Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 73
Filtrar
1.
Int J Mol Sci ; 24(12)2023 Jun 14.
Artigo em Inglês | MEDLINE | ID: mdl-37373258

RESUMO

Mitochondrial RNA editing in trypanosomes represents an attractive target for developing safer and more efficient drugs for treating infections with trypanosomes because this RNA editing pathway is not found in humans. Other workers have targeted several enzymes in this editing system, but not the RNA. Here, we target a universal domain of the RNA editing substrate, which is the U-helix formed between the oligo-U tail of the guide RNA and the target mRNA. We selected a part of the U-helix that is rich in G-U wobble base pairs as the target site for the virtual screening of 262,000 compounds. After chemoinformatic filtering of the top 5000 leads, we subjected 50 representative complexes to 50 nanoseconds of molecular dynamics simulations. We identified 15 compounds that retained stable interactions in the deep groove of the U-helix. The microscale thermophoresis binding experiments on these five compounds show low-micromolar to nanomolar binding affinities. The UV melting studies show an increase in the melting temperatures of the U-helix upon binding by each compound. These five compounds can serve as leads for drug development and as research tools to probe the role of the RNA structure in trypanosomal RNA editing.


Assuntos
Edição de RNA , Bibliotecas de Moléculas Pequenas , Tripanossomicidas , Trypanosoma , Trypanosoma/efeitos dos fármacos , Edição de RNA/efeitos dos fármacos , RNA de Protozoário/química , RNA Mitocondrial/química , Tripanossomicidas/química , Tripanossomicidas/farmacologia , Conformação de Ácido Nucleico/efeitos dos fármacos , Simulação de Dinâmica Molecular , Bibliotecas de Moléculas Pequenas/química , Bibliotecas de Moléculas Pequenas/farmacologia
2.
J Biol Chem ; 299(7): 104840, 2023 07.
Artigo em Inglês | MEDLINE | ID: mdl-37209819

RESUMO

Adenosine-to-inosine RNA editing is catalyzed by nuclear adenosine deaminase acting on RNA 1 (ADAR1) p110 and ADAR2, and cytoplasmic ADAR1 p150 in mammals, all of which recognize dsRNAs as targets. RNA editing occurs in some coding regions, which alters protein functions by exchanging amino acid sequences, and is therefore physiologically significant. In general, such coding sites are edited by ADAR1 p110 and ADAR2 before splicing, given that the corresponding exon forms a dsRNA structure with an adjacent intron. We previously found that RNA editing at two coding sites of antizyme inhibitor 1 (AZIN1) is sustained in Adar1 p110/Aadr2 double KO mice. However, the molecular mechanisms underlying RNA editing of AZIN1 remain unknown. Here, we showed that Azin1 editing levels were increased upon type I interferon treatment, which activated Adar1 p150 transcription, in mouse Raw 264.7 cells. Azin1 RNA editing was observed in mature mRNA but not precursor mRNA. Furthermore, we revealed that the two coding sites were editable only by ADAR1 p150 in both mouse Raw 264.7 and human embryonic kidney 293T cells. This unique editing was achieved by forming a dsRNA structure with a downstream exon after splicing, and the intervening intron suppressed RNA editing. Therefore, deletion of a nuclear export signal from ADAR1 p150, shifting its localization to the nucleus, decreased Azin1 editing levels. Finally, we demonstrated that Azin1 RNA editing was completely absent in Adar1 p150 KO mice. Thus, these findings indicate that RNA editing of AZIN1 coding sites is exceptionally catalyzed by ADAR1 p150 after splicing.


Assuntos
Adenosina Desaminase , Proteínas de Transporte , Edição de RNA , Animais , Humanos , Camundongos , Adenosina Desaminase/metabolismo , Proteínas de Transporte/genética , Proteínas de Transporte/metabolismo , Catálise , Edição de RNA/efeitos dos fármacos , Edição de RNA/genética , RNA de Cadeia Dupla/genética , RNA Mensageiro/metabolismo , Células HEK293 , Camundongos Knockout , Células RAW 264.7 , Interferons/farmacologia , Transporte Proteico
3.
Toxicol Lett ; 331: 22-32, 2020 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-32439581

RESUMO

Adenosine-to-inosine (A-to-I) RNA editing, catalyzed by adenosine deaminase acting on RNA (ADAR) enzymes, is the most frequent type of post-transcriptional nucleotide conversion in humans. It is known that innate abnormalities of A-to-I RNA editing are associated with the risk of certain diseases, such as amyotrophic lateral sclerosis. Extrinsic factors that modulate ADAR-mediated RNA editing remain to be clarified. In this study, we investigated the possibility that cigarette smoking may influence the expression of ADAR and that the changes may be biologically significant. Treatment of human lung adenocarcinoma A549 cells with cigarette smoke extract (CSE) induced a significant 50% decrease in ADAR1 protein levels. Since the decrease was counteracted by cotreatment with chloroquine, the CSE-dependent decrease in the ADAR1 protein levels may be due to the activation of autophagy. In addition to the in vitro study, we performed an in vivo study in mice and found a decrease in pulmonary Adar1 protein expression induced by cigarette smoking. Then, we investigated the biological significance of decreased ADAR1 expression. We found that knockdown of ADAR1 in A549 cells by siRNA resulted in an increase in the levels of protein carbonyl, a marker of oxidative stress. Moreover, knockdown of ADAR1 triggered a decrease in super oxide dismutase activity and heme oxygenase-1 expression, suggesting that ADAR1 plays a role to suppress oxidative stress. In conclusion, we show that ADAR1 expression is decreased by cigarette smoking and is a factor that contributes to the enhanced intracellular oxidative stress caused by cigarette smoking.


Assuntos
Adenosina Desaminase/genética , Estresse Oxidativo/efeitos dos fármacos , Edição de RNA/efeitos dos fármacos , Proteínas de Ligação a RNA/genética , Fumaça/efeitos adversos , Produtos do Tabaco , Células A549 , Técnicas de Cultura de Células , Sobrevivência Celular/efeitos dos fármacos , Sobrevivência Celular/genética , Humanos , Estresse Oxidativo/genética
4.
RNA ; 26(7): 827-835, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32276989

RESUMO

The RNA editing core complex (RECC) catalyzes mitochondrial U-insertion/deletion mRNA editing in trypanosomatid flagellates. Some naphthalene-based sulfonated compounds, such as C35 and MrB, competitively inhibit the auto-adenylylation activity of an essential RECC enzyme, kinetoplastid RNA editing ligase 1 (KREL1), required for the final step in editing. Previous studies revealed the ability of these compounds to interfere with the interaction between the editosome and its RNA substrates, consequently affecting all catalytic activities that comprise RNA editing. This observation implicates a critical function for the affected RNA binding proteins in RNA editing. In this study, using the inhibitory compounds, we analyzed the composition and editing activities of functional editosomes and identified the mitochondrial RNA binding proteins 1 and 2 (MRP1/2) as their preferred targets. While the MRP1/2 heterotetramer complex is known to bind guide RNA and promote annealing to its cognate pre-edited mRNA, its role in RNA editing remained enigmatic. We show that the compounds affect the association between the RECC and MRP1/2 heterotetramer. Furthermore, RECC purified post-treatment with these compounds exhibit compromised in vitro RNA editing activity that, remarkably, recovers upon the addition of recombinant MRP1/2 proteins. This work provides experimental evidence that the MRP1/2 heterotetramer is required for in vitro RNA editing activity and substantiates the hypothesized role of these proteins in presenting the RNA duplex to the catalytic complex in the initial steps of RNA editing.


Assuntos
Ligases/antagonistas & inibidores , Proteínas Mitocondriais/genética , Proteínas de Protozoários/genética , Edição de RNA/genética , RNA Guia de Cinetoplastídeos/efeitos dos fármacos , RNA de Protozoário/genética , Proteínas de Ligação a RNA/genética , Mitocôndrias/efeitos dos fármacos , Mitocôndrias/genética , Edição de RNA/efeitos dos fármacos , RNA Mensageiro/genética , RNA Mitocondrial/genética , Proteínas Recombinantes/genética , Trypanosoma brucei brucei/efeitos dos fármacos
5.
Neurochem Int ; 134: 104689, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-31968217

RESUMO

The alcoholism and major depressive disorder are common comorbidity, with alcohol-induced depressive symptoms being eased by selective serotonin re-uptake inhibitors (SSRIs), although the mechanisms underlying pathology and therapy are poorly understood. Chronic alcohol consumption affects the activity of serotonin 2C receptors (5-HT2CR) by regulating adenosine deaminases acting on RNA (ADARs) in neurons. Astrogliopathic changes contribute to alcohol addiction, while decreased release of ATP from astrocytes can trigger depressive-like behaviours in mice. In this study, we discovered that chronic alcohol treatment increased editing of RNA of 5-HT2CR via up-regulating the expression of ADAR2, consequently reducing the release of ATP from astrocytes induced by 5-HT2CR agonist, MK212. Moreover, SSRI antidepressant fluoxetine decreased the expression of ADAR2 through the transactivation of EGFR/PI3K/AKT/cFos signalling pathway. The increased release of astroglial ATP by MK212 which was suppressed by chronic alcohol consumption, and reduction in ADAR2 activity eliminated the RNA editing of 5-HT2CR increased by alcohol in vitro and recovered the release of ATP from astrocytes induced by MK212. Meanwhile, fluoxetine improved the behavioural and motor symptoms induced by alcohol addiction and decreased the alcohol intake. Our study suggests that the astrocytic 5-HT2CR contribute to alcohol addiction; fluoxetine thus can be used to alleviate depression, treat alcohol addiction and improve motor coordination.


Assuntos
Álcoois/farmacologia , Comportamento Animal/efeitos dos fármacos , Fluoxetina/farmacologia , Receptor 5-HT2C de Serotonina/efeitos dos fármacos , Alcoolismo/tratamento farmacológico , Alcoolismo/metabolismo , Animais , Astrócitos/efeitos dos fármacos , Astrócitos/metabolismo , Encéfalo/efeitos dos fármacos , Encéfalo/metabolismo , Transtorno Depressivo Maior/tratamento farmacológico , Camundongos , Neurônios/efeitos dos fármacos , Neurônios/metabolismo , Edição de RNA/efeitos dos fármacos , Receptor 5-HT2C de Serotonina/metabolismo , Serotonina/metabolismo , Inibidores Seletivos de Recaptação de Serotonina/farmacologia , Transdução de Sinais/efeitos dos fármacos
6.
Int J Biol Macromol ; 141: 1228-1245, 2019 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-31520703

RESUMO

Lipopolysaccharide (LPS) is a bacterial endotoxin which can participate in the induction of inflammatory responses. LPS may also play a significant role in some neurodegenerative, oncological and metabolic disorders. The aim of the current study was to determine the effect of a subclinical low single dose of LPS from Salmonella Enteritidis administrated in vivo on the transcriptome of porcine adrenal cortex cells, especially gene expression levels, long non-coding RNA (lncRNA) profiles, alternative splicing events and RNA editing sites using RNA-seq technology. The subclinical dose of LPS changed the expression of 354 genes, 27 lncRNA loci and other unclassified RNAs. An analysis of alternative splicing events revealed 104 genes with differentially expressed splice junction sites, and the single nucleotide variant calling approach supported the identification of 376 canonical RNA editing candidates and 7249 allele-specific expression variants. The obtained results suggest that the RIG-I-like receptor signaling pathway, may play a more important role than the Toll-like signaling pathway after the administration of a subclinical dose of LPS. Single subclinical dose of LPS can affect the expression profiles of genes coding peptide hormones, steroidogenic enzymes and transcriptional factors, and modulate the endocrine functions of the gland.


Assuntos
Córtex Suprarrenal/efeitos dos fármacos , Córtex Suprarrenal/metabolismo , Lipopolissacarídeos/farmacologia , Salmonella enteritidis/química , Transcriptoma/efeitos dos fármacos , Processamento Alternativo/efeitos dos fármacos , Animais , Relação Dose-Resposta a Droga , Feminino , Anotação de Sequência Molecular , Edição de RNA/efeitos dos fármacos , Suínos
7.
J Neurovirol ; 25(6): 825-836, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31332697

RESUMO

Treatment-emergent depression is a common complication in patients with chronic hepatitis C virus (HCV) infection undergoing antiviral combination therapy with IFN-α and ribavirin. It has recently been shown that changes in A-to-I RNA editing rates are associated with various pathologies such as inflammatory disorders, depression and suicide. Interestingly, IFN-α induces gene expression of the RNA editing enzyme ADAR1-1 (ADAR1a-p150) and alters overall RNA editing activity. In this study, we took advantage of the high prevalence of pharmacologically induced depression in patients treated with IFN-α and ribavirin to test the interest of RNA editing-related biomarkers in white blood cells of patients. In this 16-week longitudinal study, a small cohort of patients was clinically evaluated using standard assessment methods prior to and during antiviral therapy and blood samples were collected to analyse RNA editing modifications. A-I RNA editing activity on the phosphodiesterase 8A (PDE8A) gene, a previously identified RNA editing hotspot in the context of lupus erythematosus, was quantified by using an ultra-deep next-generation sequencing approach. We also monitored gene expression levels of the ADAR enzymes and the PDE8A gene during treatment by qPCR. As expected, psychiatric evaluation could track treatment-emergent depression, which occurred in 30% of HCV patients. We show that PDE8A RNA editing is increased in all patients following interferon treatment, but differently in 30% of patients. This effect was mimicked in a cellular model using SHSY-5Y neuroblastoma cells. By combining the data of A-I RNA editing and gene expression, we generated an algorithm that allowed discrimination between the group of patients who developed a treatment-emergent depression and those who did not. The current model of drug-induced depression identified A-I RNA editing biomarkers as useful tools for the identification of individuals at risk of developing depression in an objective, quantifiable biological blood test.


Assuntos
Antivirais/efeitos adversos , Biomarcadores/sangue , Depressão/sangue , Depressão/induzido quimicamente , Hepatite C Crônica/tratamento farmacológico , Edição de RNA/efeitos dos fármacos , 3',5'-AMP Cíclico Fosfodiesterases/sangue , 3',5'-AMP Cíclico Fosfodiesterases/genética , Adenosina Desaminase/sangue , Adenosina Desaminase/genética , Adulto , Idoso , Feminino , Hepacivirus , Humanos , Interferon-alfa/efeitos adversos , Estudos Longitudinais , Masculino , Pessoa de Meia-Idade , Polietilenoglicóis/efeitos adversos , Edição de RNA/fisiologia , Proteínas Recombinantes/efeitos adversos , Ribavirina/efeitos adversos
8.
Drug Resist Updat ; 32: 16-22, 2017 05.
Artigo em Inglês | MEDLINE | ID: mdl-29145975

RESUMO

In recent years, A-to-I RNA modifications performed by the Adenosine Deaminase Acting on RNA (ADAR) protein family were found to be expressed at altered levels in multiple human malignancies. A-to-I RNA editing changes adenosine to inosine on double stranded RNA, thereby changing transcript sequence and structure. Although A-to-I RNA editing have the potential to change essential mRNA transcripts, affecting their corresponding protein structures, most of the human editing sites identified to date reside in non-coding repetitive transcripts such as Alu elements. Therefore, the impact of the hypo- or hyper-editing found in specific cancers remains unknown. Moreover, it is yet unclear whether or not changes in RNA editing and ADAR expression levels facilitate or even drive cancer progression or are just a byproduct of other affected pathways. In both cases, however, the levels of RNA editing and ADAR enzymes can possibly be used as specific biomarkers, as their levels change differently in specific malignancies. More significantly, recent studies suggest that ADAR enzymes can be used to reverse the oncogenic process, suggesting a potential for gene therapies. This review focuses on new findings that suggest that RNA editing by ADARs can affect cancer progression and even formation. We also discuss new possibilities of using ADAR enzymes and RNA editing as cancer biomarkers, indicators of chemotherapeutic drug sensitivity, and even to be themselves potential therapeutic tools.


Assuntos
Adenosina Desaminase/genética , Carcinogênese/genética , Neoplasias/genética , Edição de RNA/genética , Proteínas de Ligação a RNA/genética , Adenosina/genética , Adenosina/metabolismo , Adenosina Desaminase/metabolismo , Elementos Alu/genética , Antineoplásicos/uso terapêutico , Biomarcadores Tumorais/genética , Biomarcadores Tumorais/metabolismo , Carcinogênese/patologia , Terapia Genética/métodos , Humanos , Inosina/genética , Inosina/metabolismo , Terapia de Alvo Molecular/métodos , Terapia de Alvo Molecular/tendências , Neoplasias/patologia , Neoplasias/terapia , Oncogenes/genética , Edição de RNA/efeitos dos fármacos , RNA de Cadeia Dupla/genética , RNA Mensageiro/genética , Proteínas de Ligação a RNA/metabolismo , Proteínas Supressoras de Tumor/genética
9.
Curr Med Chem ; 24(27): 2974-2987, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28302007

RESUMO

The effective control of insect pests is based on the use of insecticides. Most of these compounds act on molecular targets in the insect nervous system. However, the largescale deployment of insecticide treatment has led to the development of resistance, which decreases insecticide efficacy. Although the resistance mechanisms are largely studied today, this review aims to point out new insights on the less-known cellular and molecular factors involved in the modulation of the sensitivity of the targets to insecticides. This review will focus on the phosphorylation/dephosphorylation process, the post-transcriptional events such as editing and alternative splicing and the influence of the association with auxiliary proteins of the receptors and/or ion channels targeted by insecticides. In addition, the involvement of calcium-dependent signaling pathways in the modulation of the sensitivity of the target to insecticides will also be considered and discussed. Finally, this review will insist on different strategies proposed to optimize the efficacy of insecticide treatment while reducing doses to decrease side effects on environment and on non-target organisms by combining two different chemical insecticides or a given active ingredient associated with biological and/or chemical synergistic agents. This review is part of the special issue "Insecticide Mode of Action: From Insect to Mammalian Toxicity".


Assuntos
Membrana Celular/efeitos dos fármacos , Inseticidas/toxicidade , Acetilcolinesterase/química , Acetilcolinesterase/metabolismo , Animais , Membrana Celular/metabolismo , Insetos/efeitos dos fármacos , Insetos/metabolismo , Inseticidas/metabolismo , Fosforilação/efeitos dos fármacos , Processamento de Proteína Pós-Traducional/efeitos dos fármacos , Edição de RNA/efeitos dos fármacos , Receptores de GABA/química , Receptores de GABA/metabolismo , Transdução de Sinais/efeitos dos fármacos
10.
RNA Biol ; 14(5): 611-619, 2017 05 04.
Artigo em Inglês | MEDLINE | ID: mdl-26786754

RESUMO

Non-coding RNAs are crucial regulators for a vast array of cellular processes and have been implicated in human disease. These biological processes represent a hitherto untapped resource in our fight against disease. In this work we identify small molecule inhibitors of a non-coding RNA uridylylation pathway. The TUTase family of enzymes is important for modulating non-coding RNA pathways in both human cancer and pathogen systems. We demonstrate that this new class of drug target can be accessed with traditional drug discovery techniques. Using the Trypanosoma brucei TUTase, RET1, we identify TUTase inhibitors and lay the groundwork for the use of this new target class as a therapeutic opportunity for the under-served disease area of African Trypanosomiasis. In a broader sense this work demonstrates the therapeutic potential for targeting RNA post-transcriptional modifications with small molecules in human disease.


Assuntos
Descoberta de Drogas , Inibidores da Síntese de Ácido Nucleico/farmacologia , Proteínas de Protozoários/antagonistas & inibidores , Edição de RNA/efeitos dos fármacos , RNA Nucleotidiltransferases/antagonistas & inibidores , RNA não Traduzido/biossíntese , Tripanossomicidas/farmacologia , Trypanosoma brucei brucei/enzimologia , Humanos , Inibidores da Síntese de Ácido Nucleico/química , Inibidores da Síntese de Ácido Nucleico/uso terapêutico , Tripanossomicidas/química , Tripanossomicidas/uso terapêutico , Trypanosoma brucei brucei/genética , Tripanossomíase Africana/tratamento farmacológico , Uridina Trifosfato/metabolismo
13.
Nat Med ; 22(10): 1140-1150, 2016 10.
Artigo em Inglês | MEDLINE | ID: mdl-27595325

RESUMO

Adenosine-to-inosine (A-to-I) RNA editing, which is catalyzed by a family of adenosine deaminase acting on RNA (ADAR) enzymes, is important in the epitranscriptomic regulation of RNA metabolism. However, the role of A-to-I RNA editing in vascular disease is unknown. Here we show that cathepsin S mRNA (CTSS), which encodes a cysteine protease associated with angiogenesis and atherosclerosis, is highly edited in human endothelial cells. The 3' untranslated region (3' UTR) of the CTSS transcript contains two inverted repeats, the AluJo and AluSx+ regions, which form a long stem-loop structure that is recognized by ADAR1 as a substrate for editing. RNA editing enables the recruitment of the stabilizing RNA-binding protein human antigen R (HuR; encoded by ELAVL1) to the 3' UTR of the CTSS transcript, thereby controlling CTSS mRNA stability and expression. In endothelial cells, ADAR1 overexpression or treatment of cells with hypoxia or with the inflammatory cytokines interferon-γ and tumor-necrosis-factor-α induces CTSS RNA editing and consequently increases cathepsin S expression. ADAR1 levels and the extent of CTSS RNA editing are associated with changes in cathepsin S levels in patients with atherosclerotic vascular diseases, including subclinical atherosclerosis, coronary artery disease, aortic aneurysms and advanced carotid atherosclerotic disease. These results reveal a previously unrecognized role of RNA editing in gene expression in human atherosclerotic vascular diseases.


Assuntos
Adenosina Desaminase/genética , Aterosclerose/genética , Catepsinas/genética , Proteína Semelhante a ELAV 1/genética , Edição de RNA/genética , RNA Mensageiro/metabolismo , Proteínas de Ligação a RNA/genética , Regiões 3' não Traduzidas , Adenosina/metabolismo , Adulto , Idoso , Idoso de 80 Anos ou mais , Aneurisma Aórtico/genética , Doenças das Artérias Carótidas/genética , Doença da Artéria Coronariana/genética , Feminino , Imunofluorescência , Regulação da Expressão Gênica , Técnicas de Introdução de Genes , Técnicas de Silenciamento de Genes , Sequenciamento de Nucleotídeos em Larga Escala , Células Endoteliais da Veia Umbilical Humana , Humanos , Hipóxia/genética , Immunoblotting , Inosina/metabolismo , Interferon gama/farmacologia , Masculino , Pessoa de Meia-Idade , Edição de RNA/efeitos dos fármacos , Processamento Pós-Transcricional do RNA/efeitos dos fármacos , Processamento Pós-Transcricional do RNA/genética , Reação em Cadeia da Polimerase em Tempo Real , Análise de Sequência de RNA , Fator de Necrose Tumoral alfa/farmacologia
14.
Dev Biol ; 409(2): 420-8, 2016 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-26632489

RESUMO

Sea urchin embryos are a useful model system for investigating early developmental processes and the underlying gene regulatory networks. Most functional studies using sea urchin embryos rely on antisense morpholino oligonucleotides to knockdown gene functions. However, major concerns related to this technique include off-target effects, variations in morpholino efficiency, and potential morpholino toxicity; furthermore, such problems are difficult to discern. Recent advances in genome editing technologies have introduced the prospect of not only generating sequence-specific knockouts, but also providing genome-engineering applications. Two genome editing tools, zinc-finger nuclease (ZFN) and transcription activator-like effector nucleases (TALENs), have been utilized in sea urchin embryos, but the resulting efficiencies are far from satisfactory. The CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 (CRISPR-associated nuclease 9) system serves as an easy and efficient method with which to edit the genomes of several established and emerging model organisms in the field of developmental biology. Here, we apply the CRISPR/Cas9 system to the sea urchin embryo. We designed six guide RNAs (gRNAs) against the well-studied nodal gene and discovered that five of the gRNAs induced the expected phenotype in 60-80% of the injected embryos. In addition, we developed a simple method for isolating genomic DNA from individual embryos, enabling phenotype to be precisely linked to genotype, and revealed that the mutation rates were 67-100% among the sequenced clones. Of the two potential off-target sites we examined, no off-target effects were observed. The detailed procedures described herein promise to accelerate the usage of CRISPR/Cas9 system for genome editing in sea urchin embryos.


Assuntos
Sistemas CRISPR-Cas/genética , Genoma , Edição de RNA/genética , Ouriços-do-Mar/embriologia , Ouriços-do-Mar/genética , Animais , Sequência de Bases , Embrião não Mamífero/metabolismo , Regulação da Expressão Gênica no Desenvolvimento/efeitos dos fármacos , Genótipo , Dados de Sequência Molecular , Morfolinos/farmacologia , Proteína Nodal/metabolismo , Ácidos Nucleicos Heteroduplexes , Fenótipo , Edição de RNA/efeitos dos fármacos , RNA Guia de Cinetoplastídeos/genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Ouriços-do-Mar/efeitos dos fármacos , Transdução de Sinais/efeitos dos fármacos
15.
BMC Syst Biol ; 9: 75, 2015 Nov 06.
Artigo em Inglês | MEDLINE | ID: mdl-26542228

RESUMO

BACKGROUND: Cellular function and diversity are orchestrated by complex interactions of fundamental biomolecules including DNA, RNA and proteins. Technological advances in genomics, epigenomics, transcriptomics and proteomics have enabled massively parallel and unbiased measurements. Such high-throughput technologies have been extensively used to carry out broad, unbiased studies, particularly in the context of human diseases. Nevertheless, a unified analysis of the genome, epigenome, transcriptome and proteome of a single human cell type to obtain a coherent view of the complex interplay between various biomolecules has not yet been undertaken. Here, we report the first multi-omic analysis of human primary naïve CD4+ T cells isolated from a single individual. RESULTS: Integrating multi-omics datasets allowed us to investigate genome-wide methylation and its effect on mRNA/protein expression patterns, extent of RNA editing under normal physiological conditions and allele specific expression in naïve CD4+ T cells. In addition, we carried out a multi-omic comparative analysis of naïve with primary resting memory CD4+ T cells to identify molecular changes underlying T cell differentiation. This analysis provided mechanistic insights into how several molecules involved in T cell receptor signaling are regulated at the DNA, RNA and protein levels. Phosphoproteomics revealed downstream signaling events that regulate these two cellular states. Availability of multi-omics data from an identical genetic background also allowed us to employ novel proteogenomics approaches to identify individual-specific variants and putative novel protein coding regions in the human genome. CONCLUSIONS: We utilized multiple high-throughput technologies to derive a comprehensive profile of two primary human cell types, naïve CD4+ T cells and memory CD4+ T cells, from a single donor. Through vertical as well as horizontal integration of whole genome sequencing, methylation arrays, RNA-Seq, miRNA-Seq, proteomics, and phosphoproteomics, we derived an integrated and comparative map of these two closely related immune cells and identified potential molecular effectors of immune cell differentiation following antigen encounter.


Assuntos
Linfócitos T CD4-Positivos/metabolismo , Imunidade Inata/fisiologia , Modelos Biológicos , Metilação de DNA , Epigenômica , Perfilação da Expressão Gênica , Variação Genética , Genoma Humano , Genômica , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Imunidade Inata/genética , Fosforilação , Proteômica , Edição de RNA/efeitos dos fármacos , RNA Mensageiro/metabolismo , Transdução de Sinais/genética , Transcriptoma
16.
J Biomol Screen ; 20(1): 92-100, 2015 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-25170016

RESUMO

Most mitochondrial messenger RNAs in trypanosomatid pathogens undergo a unique type of posttranscriptional modification involving insertion and/or deletion of uridylates. This process, RNA editing, is catalyzed by a multiprotein complex (~1.6 MDa), the editosome. Knockdown of core editosome proteins compromises mitochondrial function and, ultimately, parasite viability. Hence, because the editosome is restricted to trypanosomatids, it serves as a unique drug target in these pathogens. Currently, there is a lack of editosome inhibitors for antitrypanosomatid drug development or that could serve as unique tools for perturbing and characterizing editosome interactions or RNA editing reaction stages. Here, we screened a library of pharmacologically active compounds (LOPAC1280) using high-throughput screening to identify RNA editing inhibitors. We report that aurintricarboxylic acid, mitoxantrone, PPNDS, and NF449 are potent inhibitors of deletion RNA editing (IC50 range, 1-5 µM). However, none of these compounds could specifically inhibit the catalytic steps of RNA editing. Mitoxantrone blocked editing by inducing RNA-protein aggregates, whereas the other three compounds interfered with editosome-RNA interactions to varying extents. Furthermore, NF449, a suramin analogue, was effective at killing Trypanosoma brucei in vitro. Thus, new tools for editosome characterization and downstream RNA editing inhibitor have been identified.


Assuntos
Descoberta de Drogas/métodos , Ensaios de Triagem em Larga Escala , Edição de RNA/efeitos dos fármacos , Tripanossomicidas/farmacologia , Trypanosoma/efeitos dos fármacos , Trypanosoma/genética , Relação Dose-Resposta a Droga , Transferência Ressonante de Energia de Fluorescência/métodos , RNA Mensageiro , RNA Mitocondrial , Proteínas de Ligação a RNA/metabolismo , Bibliotecas de Moléculas Pequenas
17.
Mol Psychiatry ; 20(11): 1460-6, 2015 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-25349168

RESUMO

Activation of AMPA receptors (AMPARs) in the nucleus accumbens is necessary for the reinstatement of cocaine-seeking behavior, an animal model of drug craving and relapse. AMPARs are tetrameric protein complexes that consist of GluA1-4 subunits, of which GluA2 imparts calcium permeability. Adenosine deaminase acting on RNA 2 (ADAR2) is a nuclear enzyme that is essential for editing GluA2 pre-mRNA at Q/R site 607. Unedited GluA2(Q) subunits form calcium-permeable AMPARs (CP-AMPARs), whereas edited GluA2(R) subunits form calcium-impermeable channels (CI-AMPARs). Emerging evidence suggests that the reinstatement of cocaine seeking is associated with increased synaptic expression of CP-AMPARs in the nucleus accumbens. However, the role of GluA2 Q/R site editing and ADAR2 in cocaine seeking is unclear. In the present study, we investigated the effects of forced cocaine abstinence on GluA2 Q/R site editing and ADAR2 expression in the nucleus accumbens. Our results demonstrate that 7 days of cocaine abstinence is associated with decreased GluA2 Q/R site editing and reduced ADAR2 expression in the accumbens shell, but not core, of cocaine-experienced rats compared with yoked saline controls. To examine the functional significance of ADAR2 and GluA2 Q/R site editing in cocaine seeking, we used viral-mediated gene delivery to overexpress ADAR2b in the accumbens shell. Increased ADAR2b expression in the shell attenuated cocaine priming-induced reinstatement of drug seeking and was associated with increased GluA2 Q/R site editing and surface expression of GluA2-containing AMPARs. Taken together, these findings support the novel hypothesis that an increased contribution of accumbens shell CP-AMPARs containing unedited GluA2(Q) promotes cocaine seeking. Therefore, CP-AMPARs containing unedited GluA2(Q) represent a novel target for cocaine addiction pharmacotherapies.


Assuntos
Adenosina Desaminase/metabolismo , Cocaína/administração & dosagem , Inibidores da Captação de Dopamina/administração & dosagem , Comportamento de Procura de Droga/efeitos dos fármacos , Regulação da Expressão Gênica/efeitos dos fármacos , Receptores de AMPA/metabolismo , Adenosina Desaminase/genética , Animais , Cálcio/metabolismo , Condicionamento Operante/efeitos dos fármacos , Desoxirribonucleases de Sítio Específico do Tipo II/administração & dosagem , Regulação da Expressão Gênica/fisiologia , Masculino , Núcleo Accumbens/efeitos dos fármacos , Núcleo Accumbens/metabolismo , Edição de RNA/efeitos dos fármacos , Edição de RNA/genética , RNA Mensageiro/metabolismo , Ratos , Ratos Sprague-Dawley , Receptores de AMPA/genética , Autoadministração , Transdução Genética
18.
J Vis Exp ; (89)2014 Jul 22.
Artigo em Inglês | MEDLINE | ID: mdl-25079143

RESUMO

Substantial progress has been made in determining the mechanism of mitochondrial RNA editing in trypanosomes. Similarly, considerable progress has been made in identifying the components of the editosome complex that catalyze RNA editing. However, it is still not clear how those proteins work together. Chemical compounds obtained from a high-throughput screen against the editosome may block or affect one or more steps in the editing cycle. Therefore, the identification of new chemical compounds will generate valuable molecular probes for dissecting the editosome function and assembly. In previous studies, in vitro editing assays were carried out using radio-labeled RNA. These assays are time consuming, inefficient and unsuitable for high-throughput purposes. Here, a homogenous fluorescence-based "mix and measure" hammerhead ribozyme in vitro reporter assay to monitor RNA editing, is presented. Only as a consequence of RNA editing of the hammerhead ribozyme a fluorescence resonance energy transfer (FRET) oligoribonucleotide substrate undergoes cleavage. This in turn results in separation of the fluorophore from the quencher thereby producing a signal. In contrast, when the editosome function is inhibited, the fluorescence signal will be quenched. This is a highly sensitive and simple assay that should be generally applicable to monitor in vitro RNA editing or high throughput screening of chemicals that can inhibit the editosome function.


Assuntos
Avaliação Pré-Clínica de Medicamentos/métodos , Edição de RNA/efeitos dos fármacos , Edição de RNA/fisiologia , RNA Catalítico/análise , Trypanosoma brucei brucei/efeitos dos fármacos , Trypanosoma brucei brucei/genética , Transferência Ressonante de Energia de Fluorescência , RNA/genética , RNA/metabolismo , RNA Catalítico/metabolismo , RNA Mitocondrial , Trypanosoma brucei brucei/metabolismo
19.
ChemMedChem ; 9(9): 2021-5, 2014 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-24954543

RESUMO

RNA-guided machineries perfectly satisfy the demand for rationally programmable tools that manipulate gene function inside the cell. Over the last ten years, various natural machineries have been harnessed, with RNA interference being among the most prominent examples. It is now time to tackle the engineering of novel RNA-guided tools not provided by nature. In this respect, we highlight RNA-guided site-directed RNA editing as a new concept for the manipulation of RNA and protein function. In contrast to currently available techniques, RNA editing allows for the introduction of selected point mutations into the transcriptome without the need for genomic manipulation. In particular, the approach described using chemically stabilized, antagomir-like guideRNAs may offer advantages over others, such as specificity and circumvention of immunogenicity. These new tools have significant potential for the advancement of both basic science and medicinal application, especially in the treatment of genetic diseases.


Assuntos
Nucleosídeo Desaminases/química , Proteínas/efeitos dos fármacos , Edição de RNA/efeitos dos fármacos , RNA/efeitos dos fármacos , Animais , Humanos , Mutagênese Sítio-Dirigida , Nucleosídeo Desaminases/farmacologia , Engenharia de Proteínas , Proteínas/fisiologia , RNA/fisiologia
20.
Mol Brain ; 7: 5, 2014 Jan 21.
Artigo em Inglês | MEDLINE | ID: mdl-24443933

RESUMO

BACKGROUND: Pre-mRNAs of 2-amino-3-(3-hydroxy-5-methyl-isoxazol-4-yl)-propanoic acid (AMPA)/kainate glutamate receptors undergo post-transcriptional modification known as RNA editing that is mediated by adenosine deaminase acting on RNA type 2 (ADAR2). This modification alters the amino acid sequence and function of the receptor. Glutamatergic signaling has been suggested to have a role in mood disorders and schizophrenia, but it is unknown whether altered RNA editing of AMPA/kainate receptors has pathophysiological significance in these mental disorders. In this study, we found that ADAR2 expression tended to be decreased in the postmortem brains of patients with schizophrenia and bipolar disorder. RESULTS: Decreased ADAR2 expression was significantly correlated with decreased editing of the R/G sites of AMPA receptors. In heterozygous Adar2 knockout mice (Adar2+/- mice), editing of the R/G sites of AMPA receptors was decreased. Adar2+/- mice showed a tendency of increased activity in the open-field test and a tendency of resistance to immobility in the forced swimming test. They also showed enhanced amphetamine-induced hyperactivity. There was no significant difference in amphetamine-induced hyperactivity between Adar2+/- and wild type mice after the treatment with an AMPA/kainate receptor antagonist, 2,3-dihydroxy-6-nitro-7-sulfamoyl-benzo[f]quinoxaline. CONCLUSIONS: These findings collectively suggest that altered RNA editing efficiency of AMPA receptors due to down-regulation of ADAR2 has a possible role in the pathophysiology of mental disorders.


Assuntos
Adenosina Desaminase/metabolismo , Transtornos do Humor/enzimologia , Transtornos do Humor/genética , Edição de RNA/genética , Proteínas de Ligação a RNA/metabolismo , Receptores de Glutamato/genética , Esquizofrenia/genética , Adenosina Desaminase/deficiência , Adenosina Desaminase/genética , Animais , Comportamento Animal/efeitos dos fármacos , Encéfalo/enzimologia , Encéfalo/patologia , Humanos , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Knockout , Atividade Motora/efeitos dos fármacos , Mudanças Depois da Morte , Quinoxalinas/farmacologia , Edição de RNA/efeitos dos fármacos , Receptores de AMPA/metabolismo , Receptores de Glutamato/metabolismo , Esquizofrenia/enzimologia
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA