RNA editing, especially A-to-I RNA editing, is a common post-transcriptional modification in mammals. Adenosine deaminase acting on RNA (ADAR) is a key protein for A-to-I editing, which converts the adenosine group of a double-stranded RNA to creatinine group by deaminating it, resulting in a change of nucleotide sequence. There are 3 types of ADARs (ADAR1, ADAR2, ADAR3) that have been found in recent years. The abnormalities of ADARs are closely related to many human diseases such as viral infections, metabolic diseases, nervous system diseases, and tumors.
Adenosine ; metabolism ; Adenosine Deaminase ; physiology ; Base Sequence ; Creatinine ; metabolism ; Deamination ; Disease ; etiology ; Humans ; RNA Editing ; physiology ; RNA, Double-Stranded ; RNA-Binding Proteins ; physiology

Retinoic acid inducible gene-I (RIG-I) is a caspase recruitment domain (CARD) containing protein that acts as an intracellular RNA receptor and senses virus infection. After binding to double stranded RNA (dsRNA) or 5'-triphosphate single stranded RNA (ssRNA), RIG-I transforms into an open conformation, translocates onto mitochondria, and interacts with the downstream adaptor mitochondrial antiviral signaling (MAVS) to induce the production of type I interferon and inflammatory factors via IRF3/7 and NF-κB pathways, respectively. Recently, accumulating evidence suggests that RIG-I could function in non-viral systems and participate in a series of biological events, such as inflammation and inflammation related diseases, cell proliferation, apoptosis and even senescence. Here we review recent advances in antiviral study of RIG-I as well as the functions of RIG-I in other fields.
Antiviral Agents ; chemistry ; DEAD Box Protein 58 ; DEAD-box RNA Helicases ; chemistry ; metabolism ; physiology ; Humans ; Inflammation ; metabolism ; Interferon Regulatory Factor-3 ; metabolism ; NF-kappa B ; metabolism ; RNA Viruses ; metabolism ; RNA, Double-Stranded ; metabolism ; Signal Transduction

OBJECTIVETo investigate the role of histone acetylation in regulating influenza virus replicative intermediate double-stranded RNA (dsRNA)-induced interleukin-6 (IL-6) expression in A549 cells.

METHODSA549 cells were treated with influenza virus replicative intermediate dsRNA, histone deacetylase (HDAC) inhibitor trichostatin A (TSA), or HADC small interfering RNA (siRNA). The changes in the cellular IL-6 promoter activities were detected by dual-luciferase assay, and IL-6 mRNA and protein expressions in the cells were determined using real-time RT-PCR and ELISA, respectively.

RESULTSInfluenza virus replicative intermediate dsRNA obviously up-regulated IL-6 expression in the cells. HDAC inhibitor TSA significantly enhanced the activity of IL-6 promoter and increased IL-6 mRNA expression in A549 cells, and HDAC3 may play an important role in this process. HDAC inhibitor TSA and DNMT inhibitor DAC showed no synergic effect in regulating IL-6 expression.

CONCLUSIONSInfluenza virus replicative intermediate dsRNA-induced IL-6 expression in A549 cells is regulated by histone acetylation.

Acetylation ; Cell Line, Tumor ; Gene Expression Regulation ; Histone Deacetylase Inhibitors ; pharmacology ; Histones ; metabolism ; Humans ; Interleukin-6 ; metabolism ; Orthomyxoviridae ; genetics ; metabolism ; Promoter Regions, Genetic ; RNA, Double-Stranded ; RNA, Messenger ; genetics ; RNA, Viral

OBJECTIVE: To report the use of Dicer to cleave double-stranded RNA (dsRNAs) into small interference RNAs (D-siRNAs) that can target multiple sites within an mRNA, and to acquire an new method to cure inflammation of the airway and tumor. METHODS: Using RiboMAX Large Scale RNA Production Systems-SP6 and T7 kit were used to transcribe A549 cell COX-2 DNA into RNA (dsRNAs). We mixed dsRNAs with Dicer in the reaction buffer. We recovered siRNAs using RNA Purification Column. RESULTS: Dicer efficiently converted double-stranded RNA of COX-2 into small interference RNAs of 21 approximately 23 bp. CONCLUSION Dicer efficiently converts double-stranded RNA (dsRNA) into small interference RNAs (D-siRNAs of 21 approximately 23 bp).
Base Sequence ; Cell Line, Tumor ; Cyclooxygenase 2 ; genetics ; Humans ; Molecular Sequence Data ; RNA Interference ; RNA, Double-Stranded ; genetics ; metabolism ; RNA, Small Interfering ; genetics ; metabolism ; Ribonuclease III ; metabolism ; Sequence Analysis, DNA

Protozoan viruses may influence the function and pathogenicity of the protozoa. Trichomonas vaginalis is a parasitic protozoan that could contain a double stranded RNA (dsRNA) virus, T. vaginalis virus (TVV). However, there are few reports on the properties of the virus. To further determine variations in protein expression of T. vaginalis, we detected 2 strains of T. vaginalis; the virus-infected (V⁺) and uninfected (V⁻) isolates to examine differentially expressed proteins upon TVV infection. Using a stable isotope N-terminal labeling strategy (iTRAQ) on soluble fractions to analyze proteomes, we identified 293 proteins, of which 50 were altered in V⁺ compared with V⁻ isolates. The results showed that the expression of 29 proteins was increased, and 21 proteins decreased in V⁺ isolates. These differentially expressed proteins can be classified into 4 categories: ribosomal proteins, metabolic enzymes, heat shock proteins, and putative uncharacterized proteins. Quantitative PCR was used to detect 4 metabolic processes proteins: glycogen phosphorylase, malate dehydrogenase, triosephosphate isomerase, and glucose-6-phosphate isomerase, which were differentially expressed in V⁺ and V⁻ isolates. Our findings suggest that mRNA levels of these genes were consistent with protein expression levels. This study was the first which analyzed protein expression variations upon TVV infection. These observations will provide a basis for future studies concerning the possible roles of these proteins in host-parasite interactions.
Glucose-6-Phosphate Isomerase ; Glycogen Phosphorylase ; Heat-Shock Proteins ; Host-Parasite Interactions ; Malate Dehydrogenase ; Metabolism ; Polymerase Chain Reaction ; Proteome ; Reticuloendotheliosis virus ; Ribosomal Proteins ; RNA, Double-Stranded ; RNA, Messenger ; Trichomonas vaginalis* ; Trichomonas* ; Triose-Phosphate Isomerase ; Virulence

Asthma is characterized by airway inflammation induced by immune dysfunction to inhaled antigens. Although respiratory viral infections are the most common cause of asthma exacerbation, immunologic mechanisms underlying virus-associated asthma exacerbation are controversial. Clinical evidence indicates that nitric oxide (NO) levels in exhaled air are increased in exacerbated asthma patients compared to stable patients. Here, we evaluated the immunologic mechanisms and the role of NO synthases (NOSs) in the development of virus-associated asthma exacerbation. A murine model of virus-associated asthma exacerbation was established using intranasal challenge with ovalbumin (OVA) plus dsRNA for 4 weeks in mice sensitized with OVA plus dsRNA. Lung infiltration of inflammatory cells, especially neutrophils, was increased by repeated challenge with OVA plus dsRNA, as compared to OVA alone. The neutrophilic inflammation enhanced by dsRNA was partly abolished in the absence of IFN-gamma or IL-17 gene expression, whereas unaffected in the absence of IL-13. In terms of the roles of NOSs, dsRNA-enhanced neutrophilic inflammation was significantly decreased in inducible NOS (iNOS)-deficient mice compared to wild type controls; in addition, this phenotype was inhibited by treatment with a non-specific NOS inhibitor (L-NAME) or an specific inhibitor (1400 W), but not with a specific endothelial NOS inhibitor (AP-CAV peptide). Taken together, these findings suggest that iNOS pathway is important in the development of virus-associated exacerbation of neutrophilic inflammation, which is dependent on both Th1 and Th17 cell responses.
Animals ; Asthma/*immunology/virology ; Imines/pharmacology ; Mice ; Mice, Inbred BALB C ; NG-Nitroarginine Methyl Ester/pharmacology ; Nitric Oxide Synthase Type II/antagonists & inhibitors/*metabolism ; RNA, Double-Stranded/metabolism ; Th1 Cells/*immunology ; Th17 Cells/*immunology

Animals ; Apoptosis ; Cadherins ; genetics ; metabolism ; Epigenesis, Genetic ; Gene Expression Regulation, Neoplastic ; Humans ; MicroRNAs ; genetics ; metabolism ; physiology ; Neoplasm Invasiveness ; Neoplasms ; genetics ; metabolism ; pathology ; therapy ; RNA, Double-Stranded ; genetics ; metabolism ; physiology ; RNA, Small Interfering ; genetics ; metabolism ; physiology ; RNA, Small Untranslated ; genetics ; metabolism ; physiology ; therapeutic use ; Transcriptional Activation

Retinoic acid-inducible gene I (RIG-I) is an important pattern recognition receptor that detects viral RNA and triggers the production of type-I interferons through the downstream adaptor MAVS (also called IPS-1, CARDIF, or VISA). A series of structural studies have elaborated some of the mechanisms of dsRNA recognition and activation of RIG-I. Recent studies have proposed that K63-linked ubiquitination of, or unanchored K63-linked polyubiquitin binding to RIG-I positively regulates MAVS-mediated antiviral signaling. Conversely phosphorylation of RIG-I appears to play an inhibitory role in controlling RIG-I antiviral signal transduction. Here we performed a combined structural and biochemical study to further define the regulatory features of RIG-I signaling. ATP and dsRNA binding triggered dimerization of RIG-I with conformational rearrangements of the tandem CARD domains. Full length RIG-I appeared to form a complex with dsRNA in a 2:2 molar ratio. Compared with the previously reported crystal structures of RIG-I in inactive state, our electron microscopic structure of full length RIG-I in complex with blunt-ended dsRNA, for the first time, revealed an exposed active conformation of the CARD domains. Moreover, we found that purified recombinant RIG-I proteins could bind to the CARD domain of MAVS independently of dsRNA, while S8E and T170E phosphorylation-mimicking mutants of RIG-I were defective in binding E3 ligase TRIM25, unanchored K63-linked polyubiquitin, and MAVS regardless of dsRNA. These findings suggested that phosphorylation of RIG inhibited downstream signaling by impairing RIG-I binding with polyubiquitin and its interaction with MAVS.
Adaptor Proteins, Signal Transducing ; metabolism ; Adenosine Triphosphate ; metabolism ; DEAD Box Protein 58 ; DEAD-box RNA Helicases ; chemistry ; genetics ; metabolism ; Dimerization ; Humans ; Mutagenesis, Site-Directed ; Phosphorylation ; Polyubiquitin ; metabolism ; Protein Binding ; Protein Structure, Tertiary ; RNA, Double-Stranded ; metabolism ; Recombinant Proteins ; biosynthesis ; chemistry ; genetics ; Signal Transduction ; Transcription Factors ; metabolism ; Tripartite Motif Proteins ; Ubiquitin-Protein Ligases ; metabolism ; Ubiquitination

OBJECTIVETo silence the expression of alpha-synuclein in MN9D dopaminergic cells using vector mediated RNA interference (RNAi) and examined its effects on cell proliferation and viability.

METHODSWe identified two 19-nucleotide stretches within the coding region of the alpha-synuclein gene and designed three sets of oligonucleotides to generate double-stranded (ds) oligos. The ds oligos were inserted into the pENTR/H1/TO vector and transfected into MN9D dopaminergic cells. alpha-Synuclein expression was detected by RT-PCR, real-time PCR, immunocytochemistry staining and Western blot. In addition, we measured cell proliferation using growth curves and cell viability by 3-(4, 5)-dimethylthiahiazo (-z-y1)-3, 5-di- phenytetrazoliumromide (MTT).

RESULTSThe mRNA and protein levels of alpha-synuclein gene were significantly down-regulated in pSH2/alpha-SYN-transfected cells compared with control MN9D and pSH/CON-transfected MN9D cells, while pSH1/alpha-SYN-transfected cells showed no significant difference. Silencing alpha-synuclein expression does not affect cell proliferation but may decrease cell viability.

CONCLUSIONOur results demonstrated pSH2/alpha-SYN is an effective small interfering RNA (siRNA) sequence and potent silencing of mouse alpha-synuclein expression in MN9D cells by vector-based RNAi, which provides the tools for studying the normal function of alpha-synuclein and examining its role in Parkinson's disease (PD) pathogenesis. alpha-Synuclein may be important for the viability of MN9D cells, and loss of alpha-synuclein may induce cell injury directly or indirectly.

Animals ; Cell Line ; Cell Proliferation ; Cell Survival ; drug effects ; genetics ; Down-Regulation ; drug effects ; genetics ; Gene Silencing ; Genetic Vectors ; genetics ; Hybridomas ; Mice ; Mice, Inbred C57BL ; Nerve Degeneration ; genetics ; metabolism ; Neurons ; drug effects ; metabolism ; pathology ; Oligonucleotides ; genetics ; Parkinson Disease ; genetics ; metabolism ; Plasmids ; genetics ; RNA Interference ; RNA, Double-Stranded ; genetics ; pharmacology ; RNA, Small Interfering ; genetics ; Transfection ; methods ; alpha-Synuclein ; genetics ; metabolism

DNA damage response (DDR) is essential for maintaining genome stability and protecting cells from tumorigenesis. Ubiquitin and ubiquitin-like modifications play an important role in DDR, from signaling DNA damage to mediating DNA repair. In this report, we found that the E3 ligase ring finger protein 126 (RNF126) was recruited to UV laser micro-irradiation-induced stripes in a RNF8-dependent manner. RNF126 directly interacted with and ubiquitinated another E3 ligase, RNF168. Overexpression of wild type RNF126, but not catalytically-inactive mutant RNF126 (CC229/232AA), diminished ubiquitination of H2A histone family member X (H2AX), and subsequent bleomycin-induced focus formation of total ubiquitin FK2, TP53-binding protein 1 (53BP1), and receptor-associated protein 80 (RAP80). Interestingly, both RNF126 overexpression and RNF126 downregulation compromised homologous recombination (HR)-mediated repair of DNA double-strand breaks (DSBs). Taken together, our findings demonstrate that RNF126 negatively regulates RNF168 function in DDR and its appropriate cellular expression levels are essential for HR-mediated DSB repair.
Carrier Proteins ; metabolism ; Cell Line, Tumor ; DNA Breaks, Double-Stranded ; DNA Repair ; genetics ; DNA-Binding Proteins ; metabolism ; Genomic Instability ; HeLa Cells ; Histones ; metabolism ; Humans ; Nuclear Proteins ; metabolism ; RNA Interference ; RNA, Small Interfering ; genetics ; Signal Transduction ; Tumor Suppressor p53-Binding Protein 1 ; metabolism ; Ubiquitin ; Ubiquitin-Protein Ligases ; genetics ; metabolism ; Ubiquitination