and the latest research progress of circRNAs, which provide a new perspective for further studies of circRNAs in plants.


Assuntos
Processamento Alternativo , RNA/genética , Íntrons , MicroRNAs , Modelos Genéticos , Plantas/genética , Proteínas de Ligação a RNA
9.
Gene ; 714: 143992, 2019 Sep 25.
Artigo em Inglês | MEDLINE | ID: mdl-31330234

RESUMO

Increasing studies have demonstrated the important roles of circular RNAs (circRNAs) in human malignancies. Nevertheless, the molecular mechanisms and functions of circRNAs in hepatocellular carcinoma (HCC) are still not fully understood. In the present study, we evaluated circ_0021093 expression in 82 pairs of HCC tissues and 5 cell lines by qRT-PCR. The clinical implications of circ_0021093 were evaluated. In addition, the viability, apoptosis, migration and invasion capacities of different HCC cells were evaluated by gain-/loss-of-function experiments. Target prediction and dual-luciferase reporter experiments were performed to identify the molecular mechanisms of circ_0021093. Upregulation of circ_0021093 was found in HCC tumor samples and cells. Additionally, upregulated circ_0021093 was related to adverse clinical characteristics and an unfavorable prognosis. Furthermore, downregulated circ_0021093 attenuated cell growth, migration and invasion but increased cell apoptosis. By contrast, ectopically expressed circ_0021093 enhanced the abovementioned malignant biological behaviors. For mechanism exploration, circ_0021093 sponges of miR-766-3p were used in HCC cells. In addition, we found that metastasis-associated protein 3 (MTA3) was a direct target of miR-766-3p and that the oncogenic function of circ_0021093 was partly dependent on the miR-766-3p/MTA3 axis according to rescue assays. In conclusion, the circ_0021093/miR-766-3p/MTA3 regulatory axis may be an effective therapeutic target for HCC.


Assuntos
Carcinoma Hepatocelular/genética , Neoplasias Hepáticas/genética , MicroRNAs/genética , Proteínas de Neoplasias/genética , RNA/genética , Apoptose/genética , Carcinoma Hepatocelular/patologia , Linhagem Celular Tumoral , Movimento Celular/genética , Proliferação de Células/genética , Progressão da Doença , Regulação para Baixo/genética , Feminino , Regulação Neoplásica da Expressão Gênica/genética , Células Hep G2 , Humanos , Neoplasias Hepáticas/patologia , Masculino , Pessoa de Meia-Idade , Prognóstico , Regulação para Cima/genética
10.
Nat Commun ; 10(1): 2909, 2019 07 02.
Artigo em Inglês | MEDLINE | ID: mdl-31266957

RESUMO

Cells form and use biomolecular condensates to execute biochemical reactions. The molecular properties of non-membrane-bound condensates are directly connected to the amino acid content of disordered protein regions. Lysine plays an important role in cellular function, but little is known about its role in biomolecular condensation. Here we show that protein disorder is abundant in protein/RNA granules and lysine is enriched in disordered regions of proteins in P-bodies compared to the entire human disordered proteome. Lysine-rich polypeptides phase separate into lysine/RNA-coacervates that are more dynamic and differ at the molecular level from arginine/RNA-coacervates. Consistent with the ability of lysine to drive phase separation, lysine-rich variants of the Alzheimer's disease-linked protein tau undergo coacervation with RNA in vitro and bind to stress granules in cells. Acetylation of lysine reverses liquid-liquid phase separation and reduces colocalization of tau with stress granules. Our study establishes lysine as an important regulator of cellular condensation.


Assuntos
Lisina/metabolismo , RNA/química , RNA/metabolismo , Proteínas tau/química , Proteínas tau/metabolismo , Acetilação , Doença de Alzheimer/genética , Doença de Alzheimer/metabolismo , Linhagem Celular , Grânulos Citoplasmáticos/genética , Grânulos Citoplasmáticos/metabolismo , Humanos , Lisina/química , Lisina/genética , RNA/genética , Proteínas tau/genética
11.
Gene ; 711: 143948, 2019 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-31255737

RESUMO

The incidence of atherosclerosis is greatly increased, which becomes the leading cause for the death and disability worldwide. Endothelial cells dysfunction plays a substantial role in the pathogenesis of atherosclerosis. MicroRNA-148a-3p (miR-148a-3p) and circular RNA 0003575 (circ_0003575) modulated lipid metabolism and proliferative function of endothelial cells, respectively. However, the role of them in modulation of endothelial cell function and progression of atherosclerosis remains unknown. Endothelial cells were isolated from the aorta of Apoe-/- mice. miR-148a-3p in atherosclerosis patients and healthy controls were measured by qRT-PCR. Overexpression and knockdown of miR-148a-3p in endothelial cells were established. The proliferation, migration and apoptosis of endothelial cells were measured by MTT, Transwell, and fluorescence microscope, respectively. Online software (miRWalk 2.0 and RegRNA2.0) and databases (miRWalk, miRanda, RNA22, and Targetscan) were used to predict potential target genes of miR-148a-3p and circ_0003575. The expression of target genes was detected through western blotting. The expression of miR-148a-3p was significantly upregulated in patients with atherosclerosis as relative to healthy people. Overexpression of miR-148a-3p exhibited stimulatory effects on endothelial cell proliferation and migration and inhibited programmed cell death. Six intersection target genes, c-MAF, FOXO4, FOXO3, MITF, ETV7, and CRX, were predicted between miR-148a-3p and circ_0003575. The opposite effects of circ_0003575 and miR-148a-3p on the expression of FOXO4 and FOXO3, which are essential for lipid metabolism. We demonstrate that miR-148a-3p suppresses FOXO4 and FOXO3 expression via interruption of circ_0003575 function, which in turn impairs the proliferative and migratory function of endothelial cells, eventually exacerbating the atherosclerosis.


Assuntos
Apolipoproteínas E/deficiência , Aterosclerose/genética , Células Endoteliais/citologia , Proteína Forkhead Box O3/metabolismo , MicroRNAs/genética , RNA/genética , Fatores de Transcrição/metabolismo , Regulação para Cima , Animais , Apolipoproteínas E/genética , Apoptose , Aterosclerose/metabolismo , Estudos de Casos e Controles , Movimento Celular , Proliferação de Células , Sobrevivência Celular , Células Cultivadas , Modelos Animais de Doenças , Células Endoteliais/metabolismo , Proteína Forkhead Box O3/genética , Redes Reguladoras de Genes , Humanos , Metabolismo dos Lipídeos , Camundongos , Fatores de Transcrição/genética
12.
Chem Commun (Camb) ; 55(58): 8402-8405, 2019 Jul 25.
Artigo em Inglês | MEDLINE | ID: mdl-31257385

RESUMO

A proof-of-principle for the application of hemi-indigo derivatives as RNA binders with photocontrollable fluorescence is presented. The photoswitch binds to the human immunodeficiency virus type 1 (HIV-1) RNA with a significant light-up effect. The fluorescence of the RNA-bound ligand can be reversibly switched ON and OFF by light without destroying the ligand-RNA associates.


Assuntos
Corantes Fluorescentes/metabolismo , HIV-1/genética , Indóis/metabolismo , RNA/metabolismo , Fluorescência , Corantes Fluorescentes/química , Corantes Fluorescentes/efeitos da radiação , Indóis/química , Indóis/efeitos da radiação , Ligantes , Luz , Estudo de Prova de Conceito , RNA/genética , Elementos de Resposta , Estereoisomerismo
13.
Zool Res ; 40(4): 293-304, 2019 Jul 18.
Artigo em Inglês | MEDLINE | ID: mdl-31271004

RESUMO

Divergence of gene expression and alternative splicing is a crucial driving force in the evolution of species; to date, however the molecular mechanism remains unclear. Hybrids of closely related species provide a suitable model to analyze allele-specific expression (ASE) and allele-specific alternative splicing (ASS). Analysis of ASE and ASS can uncover the differences in cis-regulatory elements between closely related species, while eliminating interference of trans-regulatory elements. Here, we provide a detailed characterization of ASE and ASS from 19 and 10 transcriptome datasets across five tissues from reciprocal-cross hybrids of horse×donkey (mule/hinny) and cattle×yak (dzo), respectively. Results showed that 4.8%-8.7% and 10.8%-16.7% of genes exhibited ASE and ASS, respectively. Notably, lncRNAs and pseudogenes were more likely to show ASE than protein-coding genes. In addition, genes showing ASE and ASS in mule/hinny were found to be involved in the regulation of muscle strength, whereas those of dzo were involved in high-altitude adaptation. In conclusion, our study demonstrated that exploration of genes showing ASE and ASS in hybrids of closely related species is feasible for species evolution research.


Assuntos
Alelos , Processamento Alternativo , Bovinos/genética , Equidae/genética , Hibridização Genética/genética , Animais , Sequência de Bases , Regulação da Expressão Gênica , RNA/genética , RNA/metabolismo
14.
Int Heart J ; 60(4): 964-973, 2019 07 27.
Artigo em Inglês | MEDLINE | ID: mdl-31257333

RESUMO

Acute myocardial infarction (AMI) is a serious heart disease and the main reason for heart failure and sudden death worldwide. This study investigated the effects of polysaccharides from Enteromorpha prolifera (PEP) on AMI in vitro and in vivo, as well as the underlying mechanisms.Human cardiac microvascular endothelial cells (HCMVEC) were cultured in vitro in an oxygen-glucose deprivation (OGD) environment to induce injury. The viability and apoptosis of HCMVEC were then detected using CCK-8 assay and Annexin V-FITC/PI staining, respectively. ELISA was performed to measure the concentrations of inflammatory cytokines. Cell transfection was conducted to reduce the expression of HIF-1α. Expression of key factors involving in cell proliferation, apoptosis, autophagy, MEK/ERK, and the NF-κB and mTOR pathways were evaluated using Western blotting. In vivo, Wistar rats were pre-treated by PEP and AMI was induced. The infarct size and cardiac functions (LVEDD, LVEF and LVFS) were measured.In vitro, PEP treatment significantly protected HCMVEC from OGD-induced viability loss, proliferation inhibition, apoptosis, inflammatory cytokine expression, and autophagy. Moreover, PEP enhanced the expression of HIF-1α in HCMVEC via the MEK/ERK pathway. HIF-1α participated in the protective effects of PEP on OGD-treated HCMVEC. Furthermore, PEP attenuated OGD-induced NF-κB pathway activation and promoted the mTOR pathway in HCMVEC. In vivo, PEP pre-treatment reduced the infarct size and enhanced the LVEDD, LVEF and LVFS of rats via up-regulation of HIF-1α.PEP ameliorated AMI in vitro and in vivo through up-regulation of HIF-1α. In vitro, PEP could activate the MEK/ERK and mTOR pathways, but inactivate the NF-κB pathway in OGD-treated HCMVEC.


Assuntos
Subunidade alfa do Fator 1 Induzível por Hipóxia/genética , Infarto do Miocárdio/genética , Polissacarídeos Bacterianos/farmacologia , RNA/genética , Regulação para Cima , Animais , Apoptose , Western Blotting , Proliferação de Células , Sobrevivência Celular , Células Cultivadas , Modelos Animais de Doenças , Ensaio de Imunoadsorção Enzimática , Humanos , Subunidade alfa do Fator 1 Induzível por Hipóxia/biossíntese , Masculino , Infarto do Miocárdio/metabolismo , Infarto do Miocárdio/patologia , Ratos , Ratos Wistar , Transdução de Sinais
15.
BMC Bioinformatics ; 20(1): 372, 2019 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-31266442

RESUMO

BACKGROUND: The studies of functions of circular RNAs (circRNAs) are heavily focused on the regulation of gene expression through interactions with multiple miRNAs. However, the number of predicted target genes is typically overwhelming due to the synergistic complexity caused by two factors ─ the binding of multiple miRNAs to a circRNA and the existence of multiple targets for each miRNA. Analysis of common targets (ACT) was designed to facilitate the identification of potential circRNA targets. RESULTS: We demonstrated the feasibility of the proposed feature/measurement to assess which genes are more likely to be regulated by circRNAs with given sequences by calculating the level of co-regulation by multiple miRNAs. The web service is made freely available at http://lab-x-omics.nchu.edu.tw/ACT_Server . CONCLUSIONS: ACT allows users to identify potential circRNA-regulated genes and their associated pathways for further investigation.


Assuntos
RNA/metabolismo , Interface Usuário-Computador , Animais , Metabolismo Energético/genética , Humanos , MicroRNAs/genética , MicroRNAs/metabolismo , RNA/genética
16.
BMC Bioinformatics ; 20(1): 394, 2019 Jul 16.
Artigo em Inglês | MEDLINE | ID: mdl-31311497

RESUMO

BACKGROUND: High-dimensional data of discrete and skewed nature is commonly encountered in high-throughput sequencing studies. Analyzing the network itself or the interplay between genes in this type of data continues to present many challenges. As data visualization techniques become cumbersome for higher dimensions and unconvincing when there is no clear separation between homogeneous subgroups within the data, cluster analysis provides an intuitive alternative. The aim of applying mixture model-based clustering in this context is to discover groups of co-expressed genes, which can shed light on biological functions and pathways of gene products. RESULTS: A mixture of multivariate Poisson-log normal (MPLN) model is developed for clustering of high-throughput transcriptome sequencing data. Parameter estimation is carried out using a Markov chain Monte Carlo expectation-maximization (MCMC-EM) algorithm, and information criteria are used for model selection. CONCLUSIONS: The mixture of MPLN model is able to fit a wide range of correlation and overdispersion situations, and is suited for modeling multivariate count data from RNA sequencing studies. All scripts used for implementing the method can be found at https://github.com/anjalisilva/MPLNClust .


Assuntos
Algoritmos , RNA/química , Análise por Conglomerados , Sequenciamento de Nucleotídeos em Larga Escala , Cadeias de Markov , Modelos Teóricos , Método de Monte Carlo , RNA/genética , RNA/metabolismo , Análise de Sequência de RNA , Interface Usuário-Computador
17.
Toxicol Lett ; 314: 89-97, 2019 Oct 10.
Artigo em Inglês | MEDLINE | ID: mdl-31325635

RESUMO

Ethanol is a key factor in the pathogenesis of alcoholic liver disease (ALD), commonly characterized as liver inflammation. Recently, circular (circ)RNAs have emerged as important targets to cure liver diseases. However, there are no studies investigating the role of circ_1639 in reducing inflammatory responses in ALD. In this study, we found that circ_1639 was upregulated in Kupffer cells from the livers of alcohol fed mice. We hypothesized that circ_1639 inhibition is a potential novel therapy for treating ALD. To test this hypothesis, RAW 264.7 cells were treated with ethanol and transfected with circ_1639 overexpression or knockdown plasmids. We present western blotting, qRT-PCR, and ELISA data that suggest that circ_1639 is a proinflammatory factor in the liver and is involved in the activation of the NF-κB signaling pathway. Using luciferase reporter assay, we confirmed that microRNA (miR)-122 is a target gene of circ_1639. We also show that TNFRSF13C is a key regulator of RAW 264.7 cell activation, and acts as a downstream target for miR-122. In summary, our results suggest that inhibition of circ_1639 expression may reduce inflammatory responses in ALD.


Assuntos
Mediadores da Inflamação/metabolismo , Hepatopatias Alcoólicas/metabolismo , Fígado/metabolismo , MicroRNAs/metabolismo , RNA/metabolismo , Animais , Receptor do Fator Ativador de Células B/genética , Receptor do Fator Ativador de Células B/metabolismo , Citocinas/metabolismo , Modelos Animais de Doenças , Regulação da Expressão Gênica , Técnicas de Silenciamento de Genes , Macrófagos do Fígado/metabolismo , Fígado/patologia , Hepatopatias Alcoólicas/genética , Hepatopatias Alcoólicas/patologia , Hepatopatias Alcoólicas/prevenção & controle , Ativação de Macrófagos , Masculino , Camundongos , Camundongos Endogâmicos C57BL , MicroRNAs/genética , Células RAW 264.7 , RNA/genética , Transdução de Sinais
18.
BMC Bioinformatics ; 20(1): 388, 2019 Jul 12.
Artigo em Inglês | MEDLINE | ID: mdl-31299886

RESUMO

BACKGROUND: Single-cell RNA-sequencing technologies provide a powerful tool for systematic dissection of cellular heterogeneity. However, the prevalence of dropout events imposes complications during data analysis and, despite numerous efforts from the community, this challenge has yet to be solved. RESULTS: Here we present a computational method, called RESCUE, to mitigate the dropout problem by imputing gene expression levels using information from other cells with similar patterns. Unlike existing methods, we use an ensemble-based approach to minimize the feature selection bias on imputation. By comparative analysis of simulated and real single-cell RNA-seq datasets, we show that RESCUE outperforms existing methods in terms of imputation accuracy which leads to more precise cell-type identification. CONCLUSIONS: Taken together, these results suggest that RESCUE is a useful tool for mitigating dropouts in single-cell RNA-seq data. RESCUE is implemented in R and available at https://github.com/seasamgo/rescue .


Assuntos
Análise de Sequência de RNA/métodos , Análise de Célula Única/métodos , Software , Viés , Células/metabolismo , Simulação por Computador , Regulação da Expressão Gênica , Humanos , RNA/genética , RNA/metabolismo
19.
BMC Bioinformatics ; 20(1): 405, 2019 Jul 25.
Artigo em Inglês | MEDLINE | ID: mdl-31345161

RESUMO

BACKGROUND: Next-generation sequencing technologies can produce tens of millions of reads, often paired-end, from transcripts or genomes. But few programs can align RNA on the genome and accurately discover introns, especially with long reads. We introduce Magic-BLAST, a new aligner based on ideas from the Magic pipeline. RESULTS: Magic-BLAST uses innovative techniques that include the optimization of a spliced alignment score and selective masking during seed selection. We evaluate the performance of Magic-BLAST to accurately map short or long sequences and its ability to discover introns on real RNA-seq data sets from PacBio, Roche and Illumina runs, and on six benchmarks, and compare it to other popular aligners. Additionally, we look at alignments of human idealized RefSeq mRNA sequences perfectly matching the genome. CONCLUSIONS: We show that Magic-BLAST is the best at intron discovery over a wide range of conditions and the best at mapping reads longer than 250 bases, from any platform. It is versatile and robust to high levels of mismatches or extreme base composition, and reasonably fast. It can align reads to a BLAST database or a FASTA file. It can accept a FASTQ file as input or automatically retrieve an accession from the SRA repository at the NCBI.


Assuntos
RNA/genética , Alinhamento de Sequência , Análise de Sequência de RNA/métodos , Software , Algoritmos , Sequência de Bases , Bases de Dados de Ácidos Nucleicos , Humanos , Íntrons/genética , Curva ROC , Fatores de Tempo
20.
Life Sci ; 231: 116660, 2019 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-31319086

RESUMO

Hepatocellular carcinoma (HCC), a leading cause of cancer-related death with high invasive and metastatic potential, has a low survival rate. To improve the survival and quality of life in HCC patients, it is urgently needed to explore novel biomarkers for early diagnosis and prognosis of HCC, as well as therapeutic strategies. Circular RNAs (circRNAs) are a class of highly conserved, stable and abundant non-coding RNAs (ncRNAs) that can regulate gene expression at transcriptional or post-transcriptional levels. Recently, some circRNAs are identified to be potential biomarkers for HCC diagnosis and prognosis. Furthermore, some circRNAs are found to play oncogenic or suppressive roles in HCC progression by regulating various biological processes, including cell proliferation, migration, invasion and metastasis, epithelial-mesenchymal transition (EMT), as well as apoptosis. In this review, we summarize recent findings of deregulated circRNAs, their functions and molecular mechanisms in HCC, and discuss their potential roles as diagnostic biomarkers, prognostic biomarkers, as well as therapeutic targets for HCC.


Assuntos
Carcinoma Hepatocelular/genética , Neoplasias Hepáticas/genética , RNA/metabolismo , Biomarcadores Tumorais/genética , Biomarcadores Tumorais/metabolismo , Carcinoma Hepatocelular/diagnóstico , Carcinoma Hepatocelular/patologia , Linhagem Celular Tumoral , Progressão da Doença , Humanos , Neoplasias Hepáticas/diagnóstico , Neoplasias Hepáticas/patologia , MicroRNAs/genética , Invasividade Neoplásica , Prognóstico , RNA/genética
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