Your browser doesn't support javascript.
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 62.542
Filtrar
1.
Nature ; 571(7765): 424-428, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-31292544

RESUMO

N6-methyladenosine (m6A) is the most prevalent modified nucleotide in mRNA1,2, with around 25% of mRNAs containing at least one m6A. Methylation of mRNA to form m6A is required for diverse cellular and physiological processes3. Although the presence of m6A in an mRNA can affect its fate in different ways, it is unclear how m6A directs this process and why the effects of m6A can vary in different cellular contexts. Here we show that the cytosolic m6A-binding proteins-YTHDF1, YTHDF2 and YTHDF3-undergo liquid-liquid phase separation in vitro and in cells. This phase separation is markedly enhanced by mRNAs that contain multiple, but not single, m6A residues. Polymethylated mRNAs act as a multivalent scaffold for the binding of YTHDF proteins, juxtaposing their low-complexity domains and thereby leading to phase separation. The resulting mRNA-YTHDF complexes then partition into different endogenous phase-separated compartments, such as P-bodies, stress granules or neuronal RNA granules. m6A-mRNA is subject to compartment-specific regulation, including a reduction in the stability and translation of mRNA. These studies reveal that the number and distribution of m6A sites in cellular mRNAs can regulate and influence the composition of the phase-separated transcriptome, and suggest that the cellular properties of m6A-modified mRNAs are governed by liquid-liquid phase separation principles.


Assuntos
Adenosina/análogos & derivados , Compartimento Celular , RNA Mensageiro/química , RNA Mensageiro/metabolismo , Adenosina/metabolismo , Animais , Transporte Biológico , Linhagem Celular , Grânulos Citoplasmáticos/química , Grânulos Citoplasmáticos/metabolismo , Humanos , Metilação , Metiltransferases/deficiência , Camundongos , Transição de Fase , RNA Mensageiro/análise , Proteínas de Ligação a RNA/química , Proteínas de Ligação a RNA/metabolismo , Estresse Fisiológico
2.
Biol Res ; 52(1): 35, 2019 Jul 11.
Artigo em Inglês | MEDLINE | ID: mdl-31296259

RESUMO

BACKGROUND: Non-small cell lung cancer (NSCLC) is one of the leading causes of death in the world. NSCLC diagnosed at an early stage can be highly curable with a positive prognosis, but biomarker limitations make it difficult to diagnose lung cancer at an early stage. To identify biomarkers for lung cancer development, we previously focused on the oncogenic roles of transcription factor TFAP2C in lung cancers and revealed the molecular mechanism of several oncogenes in lung tumorigenesis based on TFAP2C-related microarray analysis. RESULTS: In this study, we analyzed microarray data to identify tumor suppressor genes and nine genes downregulated by TFAP2C were screened. Among the nine genes, we focused on growth arrest and DNA-damage-inducible beta (GADD45B) and phorbol-12-myristate-13-acetate-induced protein 1 (PMAIP1) as representative TFAP2C-regulated tumor suppressor genes. It was observed that overexpressed TFAP2C resulted in inhibition of GADD45B and PMAIP1 expressions at both the mRNA and protein levels in NSCLC cells. In addition, downregulation of GADD45B and PMAIP1 by TFAP2C promoted cell proliferation and cell motility, which are closely associated with NSCLC tumorigenesis. CONCLUSION: This study indicates that GADD45B and PMAIP1 could be promising tumor suppressors for NSCLC and might be useful as prognostic markers for use in NSCLC therapy.


Assuntos
Antígenos de Diferenciação/genética , Carcinoma Pulmonar de Células não Pequenas/genética , Proliferação de Células/genética , Regulação para Baixo/genética , Neoplasias Pulmonares/genética , Fator de Transcrição AP-2/genética , Biomarcadores Tumorais/análise , Linhagem Celular Tumoral , Regulação Neoplásica da Expressão Gênica , Genes Supressores de Tumor/fisiologia , Humanos , RNA Mensageiro/análise , RNA Interferente Pequeno/análise
3.
Exp Parasitol ; 204: 107727, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31344389

RESUMO

BACKGROUND: Trypanosoma rangeli is a protozoan parasite that is non-virulent to the mammalian host and is morphologically and genomically related to Trypanosoma cruzi, whose proliferation within the mammalian host is controversially discussed. OBJECTIVES: We aimed to investigate the T. rangeli cell cycle in vitro and in vivo by characterizing the timespan of the parasite life cycle and by proposing a molecular marker to assess cytokinesis. METHODOLOGY: The morphological events and their timing during the cell cycle of T. rangeli epimastigotes were assessed using DNA staining, flagellum labelling and bromodeoxyuridine incorporation. Messenger RNA levels of four genes previously associated with the cell cycle of trypanosomatids (AUK1, PLK, MOB1 and TRACK) were evaluated in the different T. rangeli forms. FINDINGS: T. rangeli epimastigotes completed the cell cycle in vitro in 20.8 h. PLK emerged as a potential molecular marker for cell division, as its mRNA levels were significantly increased in exponentially growing epimastigotes compared with growth-arrested parasites or in vitro-differentiated trypomastigotes. PLK expression in T. rangeli can be detected near the flagellum protrusion site, reinforcing its role in the cell cycle. Interestingly, T. rangeli bloodstream trypomastigotes exhibited very low mRNA levels of PLK and were almost entirely composed of parasites in G1 phase. MAIN CONCLUSIONS: Our work is the first to describe the T. rangeli cell cycle in vitro and proposes that PLK mRNA levels could be a useful tool to investigate the T. rangeli ability to proliferate within the mammalian host bloodstream.


Assuntos
Proteínas de Ciclo Celular/genética , Ciclo Celular/genética , Citocinese/fisiologia , Proteínas Serina-Treonina Quinases/genética , Proteínas Proto-Oncogênicas/genética , RNA Mensageiro/análise , Trypanosoma rangeli/citologia , Animais , Bromodesoxiuridina/metabolismo , Ciclo Celular/efeitos dos fármacos , Citocinese/genética , DNA de Protozoário/química , DNA de Protozoário/isolamento & purificação , Citometria de Fluxo , Imunofluorescência , Hidroxiureia/farmacologia , Camundongos , Camundongos Endogâmicos BALB C , Inibidores da Síntese de Ácido Nucleico/farmacologia , RNA de Protozoário/genética , RNA de Protozoário/isolamento & purificação , Fatores de Tempo , Trypanosoma rangeli/efeitos dos fármacos , Trypanosoma rangeli/enzimologia , Trypanosoma rangeli/genética , Tripanossomíase/parasitologia
4.
Sci Data ; 6(1): 94, 2019 06 17.
Artigo em Inglês | MEDLINE | ID: mdl-31209217

RESUMO

Transcript levels powerfully influence cell behavior and phenotype and are carefully regulated at several steps. Recently developed single cell approaches such as RNA single molecule fluorescence in-situ hybridization (smFISH) have produced advances in our understanding of how these steps work within the cell. In comparison to single-cell sequencing, smFISH provides more accurate quantification of RNA levels. Additionally, transcript subcellular localization is directly visualized, enabling the analysis of transcription (initiation and elongation), RNA export and degradation. As part of our efforts to investigate how this type of analysis can generate improved models of gene expression, we used smFISH to quantify the kinetic expression of STL1 and CTT1 mRNAs in single Saccharomyces cerevisiae cells upon 0.2 and 0.4 M NaCl osmotic stress. In this Data Descriptor, we outline our procedure along with our data in the form of raw images and processed mRNA counts. We discuss how these data can be used to develop single cell modelling approaches, to study fundamental processes in transcription regulation and develop single cell image processing approaches.


Assuntos
Hibridização in Situ Fluorescente , RNA Fúngico , RNA Mensageiro , Saccharomyces cerevisiae/genética , Análise de Célula Única , Proteínas de Membrana Transportadoras/análise , Proteínas de Membrana Transportadoras/genética , RNA Fúngico/análise , RNA Fúngico/genética , RNA Mensageiro/análise , RNA Mensageiro/genética , Proteínas de Saccharomyces cerevisiae/análise , Proteínas de Saccharomyces cerevisiae/genética , Análise de Célula Única/métodos , Análise de Célula Única/normas
5.
Gen Physiol Biophys ; 38(4): 365-368, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31219430

RESUMO

The role of vascular endothelial growth factor (VEGF) in chronic stress and neurodevelopmental disorders is of growing research interest. Here we show that post-weaning isolation rearing of rats decreased gene expression of VEGF in the hippocampus. Gene expression of VEGF upstream regulator fibroblast growth factor-2 (FGF-2) or its downstream mediator endothelial nitric oxide synthase (eNOS) was unchanged. Other signaling pathways appear to be involved in isolation-induced reduction in VEGF gene expression. Sex differences in VEGF and eNOS gene expression with significantly higher mRNA levels in females than males were revealed.


Assuntos
Regulação para Baixo , Hipocampo/metabolismo , Isolamento Social , Fator A de Crescimento do Endotélio Vascular/genética , Desmame , Animais , Feminino , Fator 2 de Crescimento de Fibroblastos/genética , Masculino , Óxido Nítrico Sintase Tipo III/genética , RNA Mensageiro/análise , RNA Mensageiro/genética , Ratos
6.
Histochem Cell Biol ; 152(2): 155-166, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31111198

RESUMO

Trace amine-associated receptors are G protein-coupled receptors of which TAAR1 is the most well-studied. Recently, Vattai et al. (J Cancer Res Clin Oncol 143:1637-1647 https://doi.org/10.1007/s00432-017-2420-8 , 2017) reported that expression of TAAR1 may be a marker of breast cancer (BC) survival, with a positive correlation also suggested between TAAR1 expression and HER2 positivity. Neither a role for TAAR1 in breast tissue, nor in cancer, had previously been suspected. We, therefore, sought to provide independent validation and to further examine these putative relationships. First, a bioinformatic analysis on 58 total samples including normal breast tissue, BC-related cell lines, and tumour samples representing different BC sub-types found no clear correlation between TAAR1 mRNA levels and any BC subtype, including HER2 + . We next confirmed the bioinformatics data correlated to protein expression using a well validated anti-human TAAR1 antibody. TAAR1 mRNA levels correlated with the relative intensity of immunofluorescence staining in six BC cell lines (MCF-7, T47D, MDA-MB-231, SKBR3, MDA-MB-468, BT-474), but not in the MCF-10A immortalized mammary gland line, which had high mRNA but low protein levels. As expected, TAAR1 protein was intracellular in all cell lines. Surprisingly MCF-7, SKBR3, and MDA-MB-468 showed pronounced nuclear localization. The relative protein expression in MCF-7, MDA-MB-231, and MCF-10A lines was further confirmed by semi-quantitative flow cytometry. Finally, we demonstrate that the commercially available anti-TAAR1 antibody has poor selectivity, which likely explains the lack of correlation with the previous study. Therefore, while we clearly demonstrate variable expression and sub-cellular localization of TAAR1 across BC cell lines, we find no evidence for association with BC subtype.


Assuntos
Neoplasias da Mama/genética , Receptores Acoplados a Proteínas-G/análise , Receptores Acoplados a Proteínas-G/genética , Neoplasias da Mama/diagnóstico , Neoplasias da Mama/metabolismo , Linhagem Celular , Biologia Computacional , Feminino , Citometria de Fluxo , Imunofluorescência , Humanos , RNA Mensageiro/análise , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Receptores Acoplados a Proteínas-G/metabolismo
7.
J Dairy Sci ; 102(7): 6263-6275, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31103297

RESUMO

Domestic yaks (Bos grunniens) and domestic Taurus cattle (Bos taurus) are closely related. An interesting phenomenon in interspecific crossings is male sterility in the F1 hybrid (yattle) and F2 backcross, with no late meiotic cells or spermatids in the seminiferous tubules. The mammalian Y chromosome is crucial for spermatogenesis and male fertility. This study investigated the copy number variations and mRNA of Y-transitional region genes TSPY2 (testis specific protein, Y-linked 2 and testis-specific Y-encoded protein 3-like) and PRAMEY (preferentially expressed antigen in melanoma, Y-linked), and Y-ampliconic region genes TSPY (testis-specific Y-encoded protein 1-like), ZNF280BY (zinc finger protein 280B, Y-linked) and HSFY (heat-shock transcription factor, Y-linked) in mature testes from Taurus cattle, yaks, and yattle. Phylogenetic trees divided 33 copies of TSPY into major 2 types (TSPY-T1 and TSPY-T2), 19 copies of TSPY2 into 2 types (TSPY2-T1 and T2), and 8 copies of PRAMEY into 4 types (PRAMEY-T1 to T4). Searching by the Basic Local Alignment Search Tool of the TSPY2 coding sequences in GenBank revealed that TSPY2 was conserved in Bovidae. The TSPY2-T2 sequences were absent, whereas PRAMEY-T2 and PRAMEY-T4 were amplified on the yak Y chromosome. The average copy numbers of TSPY-T2 and ZNF280BY were significantly different between cattle and yaks. The TSPY-T2, TSPY2, PRAMEY, ZNF280BY, and HSFY genes were uniquely or predominantly expressed in testes. Reverse-transcription quantitative PCR showed that the TSPY-T2, PRAMEY-T2, HSFY, ZNF280BY, protamine 1 (PRM1), and protamine 2 (PRM2) genes were almost not expressed in yattle. The PRM1 and PRM2 genes are used as positive markers for spermatozoa. Thus, our results showed that the genomic structure of the Y-transitional and Y-ampliconic region differed between Taurus cattle and yaks. Dysregulated expression of Y-ampliconic region genes TSPY-T2, HSPY, ZNF280BY, and Y-transitional region gene PRAMEY-T2 may be associated with hybrid male sterility in yattle.


Assuntos
Antígenos de Neoplasias/genética , Bovinos/genética , Proteínas de Ciclo Celular/genética , Ligação Genética/genética , Hibridização Genética/genética , Cromossomo Y/genética , Animais , Cruzamentos Genéticos , Variações do Número de Cópias de DNA , Expressão Gênica , Regulação da Expressão Gênica , Variação Genética/genética , Infertilidade Masculina/genética , Masculino , Filogenia , RNA Mensageiro/análise , Espermatogênese/genética , Testículo/metabolismo
8.
Sci Total Environ ; 677: 590-598, 2019 Aug 10.
Artigo em Inglês | MEDLINE | ID: mdl-31071664

RESUMO

Metals and heavy metals are natural contaminants with an increasing presence in aquatic ecosystems as a result of human activities. Although they are mixed in the water, research is usually focused on analyzing them in isolation, so there is a lack of knowledge about their combined effects. The aim of this work was to assess the damage produced by mixtures of cadmium and copper, two frequent metals used in industry, in the harlequin midge Chironomus riparius (Diptera). The effects of acute doses of cadmium and copper were evaluated in fourth instar larvae by analyzing the mRNA levels of six genes related to apoptosis (DRONC, IAP1), immune system (PO1, Defensin), stress (Gp93), and copper homeostasis (Ctr1). DRONC, Ctr1, and IAP1 transcripts are described here for first time in this species. Individual fourth instar larvae were submitted to 10 µM, 1 µM and 0.1 µM of CdCl2 or CuCl2, and mixture. The employed individuals came from different egg masses. Real-time PCR analysis showed a complex pattern of alterations in transcriptional activity for two genes, DRONC and Gp93, while the rest of them did not show any statistically significant differences. The effector caspase DRONC showed upregulation with the highest concentration tested of the mixture. In case of gp93, chaperone involved in regulation of immune response, differences in expression levels were found with 1 and 10 µM Cu and 0.1 and 10 µM of mixtures, compared to control samples. These results suggest that mixtures affect the transcriptional activity differently and produce changes in apoptosis and stress processes, although it is also possible that Gp93 alteration could be related to the immune system since it is homologous to human protein Gp96, which has been related with Toll-like receptors. In conclusion, cadmium and copper mixtures can affect the population by affecting the ability of larvae to respond to the infection and the apoptosis, an important process in the metamorphosis of insects.


Assuntos
Apoptose/efeitos dos fármacos , Cloreto de Cádmio/efeitos adversos , Chironomidae/efeitos dos fármacos , Cobre/efeitos adversos , Proteínas de Insetos/genética , Transcrição Genética/efeitos dos fármacos , Poluentes Químicos da Água/efeitos adversos , Animais , Apoptose/genética , Chironomidae/genética , Chironomidae/crescimento & desenvolvimento , Chironomidae/fisiologia , Relação Dose-Resposta a Droga , Proteínas de Insetos/metabolismo , Larva/efeitos dos fármacos , Larva/fisiologia , RNA Mensageiro/análise , Reação em Cadeia da Polimerase em Tempo Real , Regulação para Cima
9.
Eur J Endocrinol ; 181(1): 69-78, 2019 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-31096184

RESUMO

Objective: The pathophysiology of aldosterone-producing adenomas (APAs) has been intensively investigated using genetic and epigenetic approaches. However, the role of miRNAs in APA is not fully understood. The present study profiled miRNAs in APAs as an exploratory approach to elucidate their pathophysiological roles in APAs. Design: Tissues of APAs and other adrenocortical adenomas were obtained from patients who underwent adrenalectomy. Methods: Candidate miRNAs differentially detected from samples were examined by whole miRNA sequencing. The expression of candidate miRNAs in APA tissues were further validated by real-time quantitative polymerase chain reaction (qPCR). Further, differential miRNA expression between APAs with and without KCNJ5 somatic mutations was examined. Prediction of miRNA target genes was performed by bioinformatics analysis. For specific miRNAs, correlation analysis between the levels of their target genes and CYP11B2 was analyzed in APA tissues. Results: Our study determined differential expression of six miRNAs in APA or APA with KCNJ5 mutations. We further demonstrated that miR299 levels were negatively correlated with mRNA levels of CACNB2, which encodes the beta-subunit of the L-type calcium channel. Additionally, we found significant correlations among miR299, CACNB2, and CYP11B2 levels in APA tissues. Conclusions: Our study suggests the possible pathophysiological involvement of specific miRNAs in calcium signaling and aldosterone hypersecretion in APAs. Further studies, including in vitro analyses, are required to clarify these findings.


Assuntos
Adenoma Adrenocortical/genética , Aldosterona/biossíntese , Citocromo P-450 CYP11B2/genética , Perfilação da Expressão Gênica , MicroRNAs/fisiologia , Adrenalectomia , Adenoma Adrenocortical/metabolismo , Idoso , Canais de Cálcio Tipo L/genética , Feminino , Canais de Potássio Corretores do Fluxo de Internalização Acoplados a Proteínas G/genética , Expressão Gênica/fisiologia , Humanos , Masculino , MicroRNAs/análise , Pessoa de Meia-Idade , Mutação , RNA Mensageiro/análise , Reação em Cadeia da Polimerase em Tempo Real
10.
Acta Cir Bras ; 34(4): e201900403, 2019 Apr 29.
Artigo em Inglês | MEDLINE | ID: mdl-31038583

RESUMO

PURPOSE: To investigate the long non-coding RNAs (lncRNAs) profile on renal ischemia reperfusion in a mouse model. METHODS: Microarray analysis was used to study the expression of misregulated lncRNA in a mouse model of renal ischemia reperfusion(I/R) with long ischemia time. Quantitative real-time PCR (qPCR) was used to verify the expression of selected lncRNAs and mRNAs.The potential functions of the lncRNA was analyzed by bioinformatics tools and databases. RESULTS: Kidney function was impaired in I/R group compared to the normal group. Analysis showed that a total of 2267 lncRNAs and 2341 messenger RNAs (mRNAs) were significantly expressed in I/R group (≥2.0-fold, p < 0.05).The qPCR result showed that lncRNAs and mRNAs expression were consistent with the microarray analysis. The co-expression network profile analysis based on five validated lncRNAs and 203 interacted mRNAs showed it existed a total of 208 nodes and 333 connections. The GO and KEEG pathway analysis results showed that multiple lncRNAs are involved the mechanism of I/R. CONCLUSION: Multiple lncRNAs are involved in the mechanism of I/R.These analysis results will help us to further understand the mechanism of I/R and promote the new methods targeted at lncRNA to improve I/R injury.


Assuntos
Rim/irrigação sanguínea , RNA Longo não Codificante/análise , RNA Mensageiro/análise , Traumatismo por Reperfusão/genética , Animais , Regulação para Baixo , Expressão Gênica , Perfilação da Expressão Gênica , Redes Reguladoras de Genes , Camundongos , Camundongos Endogâmicos C57BL , Reação em Cadeia da Polimerase em Tempo Real , Valores de Referência , Análise Serial de Tecidos/métodos , Regulação para Cima
11.
Cell Physiol Biochem ; 52(6): 1484-1502, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31099508

RESUMO

BACKGROUND/AIMS: The transient receptor potential cation channel subfamily C member 6 (TRPC6) is a Ca2+-permeable nonselective cation channel and has received recent attention because of its capability to promote chronic kidney disease (CKD). The aims of this study were (i) to examine whether deletion of TRPC6 impacts on renal fibrosis and inflammatory cell infiltration in an early CKD model of unilateral ureter obstruction (UUO) in mice; and (ii) whether TRPC6-deficiency as well as UUO affect the regulation of TRPC expression in murine kidneys. METHODS: Wild-type (WT), Trpc6-knockout (Trpc6-/-) and New Zealand obese (NZO) mice underwent sham operation or unilateral ureteral obstruction (UUO). The kidneys were harvested 7 days after surgery. We examined renal fibrosis and inflammatory cell infiltration by histological and immunohistochemical staining. The mRNA expression of TRPC members and markers of fibrosis and inflammation in kidney were assessed by using real-time quantitative reverse transcription PCR. RESULTS: Histological and immunohistochemical analyses revealed less inflammatory cell infiltration (F4/80 and CD3) in UUO kidneys of Trpc6-/- mice compared to UUO kidneys of WT mice as well as less fibrosis. Genomic deletion of TRPC6 also affected the expression of pro-fibrotic genes in UUO Trpc6-/- kidneys compared to UUO WT kidneys while the expression of pro-inflammatory genes did not differ. UUO caused marked up-regulation of Trpc6 and down-regulation of Trpc1 mRNA in kidneys of WT and NZO mice. Trpc3 mRNA expression was significantly elevated in kidneys of Trpc6-/- mice underwent UUO while the levels did not change in kidneys of neither WT nor in NZO mice underwent UUO. CONCLUSION: TRPC6 contributes to renal fibrosis and immune cell infiltration in the UUO mouse model. Therefore, inhibition of TRPC6 emerges as a promising novel therapeutic strategy for treatment of chronic kidney failure in chronic obstructive nephropathy. However, confounding genomic and non-genomic effects of other TRPC channels should be taken into consideration to fully comprehend the renoprotective potential of targeting TRPC6 therapeutically under chronic kidney damaging conditions.


Assuntos
Regulação da Expressão Gênica , Rim/patologia , Canais de Cátion TRPC/genética , Obstrução Ureteral/genética , Animais , Modelos Animais de Doenças , Fibrose , Deleção de Genes , Inflamação/complicações , Inflamação/genética , Inflamação/patologia , Rim/metabolismo , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Knockout , Camundongos Obesos , RNA Mensageiro/análise , RNA Mensageiro/genética , Insuficiência Renal Crônica/complicações , Insuficiência Renal Crônica/genética , Insuficiência Renal Crônica/patologia , Regulação para Cima , Obstrução Ureteral/complicações , Obstrução Ureteral/patologia
12.
Methods Mol Biol ; 1970: 315-330, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30963500

RESUMO

MicroRNAs (miRNAs) are small noncoding RNAs of 22-25 nucleotides that control gene expression at the posttranscriptional level through the degradation of mRNAs or translational repression. In the last 15 years, the study of these small molecules helped elucidate their role in the regulation of many cellular processes and the onset and development of several diseases. Therefore, many computational tools based on algorithms for target prediction have been developed to identify potential miRNA-target interactions. The improvement of experimental approaches to more easily and quickly confirm in silico predictions has become essential for the study of these small RNAs and their molecular functions. In this chapter, we summarized the principal steps of one of the most used techniques for the validation of microRNA targets, the Luciferase assay, thus explaining the underlying principles and the procedures to apply it best.


Assuntos
Biologia Computacional/métodos , Luciferases/metabolismo , MicroRNAs/genética , RNA Mensageiro/análise , Regulação da Expressão Gênica , Genes Reporter , Humanos , Luciferases/genética , MicroRNAs/metabolismo , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Estudos de Validação como Assunto
13.
Methods Mol Biol ; 1970: 341-353, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30963502

RESUMO

MicroRNAs are a class of small noncoding RNA involved in the mechanism of RNA silencing and regulation of gene expression at a posttranscriptional level. Recently, the discovery of their targets led to the understanding of the molecular role of these small molecules and their involvement in the pathogenesis of numerous diseases, including cancer. Not long ago, the improvement of several informatics tools for microRNA target prediction has supported the experimental research through the selection of potential mRNA as microRNA target candidates. Since the regulation mediated by microRNA affects gene expression at a posttranscriptional level, the analysis of the proteins encoded by the gene targets is essential in understanding the involvement of these small molecules in biological processes and their role in several diseases. In this chapter, we describe the experimental procedure of Western blotting applied to the validation of microRNA targets. Western blotting is one of the most common and largest know technique for protein analysis. This method, coupled with the luciferase assay, represents the standard procedure for the experimental confirmation of microRNA targeting.


Assuntos
Western Blotting/métodos , Biologia Computacional/métodos , Luciferases/metabolismo , MicroRNAs/genética , RNA Mensageiro/análise , Regulação da Expressão Gênica , Humanos , MicroRNAs/metabolismo , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Estudos de Validação como Assunto
14.
Fish Shellfish Immunol ; 90: 275-287, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-30936049

RESUMO

JAK/STAT signaling pathways are associated with the innate immune system and play important roles in mediating immune responses to virus infection. In this study, a Janus kinase gene from Scylla paramamosain (SpJAK) was cloned and characterized. The full length of SpJAK mRNA contains a 5' untranslated region (UTR) of 304 bp, an open reading frame of 3300 bp and a 3' UTR of 302 bp. The SpJAK protein contains seven characteristic JAK homology domains (JH1 to JH7) and showed 60% identity (78% similarity), 20% identity (35% similarity), and 21% identity (37% similarity) to the Litopenaeus vannamei JAK (LvJAK) protein, the Drosophila melanogaster hopscotch protein, and the Homo sapiens JAK2 protein, respectively. The mRNA of SpJAK showed high expression in the brain and nerve but low expression in the hemocyte and muscle. Moreover, the expression of SpJAK was significantly upregulated by stimulation with mud crab reovirus (MCRV), poly(I:C), and Vibrio parahaemolyticus. SpJAK significantly activated the STAT of S. paramamosain (SpSTAT) to translocate to the nucleus of Drosophila Schneider 2 cells. SpJAK significantly enhanced the activity of the promoter of the WSSV wsv069 gene that was activated significantly by SpSTAT by acting on the STAT-binding DNA motif. These results suggest that SpJAK activates the JAK/STAT pathway. Furthermore, silencing SpJAK in vivo resulted in the high mortality rate of MCRV-infected mud crabs and increased the viral load in tissues. Hence, SpJAK could play an important role in defense against MCRV in mud crab.


Assuntos
Braquiúros/genética , Braquiúros/imunologia , Regulação da Expressão Gênica/imunologia , Imunidade Inata/genética , Janus Quinases/genética , Janus Quinases/imunologia , Reoviridae/fisiologia , Sequência de Aminoácidos , Animais , Proteínas de Artrópodes/química , Proteínas de Artrópodes/genética , Proteínas de Artrópodes/imunologia , Sequência de Bases , Perfilação da Expressão Gênica , Janus Quinases/química , Filogenia , RNA Mensageiro/análise , RNA Mensageiro/genética , Alinhamento de Sequência , Transdução de Sinais
15.
Med Sci Monit ; 25: 2386-2396, 2019 Apr 02.
Artigo em Inglês | MEDLINE | ID: mdl-30938333

RESUMO

BACKGROUND Cisplatin-resistant gastric cancer (GC) occurs in patients with GC treated with cisplatin-based chemotherapy, which results in disease progression and early recurrence during the treatment. MATERIAL AND METHODS To understand the initiation and developmental mechanism underlying cisplatin-resistant GC, we developed cisplatin-resistant SGC7901 cells (SGC7901/DDP) from the parental cells (SGC7901/S) by continuous exposure to increasing concentrations of cisplatin and subjected these 2 cell lines to RNA sequencing analysis. The data were verified by quantitative polymerase chain reaction and their functional role was evaluated by cell counting kit 8 assay and cell apoptosis and cell cycle flow cytometric analysis. Bioinformatics analysis was performed to classify the differentially-expressed genes (DEGs) involved in the development of cisplatin resistance. RESULTS In comparison with SGC7901/S cells, SGC7901/DDP cells showed a total of 3165 DEGs (2014 upregulated and 1151 downregulated, fold change ≥2, and adjusted P value <0.001). qRT-PCR confirmed the reliability of the RNA sequencing results. Depletion of the top 5 upregulated mRNAs reversed the resistant index, increased apoptotic SGC7901/DDP cells, and arrested the cells at G2/M phase. Gene ontology analysis revealed that the DEGs mainly regulate metabolic process, immune system, locomotion, cell adhesion, cell growth, cell death, cytoskeleton organization, cell binding, signal transducing activity, and antioxidant activity. Kyoto Encyclopedia of Genes and Genomes analysis showed that the DEGs were mainly involved in the PI3K-Akt signaling pathway, Rap1 signaling pathway, proteoglycans in cancer, regulation of actin cytoskeleton, and pathways in cancer. CONCLUSIONS The present study is the first to interrogate mRNAs profiles in human GC cells with cisplatin resistance using RNA sequencing, which may assist in discovering potential therapeutic targets for cisplatin-resistant GC patients.


Assuntos
Resistencia a Medicamentos Antineoplásicos/genética , Perfilação da Expressão Gênica/métodos , Neoplasias Gástricas/genética , Apoptose/efeitos dos fármacos , Linhagem Celular Tumoral , Proliferação de Células/efeitos dos fármacos , Cisplatino/metabolismo , Cisplatino/farmacologia , Resistência a Múltiplos Medicamentos/genética , Regulação Neoplásica da Expressão Gênica/efeitos dos fármacos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , RNA Mensageiro/análise , Reprodutibilidade dos Testes , Transcriptoma/genética
16.
Biol Res ; 52(1): 23, 2019 Apr 16.
Artigo em Inglês | MEDLINE | ID: mdl-30992080

RESUMO

BACKGROUND: Conjunctival filtering bleb scar formation is the main reason for the failure of glaucoma filtration surgery. Cytoglobin (Cygb) has been reported to play an important role in extracellular matrix (ECM) remodeling, fibrosis and tissue damage repairing. This study aimed to investigate the role of Cygb in anti-scarring during excessive conjunctival wound healing after glaucoma filtration surgery. METHODS: Cygb was overexpressed in human tenon fibroblasts (hTFs) by transfecting hTFs with lentiviral particles encoding pLenti6.2-FLAG-Cygb. Changes in the mRNA and protein levels of fibronectin, collagen I, collagen III, TGF-ß1, and HIF1α were determined by RT-PCR and western blotting respectively. RESULTS: After Cygb overexpression, hTFs displayed no significant changes in visual appearance and cell counts compared to controls. Whereas, Cygb overexpression significantly decreased the mRNA and protein expression levels of collagen I, collagen III and fibronectin compared with control (p < 0.01). There was also a statistically significant decrease in the mRNA and protein levels of TGF-ß1 and HIF-1α in hTFs with overexpressed Cygb compared with control group (p < 0.05). CONCLUSION: Our study provided evidence that overexpression of Cygb decreased the expression levels of fibronectin, collagen I, collagen III, TGF-ß1 and HIF-1α in hTFs. Therefore, therapies targeting Cygb expression in hTFs may pave a new way for clinicians to solve the problem of post-glaucoma surgery scarring.


Assuntos
Citoglobina/metabolismo , Matriz Extracelular/metabolismo , Fibroblastos/metabolismo , Cápsula de Tenon/metabolismo , Colágeno/análise , Citoglobina/farmacologia , Matriz Extracelular/efeitos dos fármacos , Fibronectinas/análise , Humanos , RNA Mensageiro/análise , Fator A de Crescimento do Endotélio Vascular/metabolismo
17.
Adv Exp Med Biol ; 1129: 63-79, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30968361

RESUMO

In this review, we describe the BD Rhapsody™ Single-Cell Analysis System, a platform that allows high-throughput capture of nucleic acids from single cells using a simple cartridge workflow and a multitier barcoding system. The resulting captured information can be used to generate various types of next-generation sequencing (NGS) libraries, including whole transcriptome analysis for discovery biology and targeted RNA analysis for high sensitivity transcript detection. The BD Rhapsody system can be used with emerging applications, such as BD™ AbSeq assays, to profile gene expression in both mRNA and protein level to provide ultra-high resolution analysis of single cells.


Assuntos
Perfilação da Expressão Gênica , Sequenciamento de Nucleotídeos em Larga Escala , RNA Mensageiro/análise , Análise de Célula Única/instrumentação , Análise de Célula Única/métodos , Análise de Sequência de RNA , Transcriptoma
18.
Int J Mol Sci ; 20(8)2019 Apr 15.
Artigo em Inglês | MEDLINE | ID: mdl-30991638

RESUMO

The cerebellum contains a circadian clock, generating internal temporal signals. The daily oscillations of cerebellar proteins were investigated in mice using a large-scale two-dimensional difference in gel electrophoresis (2D-DIGE). Analysis of 2D-DIGE gels highlighted the rhythmic variation in the intensity of 27/588 protein spots (5%) over 24 h based on cosinor regression. Notably, the rhythmic expression of most abundant cerebellar proteins was clustered in two main phases (i.e., midday and midnight), leading to bimodal distribution. Only six proteins identified here to be rhythmic in the cerebellum are also known to oscillate in the suprachiasmatic nuclei, including two proteins involved in the synapse activity (Synapsin 2 [SYN2] and vesicle-fusing ATPase [NSF]), two others participating in carbohydrate metabolism (triosephosphate isomerase (TPI1] and alpha-enolase [ENO1]), Glutamine synthetase (GLUL), as well as Tubulin alpha (TUBA4A). Most oscillating cerebellar proteins were not previously identified in circadian proteomic analyses of any tissue. Strikingly, the daily accumulation of mitochondrial proteins was clustered to the mid-resting phase, as previously observed for distinct mitochondrial proteins in the liver. Moreover, a number of rhythmic proteins, such as SYN2, NSF and TPI1, were associated with non-rhythmic mRNAs, indicating widespread post-transcriptional control in cerebellar oscillations. Thus, this study highlights extensive rhythmic aspects of the cerebellar proteome.


Assuntos
Cerebelo/metabolismo , Relógios Circadianos , Regulação da Expressão Gênica , Proteoma/análise , Proteoma/genética , Animais , Cerebelo/química , Ritmo Circadiano , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Proteômica , RNA Mensageiro/análise , RNA Mensageiro/genética , Eletroforese em Gel Diferencial Bidimensional
19.
Int J Mol Sci ; 20(8)2019 Apr 17.
Artigo em Inglês | MEDLINE | ID: mdl-30999696

RESUMO

MicroRNA-21 (miR-21) is upregulated in many cancers including colon cancers and is a prognostic indicator of recurrence and poor prognosis. In colon cancers, miR-21 is highly expressed in stromal fibroblastic cells and more weakly in a subset of cancer cells, particularly budding cancer cells. Exploration of the expression of inflammatory markers in colon cancers revealed tumor necrosis factor alpha (TNF-α) mRNA expression at the invasive front of colon cancers. Surprisingly, a majority of the TNF-α mRNA expressing cells were found to be cancer cells and not inflammatory cells. Because miR-21 is positively involved in cell survival and TNF-α promotes necrosis, we found it interesting to analyze the presence of miR-21 in areas of TNF-α mRNA expression at the invasive front of colon cancers. For this purpose, we developed an automated procedure for the co-staining of miR-21, TNF-α mRNA and the cancer cell marker cytokeratin based on analysis of frozen colon cancer tissue samples (n = 4) with evident cancer cell budding. In all four cases, TNF-α mRNA was seen in a small subset of cancer cells at the invasive front. Evaluation of miR-21 and TNF-α mRNA expression was performed on digital slides obtained by confocal slide scanning microscopy. Both co-expression and lack of co-expression with miR-21 in the budding cancer cells was noted, suggesting non-correlated expression. miR-21 was more often seen in cancer cells than TNF-α mRNA. In conclusion, we report that miR-21 is not linked to expression of the pro-inflammatory cytokine TNF-α mRNA, but that miR-21 and TNF-α both take part in the cancer expansion at the invasive front of colon cancers. We hypothesize that miR-21 may protect both fibroblasts and cancer cells from cell death directed by TNF-α paracrine and autocrine activity.


Assuntos
Colo/patologia , Neoplasias Colorretais/patologia , MicroRNAs/análise , RNA Mensageiro/análise , Fator de Necrose Tumoral alfa/genética , Neoplasias Colorretais/genética , Regulação Neoplásica da Expressão Gênica , Humanos , Inflamação/genética , Inflamação/patologia , MicroRNAs/genética , Microscopia Confocal , RNA Mensageiro/genética
20.
BMC Bioinformatics ; 20(1): 190, 2019 Apr 16.
Artigo em Inglês | MEDLINE | ID: mdl-30991937

RESUMO

BACKGROUND: The rapid increase in High-throughput sequencing of RNA (RNA-seq) has led to tremendous improvements in the detection and reconstruction of both expressed coding and non-coding RNA transcripts. Yet, the complete and accurate annotation of the complex transcriptional output of not only the human genome has remained elusive. One of the critical bottlenecks in this endeavor is the computational reconstruction of transcript structures, due to high noise levels, technological limits, and other biases in the raw data. RESULTS: We introduce several new and improved algorithms in a novel workflow for transcript assembly and quantification. We propose an extension of the common splice graph framework that combines aspects of overlap and bin graphs and makes it possible to efficiently use both multi-splice and paired-end information to the fullest extent. Phasing information of reads is used to further resolve loci. The decomposition of read coverage patterns is modeled as a minimum-cost flow problem to account for the unavoidable non-uniformities of RNA-seq data. CONCLUSION: Its performance compares favorably with state of the art methods on both simulated and real-life datasets. Ryuto calls 1-4% more true transcripts, while calling 5-35% less false predictions compared to the next best competitor.


Assuntos
Biologia Computacional/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , RNA Mensageiro , Análise de Sequência de RNA/métodos , Transcriptoma/genética , Algoritmos , Perfilação da Expressão Gênica/métodos , Humanos , RNA Mensageiro/análise , RNA Mensageiro/genética
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA