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Rna induced silencing complex

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https://www.readbyqxmd.com/read/27924491/single-molecule-fluorescence-energy-transfer-assays-for-the-characterization-of-reaction-pathways-of-mirna-argonaute-complex
#1
Myung Hyun Jo, Sungchul Hohng
Argonaute proteins are key components of the microRNA-induced silencing complexes (miRISCs) that mediate the posttranscriptional gene silencing of microRNAs and small interfering RNA (siRNAs). The complex reaction mechanism of miRISC is expected to be characterized by tracing the reaction pathways of miRISC at the single-molecule level in real time. In this chapter, we describe single-molecule fluorescence resonance energy transfer (FRET) assays to observe the target binding and reaction pathways of miRISC composed of a recombinant Argonaute and a small RNA...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924488/elucidating-mechanisms-of-molecular-recognition-between-human-argonaute-and-mirna-using-computational-approaches
#2
Hanlun Jiang, Lizhe Zhu, Amélie Héliou, Xin Gao, Julie Bernauer, Xuhui Huang
MicroRNA (miRNA) and Argonaute (AGO) protein together form the RNA-induced silencing complex (RISC) that plays an essential role in the regulation of gene expression. Elucidating the underlying mechanism of AGO-miRNA recognition is thus of great importance not only for the in-depth understanding of miRNA function but also for inspiring new drugs targeting miRNAs. In this chapter we introduce a combined computational approach of molecular dynamics (MD) simulations, Markov state models (MSMs), and protein-RNA docking to investigate AGO-miRNA recognition...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27919963/expression-levels-of-piwi-interacting-rna-pir-823-are-deregulated-in-tumor-tissue-blood-serum-and-urine-of-patients-with-renal-cell-carcinoma
#3
Robert Iliev, Michal Fedorko, Tana Machackova, Hana Mlcochova, Marek Svoboda, Dalibor Pacik, Jan Dolezel, Michal Stanik, Ondrej Slaby
BACKGROUND: Renal cell carcinoma (RCC) is the most common neoplasm of adult kidney accounting for about 3% of adult malignancies. P-Element induced wimpy testis (PIWI)-interacting RNAs (piRNAs) are a new class of naturally occurring, short non-coding RNAs involved in silencing of transposable elements and in sequence-specific chromatin modifications. There were preliminary data published indicating that piR-823 expression is deregulated in circulating tumor cells and tumor tissue in gastric and kidney cancer, respectively...
December 2016: Anticancer Research
https://www.readbyqxmd.com/read/27911568/nf%C3%AE%C2%BAb-mediates-mesenchymal-transition-remodeling-and-pulmonary-fibrosis-in-response-to-chronic-inflammation-by-viral-rna-patterns
#4
Bing Tian, Igor Patrikeev, Lorenzo Ochoa, Gracie Vargas, KarryAnne K Belanger, Julia Litvinov, Istvan Boldogh, Bill T Ameredes, Massoud Motamedi, Allan R Brasier
Airway remodeling is resultant of a complex multi-cellular response associated with a progressive decline of pulmonary function in patients with chronic airway disease. Here, repeated infections with respiratory viruses are linked with airway remodeling through largely unknown mechanisms. Although acute activation of the Toll like receptor (TLR)3 pathway by extracellular poly(I:C) induces innate signaling through the NFkB transcription factor in human small airway epithelial cells (hSAECs), prolonged (repetitive or tonic) poly(I:C) stimulation produces chronic stress fiber formation, mesenchymal transition and activation of a fibrotic program...
December 2, 2016: American Journal of Respiratory Cell and Molecular Biology
https://www.readbyqxmd.com/read/27911494/determining-functional-aptamer-protein-interaction-by-biolayer-interferometry
#5
Xinhui Lou, Martin Egli, Xianbin Yang
Short single-stranded nucleic acids called aptamers are widely being explored as recognition molecules of high affinity and specificity for binding a wide range of target molecules, particularly protein targets. In biolayer interferometry (BLI), a simple Dip-and-Read approach in which the aptamer-coated biosensors are dipped into microplate wells is used to study the interactions between an aptamer and its target protein. Here we describe the protocol for the analysis of the interaction between a well-characterized anti-thrombin RNA aptamer with thrombin (Basic Protocol)...
December 1, 2016: Current Protocols in Nucleic Acid Chemistry
https://www.readbyqxmd.com/read/27886048/interactions-between-the-hiv-1-unspliced-mrna-and-host-mrna-decay-machineries
#6
REVIEW
Daniela Toro-Ascuy, Bárbara Rojas-Araya, Fernando Valiente-Echeverría, Ricardo Soto-Rifo
The human immunodeficiency virus type-1 (HIV-1) unspliced transcript is used both as mRNA for the synthesis of structural proteins and as the packaged genome. Given the presence of retained introns and instability AU-rich sequences, this viral transcript is normally retained and degraded in the nucleus of host cells unless the viral protein REV is present. As such, the stability of the HIV-1 unspliced mRNA must be particularly controlled in the nucleus and the cytoplasm in order to ensure proper levels of this viral mRNA for translation and viral particle formation...
November 23, 2016: Viruses
https://www.readbyqxmd.com/read/27878651/messages-on-small-rna-duplexes-in-plants
#7
Taichiro Iki
Small RNA-mediated gene silencing encompasses diverse developmental events, stress responses, defense against pathogens, and maintenance of genome integrity. Extensive studies in model organisms have unveiled the molecular mechanisms underpinning the RNA silencing phenomena, and the accumulating knowledge have characterized the intricate pathways and the repertoire of proteins responsible for the actions of small RNAs characterized as microRNAs (miRNAs) or small interfering RNAs (siRNAs). Although the single-stranded, matured guide small RNAs direct the effector ribonucleoprotein complexes to induce gene silencing in sequence-specific manner, the double-stranded intermediate, the small RNA duplexes, which are processed as nascent products of the RNase III enzyme activities, act as key to determine the downstream molecular pathways and the fate of small RNAs...
November 23, 2016: Journal of Plant Research
https://www.readbyqxmd.com/read/27873317/b-cell-activating-factor-signalling-pathway-is-associated-with-h-pylori-independence-in-gastric-malt-lymphoma-without-t-11-18-q21-q21
#8
Sung-Hsin Kuo, Hui-Jen Tsai, Chung-Wu Lin, Kun-Huei Yeh, Hsiao-Wei Lee, Ming-Feng Wei, Chia-Tung Shun, Ming-Shiang Wu, Ping-Ning Hsu, Li-Tzong Chen, Ann-Lii Cheng
We previously reported that activation of the B cell-activating factor (BAFF) pathway upregulates NF-κB and induces BCL3 and BCL10 nuclear translocation in H. pylori (HP)-independent gastric diffuse large B-cell lymphoma (DLBCL) tumours with evidence of mucosa-associated lymphoid tissue (DLBCL [MALT]). However, the significance of BAFF expression in HP-independence of gastric low-grade MALT lymphomas (MALT lymphoma) without t(11;18)(q21;q21) remains unexplored. Sixty-four patients who underwent successful HP eradication for localized HP-positive gastric MALT lymphomas without t(11;18)(q21;q21) were studied...
November 22, 2016: Journal of Pathology
https://www.readbyqxmd.com/read/27848206/tanshinone-i-attenuates-the-effects-of-a-challenge-with-h2o2-on-the-functions-of-tricarboxylic-acid-cycle-and-respiratory-chain-in-sh-sy5y-cells
#9
Marcos Roberto de Oliveira, Cristina Ribas Fürstenau, Izabel Cristina Custódio de Souza, Gustavo da Costa Ferreira
Tanshinone I (T-I; C18H12O3) is a cytoprotective molecule. T-I has been viewed as an antioxidant and anti-inflammatory agent exerting neuroprotective actions in several experimental models. Nonetheless, the mechanisms underlying the beneficial effects of T-I in mammalian cells are not completely understood yet. Mitochondrial dysfunction has been associated with several neurodegenerative diseases which remain uncured. Therefore, there is increasing interest in compounds that may be used in the prevention or treatment of those pathologies...
November 15, 2016: Molecular Neurobiology
https://www.readbyqxmd.com/read/27837013/partial-reconstitution-of-the-rnai-response-in-human-cells-using-drosophila-gene-products
#10
Edward M Kennedy, Anand V R Kornepati, Hal P Bogerd, Bryan R Cullen
While mammalian somatic cells are incapable of mounting an effective RNA interference (RNAi) response to viral infections, plants and invertebrates are able to generate high levels of viral short interfering RNAs (siRNAs) that can control many infections. In Drosophila, the RNAi response is mediated by the Dicer 2 enzyme (dDcr2) acting in concert with two co-factors called Loqs-PD and R2D2. To examine whether a functional RNAi response could be mounted in human somatic cells, we expressed dDcr2, in the presence or absence of Loqs-PD and/or R2D2, in a previously described human cell line, NoDice/ΔPKR, that lacks functional forms of human Dicer (hDcr) and PKR...
November 11, 2016: RNA
https://www.readbyqxmd.com/read/27833855/overexpression-of-klhl23-protein-from-read-through-transcription-of-phospho2-klhl23-in-gastric-cancer-increases-cell-proliferation
#11
Eun-Seok Choi, Hanna Lee, Chang-Hun Lee, Sung-Ho Goh
Gene fusion, as a prototypical pathognomonic mutation, contributes to genome complexity, and the cis-transcription-induced gene fusions generated by read-through transcription of adjacent genes have been found to be important for tumor development. We screened read-through transcription events from stomach adenocarcinoma RNA-seq data and selected three candidates PHOSPHO2-KLHL23, RPL17-C18orf32, and PRR5-ARHGAP8, to assess their biological role in gastric cancer. The expression of all three read-through fusion transcripts was confirmed in gastric cancer cell lines and paired normal/tumor gastric cancer tissues by real-time quantitative reverse transcription polymerase chain reaction and their expression was found to be significantly higher in the tumor (P < 0...
November 2016: FEBS Open Bio
https://www.readbyqxmd.com/read/27816966/hur-protects-nono-from-degradation-by-mir320-which-is-induced-by-p53-upon-uv-irradiation
#12
Luigi Alfano, Caterina Costa, Antonella Caporaso, Dario Antonini, Antonio Giordano, Francesca Pentimalli
UV radiations challenge genomic stability and are a recognized cancer risk factor. We previously found that the RNA-binding protein NONO regulates the intra-S phase checkpoint and its silencing impaired HeLa and melanoma cell response to UV-induced DNA damage. Here we investigated the mechanisms underlying NONO regulation upon UVC treatment. We found that UVC rays induce the expression of mir320a, which can indeed target NONO. However, despite mir320a induction, NONO mRNA and protein expression are not affected by UVC...
November 1, 2016: Oncotarget
https://www.readbyqxmd.com/read/27815492/preclinical-biodistribution-and-safety-evaluation-of-a-pbi-shrna-stmn1-lipoplex-after-subcutaneous-delivery
#13
Zhaohui Wang, Christopher M Jay, Courtney Evans, Padmasini Kumar, Connor Phalon, Donald D Rao, Neil Senzer, John Neumantis
Stathmin-1 (STMN1) is a microtubule-destabilizing protein which is overexpressed in cancer. Its overexpression is associated with poor prognosis and also serves as a predictive marker to taxane therapy. We have developed a proprietary bi-functional shRNA (bi-shRNA) platform to execute RNA interference (RNAi)-mediated gene silencing and a liposome-carrier complex to systemically deliver the pbi-shRNA plasmids. In vitro and in vivo testing demonstrated efficacy and specificity of pbi-shRNA plasmid in targeting STMN1 (Phadke et al...
November 4, 2016: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/27813562/genome-wide-identification-and-analysis-of-the-sgr-gene-family-in-cucumis-melo-l
#14
R G Bade, M L Bao, W Y Jin, Y Ma, Y D Niu, A Hasi
Chlorophyll (CHL) is present in many plant organs, and its metabolism is strongly regulated throughout plant development. Understanding the fate of CHL in senescent leaves or during fruit ripening is a complex process. The stay-green (SGR) protein has been shown to affect CHL degradation. In this study, we used the conserved sequences of STAY-GREEN domain protein (NP_567673) in Arabidopsis thaliana as a probe to search SGR family genes in the genome-wide melon protein database. Four candidate SGR family genes were identified in melon (Cucumis melo L...
October 17, 2016: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/27803482/development-of-novel-genetically-engineered-adenoviruses-based-on-functional-analyses-of-adenovirus-encoded-small-rnas
#15
Mitsuhiro Machitani
 The adenovirus (Ad) genome encodes two small noncoding RNAs, VA-RNA I and II, which support Ad replication by antagonizing the antiviral action associated with the Ad-induced activation of double-stranded RNA-dependent protein kinase (PKR). VA-RNAs are also processed in a manner similar to microRNAs (miRNAs), resulting in the production of VA-RNA-derived miRNAs (mivaRNAs). mivaRNAs are incorporated into the RNA-induced silencing complex (RISC) and exhibit posttranscriptional silencing in a manner similar to miRNAs...
2016: Yakugaku Zasshi: Journal of the Pharmaceutical Society of Japan
https://www.readbyqxmd.com/read/27801781/function-and-regulation-of-micrornas-and-their-potential-as-biomarkers-in-paediatric-liver-disease
#16
REVIEW
Diego A Calvopina, Miranda A Coleman, Peter J Lewindon, Grant A Ramm
MicroRNAs (miRNAs) are short non-coding RNAs involved in biological and pathological processes of every cell type, including liver cells. Transcribed from specific genes, miRNA precursors are processed in the cytoplasm into mature miRNAs and as part of the RNA-induced silencing complex (RISC) complex binds to messenger RNA (mRNA) by imperfect complementarity. This leads to the regulation of gene expression at a post-transcriptional level. The function of a number of different miRNAs in fibrogenesis associated with the progression of chronic liver disease has recently been elucidated...
October 27, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27795434/clec5a-mediated-enhancement-of-the-inflammatory-response-in-myeloid-cells-contributes-to-influenza-pathogenicity-in-vivo
#17
Ooiean Teng, Szu-Ting Chen, Tsui-Ling Hsu, Sin Fun Sia, Suzanne Cole, Sophie A Valkenburg, Tzu-Yun Hsu, Jian Teddy Zheng, Wenwei Tu, Roberto Bruzzone, Joseph Sriyal Malik Peiris, Shie-Liang Hsieh, Hui-Ling Yen
: Human infections with influenza viruses exhibit mild to severe clinical outcome as a result of complex virus-host interactions. Induction of inflammatory mediators via pattern recognition receptors may dictate subsequent host responses for pathogen clearance and tissue damage. We identified that human C-type lectin member 5A (CLEC5A) interacts with the hemagglutinin protein of influenza viruses expressed on lentiviral pseudoparticles through lectin screening. Silencing CLEC5A gene expression, blocking influenza-CLEC5A interactions with anti-CLEC5A antibodies, or dampening CLEC5A-mediated signaling using a spleen tyrosine kinase inhibitor consistently reduced the levels of pro-inflammatory cytokines produced by human macrophages without affecting the replication of influenza A viruses of different subtypes...
October 19, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27765623/simultaneous-regulation-of-apoptotic-gene-silencing-and-angiogenic-gene-expression-for-myocardial-infarction-therapy-single-carrier-delivery-of-shp-1-sirna-and-vegf-expressing-pdna
#18
Dongkyu Kim, Sook Hee Ku, Hyosuk Kim, Ji Hoon Jeong, Minhyung Lee, Ick Chan Kwon, Donghoon Choi, Sun Hwa Kim
Gene therapy is aimed at selectively knocking up or knocking down the target genes involved in the development of diseases. In many human diseases, dysregulation of disease-associated genes is occurred concurrently: some genes are abnormally turned up and some are turned down. In the field of non-viral gene therapy, plasmid DNA (pDNA) and small interfering RNA (siRNA) are suggested as representative regulation tools for activating and silencing the expression of genes of interest, representatively. Herein, we simultaneously loaded both siRNA (Src homology region 2 domain-containing tyrosine phosphatase-1 siRNA, siSHP-1) for anti-apoptosis and pDNA (hypoxia-inducible vascular endothelial growth factor expression vector, pHI-VEGF) for angiogenesis in a single polymeric nanocarrier and used to synergistically attenuate ischemia-reperfusion (IR)-induced myocardial infarction, which is mainly caused by dysregulating of cardiac apoptosis and angiogenesis...
October 18, 2016: Journal of Controlled Release: Official Journal of the Controlled Release Society
https://www.readbyqxmd.com/read/27734055/precise-redox-sensitive-cleavage-sites-for-improved-bioactivity-of-sirna-lipopolyplexes
#19
Philipp Michael Klein, Sören Reinhard, Dian-Jang Lee, Katharina Müller, Daniela Ponader, Laura Hartmann, Ernst Wagner
Lipo-oligomers have been proven as potent siRNA carriers based on stable electrostatic and hydrophobic complex formation and endosomal membrane destabilization. Although high stability of siRNA polyplexes is desirable in the extracellular space and cellular uptake, intracellular disassembly is important for the cytosolic release of siRNA and RNA-induced silencing complex formation. To improve the release, bioreducible sequence-defined lipo-oligomers were synthesized by solid-phase assisted synthesis using the disulfide building block Fmoc-succinoyl-cystamine for precise positioning of a disulfide unit between a lipophilic diacyl (bis-myristyl, bis-stearyl or bis-cholestanyl) domain and an ionizable oligocationic siRNA binding unit...
October 13, 2016: Nanoscale
https://www.readbyqxmd.com/read/27717233/mussel-adhesion-inspired-reverse-transfection-platform-enhances-osteogenic-differentiation-and-bone-formation-of-human-adipose-derived-stem-cells
#20
Jisoo Shin, Jung Ho Cho, Yoonhee Jin, Kisuk Yang, Jong Seung Lee, Hyun-Ji Park, Hyung-Seop Han, Jinkyu Lee, Hojeong Jeon, Heungsoo Shin, Seung-Woo Cho
Using small interfering RNA (siRNA) to regulate gene expression is an emerging strategy for stem cell manipulation to improve stem cell therapy. However, conventional methods of siRNA delivery into stem cells based on solution-mediated transfection are limited due to low transfection efficiency and insufficient duration of cell-siRNA contact during lengthy culturing protocols. To overcome these limitations, a bio-inspired polymer-mediated reverse transfection system is developed consisting of implantable poly(lactic-co-glycolic acid) (PLGA) scaffolds functionalized with siRNA-lipidoid nanoparticle (sLNP) complexes via polydopamine (pDA) coating...
December 2016: Small
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