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https://www.readbyqxmd.com/read/28103286/mirnas-do-not-regulate-circadian-protein-synthesis-in-the-dinoflagellate-lingulodinium-polyedrum
#1
Steve Dagenais-Bellefeuille, Mathieu Beauchemin, David Morse
Dinoflagellates have been shown to express miRNA by bioinformatics and RNA blot (Northern) analyses. However, it is not yet known if miRNAs are able to alter gene expression in this class of organisms. We have assessed the possibility that miRNA may mediate circadian regulation of gene expression in the dinoflagellate Lingulodinium polyedrum using the Luciferin Binding Protein (LBP) as a specific example. LBP is a good candidate for regulation by miRNA since mRNA levels are constant over the daily cycle while protein synthesis is restricted by the circadian clock to a period of several hours at the start of the night phase...
2017: PloS One
https://www.readbyqxmd.com/read/28094937/click-qms-identifies-piwil3-as-a-mechanistic-target-of-rna-interference-activator-enoxacin-in-cancer-cells
#2
Nathan Abell, Marvin Mercado, Tatiana Cañeque, Raphaël Rodriguez, Blerta Xhemalce
Enoxacin is a small molecule that stimulates RNA interference (RNAi) and acts as a growth inhibitor selectively in cancer but not in untransformed cells. Here, we used alkenox, a clickable enoxacin surrogate, coupled with quantitative Mass Spectrometry, to identify PIWIL3 as a mechanistic target of enoxacin. PIWIL3 is an Argonaut protein of the PIWI subfamily that is mainly expressed in the germline and that mediates RNAi through piRNAs. Our results suggest that cancer cells re-express PIWIL3 to repress RNAi through miRNAs and thus open a new opportunity for cancer specific targeting...
January 17, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28087710/targeting-argonaute-to-chromatin
#3
Jered M Wendte, Craig S Pikaard
In many eukaryotes, siRNAs bound to Argonaute proteins guide chromatin-modifying enzymes to complementary loci, resulting in transcriptional gene silencing. Multiple lines of evidence indicate that siRNAs base-pair with longer RNAs produced at target loci, but the possibility that siRNAs base-pair directly with DNA remains an attractive hypothesis. In a recent study, Shimada et al. (pp. 2571-2580) conducted experiments that address these alternative hypotheses, yielding additional evidence that fission yeast siRNA-Argonaute silencing complexes are recruited to target loci exclusively via interactions with nascent transcripts...
December 15, 2016: Genes & Development
https://www.readbyqxmd.com/read/28087276/drosophila-argonaute2-turnover-is-regulated-by-the-ubiquitin-proteasome-pathway
#4
Madoka Chinen, Elissa P Lei
Argonaute (AGO) proteins play a central role in the RNA interference (RNAi) pathway, which is a cytoplasmic mechanism important for post-transcriptional regulation of gene expression. In Drosophila, AGO2 also functions in the nucleus to regulate chromatin insulator activity and transcription. Although there are a number of studies focused on AGO2 function, the regulation of AGO2 turnover is not well understood. We found that mutation of T1149 or R1158 in the conserved PIWI domain causes AGO2 protein instability, but only T1149 affects RNAi activity...
January 10, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28075055/argonaute-2-immunoprecipitation-revealed-lats1-as-a-novel-pro-apoptotic-target-of-mir-21-in-t-cells
#5
Nato Teteloshvili, Katarzyna Smigielska-Czepiel, Ye Yuan, Annika Seitz, Debora de Jong, Bea Rutgers, Pytrick Jellema, Roelof Jan van der Lei, Izabella Slezak-Prochazka, Elisabeth Brouwer, Annemieke M H Boots, Bart-Jan Kroesen, Anke van den Berg, Joost Kluiver
MicroRNA (miR)-21 is an important suppressor of T-cell apoptosis that is also overexpressed in many types of cancers. The exact mechanisms underlying the anti-apoptotic effects of miR-21 are not well understood. In this study, we used the Jurkat T-cell line as a model to identify apoptosis-associated miR-21 target genes. We showed that expression of miR-21 rapidly increases upon αCD3/αCD28 activation of Jurkat cells. Inhibition of miR-21 reduced cell growth which could be explained by an increase in apoptosis...
January 11, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28062756/phylogenetic-origin-and-diversification-of-rnai-pathway-genes-in-insects
#6
Daniel Dowling, Thomas Pauli, Alexander Donath, Karen Meusemann, Lars Podsiadlowski, Malte Petersen, Ralph S Peters, Christoph Mayer, Shanlin Liu, Xin Zhou, Bernhard Misof, Oliver Niehuis
RNA interference (RNAi) refers to the set of molecular processes found in eukaryotic organisms in which small RNA molecules mediate the silencing or down-regulation of target genes. In insects, RNAi serves a number of functions, including regulation of endogenous genes, anti-viral defense, and defense against transposable elements. Despite being well studied in model organisms, such as Drosophila, the distribution of core RNAi pathway genes and their evolution in insects is not well understood. Here we present the most comprehensive overview of the distribution and diversity of core RNAi pathway genes across 100 insect species, encompassing all currently recognized insect orders...
January 6, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28059073/ros-accumulation-and-antiviral-defence-control-by-microrna528-in-rice
#7
Jianguo Wu, Rongxin Yang, Zhirui Yang, Shengze Yao, Shanshan Zhao, Yu Wang, Pingchuan Li, Xianwei Song, Lian Jin, Tong Zhou, Ying Lan, Lianhui Xie, Xueping Zhou, Chengcai Chu, Yijun Qi, Xiaofeng Cao, Yi Li
MicroRNAs (miRNAs) are key regulators of plant-pathogen interactions. Modulating miRNA function has emerged as a new strategy to produce virus resistance traits(1-5). However, the miRNAs involved in antiviral defence and the underlying mechanisms remain largely elusive. We previously demonstrated that sequestration by Argonaute (AGO) proteins plays an important role in regulating miRNA function in antiviral defence pathways(6). Here we reveal that cleavage-defective AGO18 complexes sequester microRNA528 (miR528) upon viral infection...
January 6, 2017: Nature Plants
https://www.readbyqxmd.com/read/28053190/phobf1-a-petunia-ocs-element-binding-factor-plays-an-important-role-in-antiviral-rna-silencing
#8
Daoyang Sun, Shaohua Li, Lixin Niu, Michael S Reid, Yanlong Zhang, Cai-Zhong Jiang
Virus-induced gene silencing (VIGS) is a common reverse genetics strategy for characterizing the function of genes in plants. The detailed mechanism governing RNA silencing efficiency triggered by viruses is largely unclear. Here, we reveal that a petunia (Petunia hybrida) ocs element binding factor, PhOBF1, one of the basic leucine zipper (bZIP) transcription factors, was up-regulated by Tobacco rattle virus (TRV) infection. Simultaneous silencing of PhOBF1 and a reporter gene, phytoene desaturase (PDS) or chalcone synthase (CHS), by TRV-based VIGS led to a failure of the development of leaf photobleaching or the white-corollas phenotype...
January 4, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28046132/transcriptome-wide-discovery-of-pasrs-promoter-associated-small-rnas-and-tasrs-terminus-associated-small-rnas-in-arabidopsis-thaliana
#9
Xiaoxia Ma, Ning Han, Chaogang Shao, Yijun Meng
Hints from animals point to the existence of two novel small RNA (sRNA) species surrounding the transcription start sites (TSSs) and the termini of the genes, respectively. In this study, we performed a comprehensive search for the two sRNA species named promoter-associated sRNAs (PASRs) and terminus-associated sRNAs (TASRs) in Arabidopsis. By using sRNA sequencing data from wild type plants and several mutants related to the sRNA biogenesis, Argonaute (AGO) 1- and AGO4-associated sRNA sequencing data, double-stranded RNA sequencing (dsRNA-seq) data, and DNA methylation profiling data, the biogenesis and action pathways of the PASRs and the TASRs were investigated...
2017: PloS One
https://www.readbyqxmd.com/read/28008821/cooperative-enhancement-of-translation-by-two-adjacent-microrna-122-argonaute-2-complexes-binding-to-the-5%C3%A2-untranslated-region-of-hepatitis-c-virus-rna
#10
Anika Nieder-Röhrmann, Nadia Dünnes, Gesche K Gerresheim, Lyudmila A Shalamova, Andreas Herchenröther, Michael Niepmann
The liver-specific microRNA-122 (miR-122) binds to two conserved binding sites in the 5´-untranslated region (5´UTR) of Hepatitis C Virus (HCV) RNA. This binding was reported to enhance HCV RNA replication, translation and stability. We have analyzed binding of miR-122/Argonaute 2 (Ago2) complexes to these sites using anti-Ago2-co-immunoprecipitation of radioactively labeled HCV RNAs along with ectopic miR-122 in HeLa cells. Our results show that the miR-122 target sites can be addressed separately. When both target sites were addressed simultaneously, we observed a synergistic binding of both miR/Ago2 complexes...
December 23, 2016: Journal of General Virology
https://www.readbyqxmd.com/read/28003477/argonaute-proteins-regulate-hiv-1-multiply-spliced-rna-and-viral-production-in-a-dicer-independent-manner
#11
Agathe Eckenfelder, Emmanuel Ségéral, Natalia Pinzón, Damien Ulveling, Céline Amadori, Marine Charpentier, Sabine Nidelet, Jean-Paul Concordet, Jean-François Zagury, Jean-Christophe Paillart, Clarisse Berlioz-Torrent, Hervé Seitz, Stéphane Emiliani, Sarah Gallois-Montbrun
Argonaute (Ago) proteins associate with microRNAs (miRNAs) to form the core of the RNA-induced silencing complex (RISC) that mediates post-transcriptional gene silencing of target mRNAs. As key players in anti-viral defense, Ago proteins are thought to have the ability to interact with human immunodeficiency virus type 1 (HIV-1) RNA. However, the role of this interaction in regulating HIV-1 replication has been debated. Here, we used high throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP) to explore the interaction between Ago2 and HIV-1 RNA in infected cells...
December 20, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/28000665/a-somatic-pirna-pathway-in-the-drosophila-fat-body-ensures-metabolic-homeostasis-and-normal-lifespan
#12
Brian C Jones, Jason G Wood, Chengyi Chang, Austin D Tam, Michael J Franklin, Emily R Siegel, Stephen L Helfand
In gonadal tissues, the Piwi-interacting (piRNA) pathway preserves genomic integrity by employing 23-29 nucleotide (nt) small RNAs complexed with argonaute proteins to suppress parasitic mobile sequences of DNA called transposable elements (TEs). Although recent evidence suggests that the piRNA pathway may be present in select somatic cells outside the gonads, the role of a non-gonadal somatic piRNA pathway is not well characterized. Here we report a functional somatic piRNA pathway in the adult Drosophila fat body including the presence of the piRNA effector protein Piwi and canonical 23-29 nt long TE-mapping piRNAs...
December 21, 2016: Nature Communications
https://www.readbyqxmd.com/read/27986853/sirna-carrying-an-e-vinylphosphonate-moiety-at-the-5-end-of-the-guide-strand-augments-gene-silencing-by-enhanced-binding-to-human-argonaute-2
#13
Elad Elkayam, Rubina Parmar, Christopher R Brown, Jennifer L Willoughby, Christopher S Theile, Muthiah Manoharan, Leemor Joshua-Tor
No abstract text is available yet for this article.
December 15, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27984744/survival-in-quiescence-requires-the-euchromatic-deployment-of-clr4-suv39h-by-argonaute-associated-small-rnas
#14
Richard I Joh, Jasbeer S Khanduja, Isabel A Calvo, Meeta Mistry, Christina M Palmieri, Andrej J Savol, Shannan J Ho Sui, Ruslan I Sadreyev, Martin J Aryee, Mo Motamedi
Quiescence (G0) is a ubiquitous stress response through which cells enter reversible dormancy, acquiring distinct properties including reduced metabolism, resistance to stress, and long life. G0 entry involves dramatic changes to chromatin and transcription of cells, but the mechanisms coordinating these processes remain poorly understood. Using the fission yeast, here, we track G0-associated chromatin and transcriptional changes temporally and show that as cells enter G0, their survival and global gene expression programs become increasingly dependent on Clr4/SUV39H, the sole histone H3 lysine 9 (H3K9) methyltransferase, and RNAi proteins...
December 15, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27941123/the-rna-induced-transcriptional-silencing-complex-targets-chromatin-exclusively-via-interacting-with-nascent-transcripts
#15
Yukiko Shimada, Fabio Mohn, Marc Bühler
Small RNAs regulate chromatin modification and transcriptional gene silencing across the eukaryotic kingdom. Although these processes have been well studied, fundamental mechanistic aspects remain obscure. Specifically, it is unclear exactly how small RNA-loaded Argonaute protein complexes target chromatin to mediate silencing. Here, using fission yeast, we demonstrate that transcription of the target locus is essential for RNA-directed formation of heterochromatin. However, high transcriptional activity is inhibitory; thus, a transcriptional window exists that is optimal for silencing...
December 1, 2016: Genes & Development
https://www.readbyqxmd.com/read/27935964/gw182-free-microrna-silencing-complex-controls-post-transcriptional-gene-expression-during-caenorhabditis-elegans-embryogenesis
#16
Guillaume Jannot, Pascale Michaud, Miguel Quévillon Huberdeau, Louis Morel-Berryman, James A Brackbill, Sandra Piquet, Katherine McJunkin, Kotaro Nakanishi, Martin J Simard
MicroRNAs and Argonaute form the microRNA induced silencing complex or miRISC that recruits GW182, causing mRNA degradation and/or translational repression. Despite the clear conservation and molecular significance, it is unknown if miRISC-GW182 interaction is essential for gene silencing during animal development. Using Caenorhabditis elegans to explore this question, we examined the relationship and effect on gene silencing between the GW182 orthologs, AIN-1 and AIN-2, and the microRNA-specific Argonaute, ALG-1...
December 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27928938/sequence-and-structure-based-analysis-of-proteins-involved-in-mirna-biogenesis
#17
Chhaya Sharma, Debasisa Mohanty
miRNA biogenesis is a multistage process for generation of a mature miRNA and involves several different proteins. In this work, we have carried out sequence as well as structure based analysis for crucial proteins involved in miRNA biogenesis, namely, Dicer, Drosha, Argonaute (Ago) and Exportin-5 to understand evolution of these proteins in animal kingdom and also to identify key sequence and structural features which are determinants of their function. Our analysis reveals that in animals the miRNA biogenesis pathway first originated in molluscs...
December 8, 2016: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/27928054/the-influence-of-the-5-terminal-nucleotide-on-agoshrna-activity-and-biogenesis-importance-of-the-polymerase-iii-transcription-initiation-site
#18
Elena Herrera-Carrillo, Zong-Liang Gao, Alex Harwig, Matthias T Heemskerk, Ben Berkhout
Recent evidence indicates that shRNAs with a relatively short basepaired stem do not require Dicer processing, but instead are processed by the Argonaute 2 protein (Ago2). We named these molecules AgoshRNAs as both their processing and silencing function are mediated by Ago2. This alternative processing yields only a single RNA guide strand, which can avoid off-target effects induced by the passenger strand of regular shRNAs. It is important to understand this alternative processing route in mechanistic detail such that one can design improved RNA reagents...
December 7, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27924491/single-molecule-fluorescence-energy-transfer-assays-for-the-characterization-of-reaction-pathways-of-mirna-argonaute-complex
#19
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/27924490/site-specific-fluorescent-labeling-of-argonaute-for-fret-based-bio-assays
#20
Sarah Willkomm, Adrian Zander, Dina Grohmann
Deciphering the molecular mechanisms of eukaryotic Argonaute proteins is crucial for the understanding of RNA interference (RNAi), a posttranscriptional gene silencing process. Fluorescence-based single-molecule studies like single-molecule Förster resonance energy transfer (FRET) between a donor and acceptor dye represent a versatile tool to gain a mechanistic understanding of the structural dynamics of a biomolecular complex. Until today it was not possible to site-specifically introduce fluorophores into eukaryotic Argonaute...
2017: Methods in Molecular Biology
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