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Journal articles on the topic 'RNA-induced silencing complexes'

Author: Grafiati

Published: 29 September 2021

Last updated: 18 July 2025

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1

Pantaleo, Vitantonio, György Szittya, and József Burgyán. "Molecular Bases of Viral RNA Targeting by Viral Small Interfering RNA-Programmed RISC." Journal of Virology 81, no. 8 (2007): 3797–806. http://dx.doi.org/10.1128/jvi.02383-06.

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ABSTRACT RNA silencing is conserved in a broad range of eukaryotes and operates in the development and maintenance of genome integrity in many organisms. Plants have adapted this system for antiviral defense, and plant viruses have in turn developed mechanisms to suppress RNA silencing. RNA silencing-related RNA inactivation is likely based on target RNA cleavage or translational arrest. Although it is widely assumed that virus-induced gene silencing (VIGS) promotes the endonucleolytic cleavage of the viral RNA genome, this popular assumption has never been tested experimentally. Here we analy

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Joseph, Baby, Ajisha S.U, and Jeevitha M.V. "SiRNA Mediated Gene Silencing: A Mini Review." Aceh International Journal of Science and Technology 1, no. 3 (2012): 98–103. http://dx.doi.org/10.13170/aijst.1.3.140.

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Abstract - RNA interference (RNAi) technology has become a novel tool for silencing gene expression in cells or organisms. RNA interference is the process that double-stranded RNA induces the homology-dependent degradation of cognate mRNA mediated by 21-23 nucleotide short interfering RNA (siRNA). RNA interference is a powerful mechanism of gene silencing that underlies many aspects of eukaryotic biology. On the molecular level, RNAi is mediated by a family of ribonucleoprotein (RNP) complexes called RNA-Induced Silencing Complexes (RISCs), which can be programmed to target virtually any nucle

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3

Csorba, Tibor, Aurelie Bovi, Tamás Dalmay, and József Burgyán. "The p122 Subunit of Tobacco Mosaic Virus Replicase Is a Potent Silencing Suppressor and Compromises both Small Interfering RNA- and MicroRNA-Mediated Pathways." Journal of Virology 81, no. 21 (2007): 11768–80. http://dx.doi.org/10.1128/jvi.01230-07.

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ABSTRACT One of the functions of RNA silencing in plants is to defend against molecular parasites, such as viruses, retrotransposons, and transgenes. Plant viruses are inducers, as well as targets, of RNA silencing-based antiviral defense. Replication intermediates or folded viral RNAs activate RNA silencing, generating small interfering RNAs (siRNAs), which are the key players in the antiviral response. Viruses are able to counteract RNA silencing by expressing silencing-suppressor proteins. It has been shown that many of the identified silencing-suppressor proteins bind long double-stranded

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Lange, Heike, and Dominique Gagliardi. "Catalytic activities, molecular connections, and biological functions of plant RNA exosome complexes." Plant Cell 34, no. 3 (2021): 967–88. http://dx.doi.org/10.1093/plcell/koab310.

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Abstract RNA exosome complexes provide the main 3′–5′-exoribonuclease activities in eukaryotic cells and contribute to the maturation and degradation of virtually all types of RNA. RNA exosomes consist of a conserved core complex that associates with exoribonucleases and with multimeric cofactors that recruit the enzyme to its RNA targets. Despite an overall high level of structural and functional conservation, the enzymatic activities and compositions of exosome complexes and their cofactor modules differ among eukaryotes. This review highlights unique features of plant exosome complexes, suc

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Hong, Hao, Chunli Wang, Ying Huang, et al. "Antiviral RISC mainly targets viral mRNA but not genomic RNA of tospovirus." PLOS Pathogens 17, no. 7 (2021): e1009757. http://dx.doi.org/10.1371/journal.ppat.1009757.

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Antiviral RNA silencing/interference (RNAi) of negative-strand (-) RNA plant viruses (NSVs) has been studied less than for single-stranded, positive-sense (+)RNA plant viruses. From the latter, genomic and subgenomic mRNA molecules are targeted by RNAi. However, genomic RNA strands from plant NSVs are generally wrapped tightly within viral nucleocapsid (N) protein to form ribonucleoproteins (RNPs), the core unit for viral replication, transcription and movement. In this study, the targeting of the NSV tospoviral genomic RNA and mRNA molecules by antiviral RNA-induced silencing complexes (RISC)

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Suzuki, Junya, and Sadaki Yokota. "PRKRA Localizes to Nuage Structures and the Ectoplasmic Specialization and Tubulobulbar Complexes in Rat and Mouse Testis." Journal of Histology 2014 (February 25, 2014): 1–9. http://dx.doi.org/10.1155/2014/634290.

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The cytoplasmic RNA-induced silencing complex (RISC) contains dsRNA binding proteins, including PRKRA, TRBP, and Dicer. RISC localizes to P-bodies. The nuage of the spermatogenic cells has function similar to the P-bodies. We study whether PRKRA localizes to nuage of spermatogenic cells of rat and mouse. PRKRA localized to four types of nuage structures, including aggregates of 60–90 nm particles, irregularly-shaped perinuclear granules, and intermitochondrial cement of pachytene spermatocytes, and chromatoid bodies of round spermatids. In addition, PRKRA is associated with dense material surr

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Tang, Fuchou, Petra Hajkova, Dónal O’Carroll, et al. "MicroRNAs are tightly associated with RNA-induced gene silencing complexes in vivo." Biochemical and Biophysical Research Communications 372, no. 1 (2008): 24–29. http://dx.doi.org/10.1016/j.bbrc.2008.04.137.

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Valli, Adrian, Gabriela Dujovny, and Juan Antonio García. "Protease Activity, Self Interaction, and Small Interfering RNA Binding of the Silencing Suppressor P1b from Cucumber Vein Yellowing Ipomovirus." Journal of Virology 82, no. 2 (2007): 974–86. http://dx.doi.org/10.1128/jvi.01664-07.

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ABSTRACT The RNA silencing pathway mediated by small interfering RNAs (siRNAs) plays an important antiviral role in eukaryotes. To counteract this defense barrier, a large number of plant viruses express proteins with RNA silencing suppression activity. Recently, it was reported that the ipomovirus Cucumber vein yellowing virus (CVYV), which lacks the typical silencing suppressor of members of the family Potyviridae, i.e., HCPro, has a duplicated P1 coding sequence and that the downstream P1 copy, named P1b, has silencing suppression activity. In this study, we provide experimental evidence th

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Piao, Xianghua, Xue Zhang, Ligang Wu, and Joel G. Belasco. "CCR4-NOT Deadenylates mRNA Associated with RNA-Induced Silencing Complexes in Human Cells." Molecular and Cellular Biology 30, no. 6 (2010): 1486–94. http://dx.doi.org/10.1128/mcb.01481-09.

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ABSTRACT MicroRNAs (miRNAs) repress gene expression posttranscriptionally by inhibiting translation and by expediting deadenylation so as to trigger rapid mRNA decay. Their regulatory influence is mediated by the protein components of the RNA-induced silencing complex (RISC), which deliver miRNAs and siRNAs to their mRNA targets. Here, we present evidence that CCR4-NOT is the deadenylase that removes poly(A) from messages destabilized by miRNAs in human cells. Overproducing a mutationally inactivated form of either of the catalytic subunits of this deadenylase (CCR4 or CAF1/POP2) significantly

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10

Grentzinger, Thomas, Stefan Oberlin, Gregory Schott, et al. "A universal method for the rapid isolation of all known classes of functional silencing small RNAs." Nucleic Acids Research 48, no. 14 (2020): e79-e79. http://dx.doi.org/10.1093/nar/gkaa472.

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Abstract Diverse classes of silencing small (s)RNAs operate via ARGONAUTE-family proteins within RNA-induced-silencing-complexes (RISCs). Here, we have streamlined various embodiments of a Q-sepharose-based RISC-purification method that relies on conserved biochemical properties of all ARGONAUTEs. We show, in multiple benchmarking assays, that the resulting 15-min benchtop extraction procedure allows simultaneous purification of all known classes of RISC-associated sRNAs without prior knowledge of the samples-intrinsic ARGONAUTE repertoires. Optimized under a user-friendly format, the method –

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Stalker, Leanne, Alanna G. Backx, Allison K. Tscherner, Stewart J. Russell, Robert A. Foster, and Jonathan LaMarre. "cDNA Cloning of Feline PIWIL1 and Evaluation of Expression in the Testis of the Domestic Cat." International Journal of Molecular Sciences 24, no. 11 (2023): 9346. http://dx.doi.org/10.3390/ijms24119346.

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The PIWI clade of Argonaute proteins is essential for spermatogenesis in all species examined to date. This protein family binds specific classes of small non-coding RNAs known as PIWI-interacting RNAs (piRNAs) which together form piRNA-induced silencing complexes (piRISCs) that are recruited to specific RNA targets through sequence complementarity. These complexes facilitate gene silencing through endonuclease activity and guided recruitment of epigenetic silencing factors. PIWI proteins and piRNAs have been found to play multiple roles in the testis including the maintenance of genomic integ

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Gartland, Siobhan, Baosheng Zeng, and Michael T. Marr. "The small RNA landscape is stable with age and resistant to loss of dFOXO signaling in Drosophila." PLOS ONE 17, no. 11 (2022): e0273590. http://dx.doi.org/10.1371/journal.pone.0273590.

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Aging can be defined as the progressive loss of physiological homeostasis that leads to a decline in cellular and organismal function. In recent years, it has become clear that small RNA pathways play a role in aging and aging related phenotypes. Small RNA pathways regulate many important processes including development, cellular physiology, and innate immunity. The pathways illicit a form of posttranscriptional gene regulation that relies on small RNAs bound by the protein components of the RNA-induced silencing complexes (RISCs), which inhibit the expression of complementary RNAs. In Drosoph

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Iki, Taichiro, Manabu Yoshikawa, Masaki Nishikiori, et al. "In Vitro Assembly of Plant RNA-Induced Silencing Complexes Facilitated by Molecular Chaperone HSP90." Molecular Cell 39, no. 2 (2010): 282–91. http://dx.doi.org/10.1016/j.molcel.2010.05.014.

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Manavella, Pablo. "Tissue-specific silencing of arabidopsis SU(VAR)3-9 HOMOLOG8 by miR171a*." Plant Physiology 161, no. 2 (2013): 805–12. https://doi.org/10.1104/pp.112.207068.

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MicroRNAs (miRNAs) are produced from double-stranded precursors, from which a short duplex is excised. The strand of the duplex that remains more abundant is usually the active form, the miRNA, while steady-state levels of the other strand, the miRNA*, are generally lower. The executive engines of miRNA-directed gene silencing are RNA-induced silencing complexes (RISCs). During RISC maturation, the miRNA/miRNA* duplex associates with the catalytic subunit, an ARGONAUTE (AGO) protein. Subsequently, the guide strand, which directs gene silencing, is retained, while the passenger strand is degrad

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Schnettler, Esther, Hans Hemmes, Rik Huismann, Rob Goldbach, Marcel Prins, and Richard Kormelink. "Diverging Affinity of Tospovirus RNA Silencing Suppressor Proteins, NSs, for Various RNA Duplex Molecules." Journal of Virology 84, no. 21 (2010): 11542–54. http://dx.doi.org/10.1128/jvi.00595-10.

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ABSTRACT The tospovirus NSs protein was previously shown to suppress the antiviral RNA silencing mechanism in plants. Here the biochemical analysis of NSs proteins from different tospoviruses, using purified NSs or NSs containing cell extracts, is described. The results showed that all tospoviral NSs proteins analyzed exhibited affinity to small double-stranded RNA molecules, i.e., small interfering RNAs (siRNAs) and micro-RNA (miRNA)/miRNA* duplexes. Interestingly, the NSs proteins from tomato spotted wilt virus (TSWV), impatiens necrotic spot virus (INSV), and groundnut ringspot virus (GRSV)

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Kourtidis, Antonis, Brian Necela, Wan-Hsin Lin, et al. "Cadherin complexes recruit mRNAs and RISC to regulate epithelial cell signaling." Journal of Cell Biology 216, no. 10 (2017): 3073–85. http://dx.doi.org/10.1083/jcb.201612125.

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Cumulative evidence demonstrates that most RNAs exhibit specific subcellular distribution. However, the mechanisms regulating this phenomenon and its functional consequences are still under investigation. Here, we reveal that cadherin complexes at the apical zonula adherens (ZA) of epithelial adherens junctions recruit the core components of the RNA-induced silencing complex (RISC) Ago2, GW182, and PABPC1, as well as a set of 522 messenger RNAs (mRNAs) and 28 mature microRNAs (miRNAs or miRs), via PLEKHA7. Top canonical pathways represented by these mRNAs include Wnt/β-catenin, TGF-β, and stem

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Lannan, Erica, Rianna Vandergaast, and Paul D. Friesen. "Baculovirus Caspase Inhibitors P49 and P35 Block Virus-Induced Apoptosis Downstream of Effector Caspase DrICE Activation in Drosophila melanogaster Cells." Journal of Virology 81, no. 17 (2007): 9319–30. http://dx.doi.org/10.1128/jvi.00247-07.

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ABSTRACT Baculoviruses induce widespread apoptosis in invertebrates. To better understand the pathways by which these DNA viruses trigger apoptosis, we have used a combination of RNA silencing and overexpression of viral and host apoptotic regulators to identify cell death components in the model system of Drosophila melanogaster. Here we report that the principal effector caspase DrICE is required for baculovirus-induced apoptosis of Drosophila DL-1 cells as demonstrated by RNA silencing. proDrICE was proteolytically cleaved and activated during infection. Activation was blocked by overexpres

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Trotman, Jackson B., David M. Lee, Rachel E. Cherney, et al. "Elements at the 5′ end of Xist harbor SPEN-independent transcriptional antiterminator activity." Nucleic Acids Research 48, no. 18 (2020): 10500–10517. http://dx.doi.org/10.1093/nar/gkaa789.

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Abstract The Xist lncRNA requires Repeat A, a conserved RNA element located in its 5′ end, to induce gene silencing during X-chromosome inactivation. Intriguingly, Repeat A is also required for production of Xist. While silencing by Repeat A requires the protein SPEN, how Repeat A promotes Xist production remains unclear. We report that in mouse embryonic stem cells, expression of a transgene comprising the first two kilobases of Xist (Xist-2kb) causes transcriptional readthrough of downstream polyadenylation sequences. Readthrough required Repeat A and the ∼750 nucleotides downstream, did not

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Sen, Merve, Marco Bassetto, Florent Poulhes, Olivier Zelphati, Marius Ueffing, and Blanca Arango-Gonzalez. "Efficient Ocular Delivery of VCP siRNA via Reverse Magnetofection in RHO P23H Rodent Retina Explants." Pharmaceutics 13, no. 2 (2021): 225. http://dx.doi.org/10.3390/pharmaceutics13020225.

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The use of synthetic RNA for research purposes as well as RNA-based therapy and vaccination has gained increasing importance. Given the anatomical seclusion of the eye, small interfering RNA (siRNA)-induced gene silencing bears great potential for targeted reduction of pathological gene expression that may allow rational treatment of chronic eye diseases in the future. However, there is yet an unmet need for techniques providing safe and efficient siRNA delivery to the retina. We used magnetic nanoparticles (MNPs) and magnetic force (Reverse Magnetofection) to deliver siRNA/MNP complexes into

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Yoshikawa, Manabu, Yong-Woon Han, Hirofumi Fujii, Shu Aizawa, Tatsuya Nishino, and Masayuki Ishikawa. "Cooperative recruitment of RDR6 by SGS3 and SDE5 during small interfering RNA amplification in Arabidopsis." Proceedings of the National Academy of Sciences 118, no. 34 (2021): e2102885118. http://dx.doi.org/10.1073/pnas.2102885118.

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Small interfering RNAs (siRNAs) are often amplified from transcripts cleaved by RNA-induced silencing complexes (RISCs) containing a small RNA (sRNA) and an Argonaute protein. Amplified siRNAs, termed secondary siRNAs, are important for reinforcement of target repression. In plants, target cleavage by RISCs containing 22-nucleotide (nt) sRNA and Argonaute 1 (AGO1) triggers siRNA amplification. In this pathway, the cleavage fragment is converted into double-stranded RNA (dsRNA) by RNA-dependent RNA polymerase 6 (RDR6), and the dsRNA is processed into siRNAs by Dicer-like proteins. Because nonsp

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Varjak, Margus, Rommel J. Gestuveo, Richard Burchmore, Esther Schnettler, and Alain Kohl. "aBravo Is a Novel Aedes aegypti Antiviral Protein That Interacts with, but Acts Independently of, the Exogenous siRNA Pathway Effector Dicer 2." Viruses 12, no. 7 (2020): 748. http://dx.doi.org/10.3390/v12070748.

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Mosquitoes, such as Aedes aegypti, can transmit arboviruses to humans. The exogenous short interfering RNA (exo-siRNA) pathway plays a major antiviral role in controlling virus infection in mosquito cells. The Dicer 2 (Dcr2) nuclease is a key effector protein in this pathway, which cleaves viral double-stranded RNA into virus-derived siRNAs that are further loaded onto an effector called Argonaute 2 (Ago2), which as part of the multiprotein RNA-induced silencing complex (RISC) targets and cleaves viral RNA. In order to better understand the effector protein Dcr2, proteomics experiments were co

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Kopek, Benjamin G., Erik W. Settles, Paul D. Friesen, and Paul Ahlquist. "Nodavirus-Induced Membrane Rearrangement in Replication Complex Assembly Requires Replicase Protein A, RNA Templates, and Polymerase Activity." Journal of Virology 84, no. 24 (2010): 12492–503. http://dx.doi.org/10.1128/jvi.01495-10.

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ABSTRACT Positive-strand RNA [(+)RNA] viruses invariably replicate their RNA genomes on modified intracellular membranes. In infected Drosophila cells, Flock House nodavirus (FHV) RNA replication complexes form on outer mitochondrial membranes inside ∼50-nm, virus-induced spherular invaginations similar to RNA replication-linked spherules induced by many (+)RNA viruses at various membranes. To better understand replication complex assembly, we studied the mechanisms of FHV spherule formation. FHV has two genomic RNAs; RNA1 encodes multifunctional RNA replication protein A and RNA interference

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Yang, Minglei, Hugh C. Woolfenden, Yueying Zhang, et al. "Intact RNA structurome reveals mRNA structure-mediated regulation of miRNA cleavage in vivo." Nucleic Acids Research 48, no. 15 (2020): 8767–81. http://dx.doi.org/10.1093/nar/gkaa577.

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Abstract MicroRNA (miRNA)-mediated cleavage is involved in numerous essential cellular pathways. miRNAs recognize target RNAs via sequence complementarity. In addition to complementarity, in vitro and in silico studies have suggested that RNA structure may influence the accessibility of mRNAs to miRNA-induced silencing complexes (miRISCs), thereby affecting RNA silencing. However, the regulatory mechanism of mRNA structure in miRNA cleavage remains elusive. We investigated the role of in vivo RNA secondary structure in miRNA cleavage by developing the new CAP-STRUCTURE-seq method to capture th

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Kennedy, Edward M., Adam W. Whisnant, Anand V. R. Kornepati, Joy B. Marshall, Hal P. Bogerd, and Bryan R. Cullen. "Production of functional small interfering RNAs by an amino-terminal deletion mutant of human Dicer." Proceedings of the National Academy of Sciences 112, no. 50 (2015): E6945—E6954. http://dx.doi.org/10.1073/pnas.1513421112.

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Although RNA interference (RNAi) functions as a potent antiviral innate-immune response in plants and invertebrates, mammalian somatic cells appear incapable of mounting an RNAi response and few, if any, small interfering RNAs (siRNAs) can be detected. To examine why siRNA production is inefficient, we have generated double-knockout human cells lacking both Dicer and protein kinase RNA-activated. Using these cells, which tolerate double-stranded RNA expression, we show that a mutant form of human Dicer lacking the amino-terminal helicase domain can process double-stranded RNAs to produce high

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Blenn, Christian, Felix R. Althaus, and Maria Malanga. "Poly(ADP-ribose) glycohydrolase silencing protects against H2O2-induced cell death." Biochemical Journal 396, no. 3 (2006): 419–29. http://dx.doi.org/10.1042/bj20051696.

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PAR [poly(ADP-ribose)] is a structural and regulatory component of multiprotein complexes in eukaryotic cells. PAR catabolism is accelerated under genotoxic stress conditions and this is largely attributable to the activity of a PARG (PAR glycohydrolase). To overcome the early embryonic lethality of parg-knockout mice and gain more insights into the biological functions of PARG, we used an RNA interference approach. We found that as little as 10% of PARG protein is sufficient to ensure basic cellular functions: PARG-silenced murine and human cells proliferated normally through several subcultu

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Pantazopoulou, Vasiliki I., Stella Georgiou, Panos Kakoulidis, et al. "From the Argonauts Mythological Sailors to the Argonautes RNA-Silencing Navigators: Their Emerging Roles in Human-Cell Pathologies." International Journal of Molecular Sciences 21, no. 11 (2020): 4007. http://dx.doi.org/10.3390/ijms21114007.

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Regulation of gene expression has emerged as a fundamental element of transcript homeostasis. Key effectors in this process are the Argonautes (AGOs), highly specialized RNA-binding proteins (RBPs) that form complexes, such as the RNA-Induced Silencing Complex (RISC). AGOs dictate post-transcriptional gene-silencing by directly loading small RNAs and repressing their mRNA targets through small RNA-sequence complementarity. The four human highly-conserved family-members (AGO1, AGO2, AGO3, and AGO4) demonstrate multi-faceted and versatile roles in transcriptome’s stability, plasticity, and funct

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Ma, Xinrong, Fadia Ibrahim, Eun-Jeong Kim, et al. "An ortholog of the Vasa intronic gene is required for small RNA-mediated translation repression inChlamydomonas reinhardtii." Proceedings of the National Academy of Sciences 117, no. 1 (2019): 761–70. http://dx.doi.org/10.1073/pnas.1908356117.

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Small RNAs (sRNAs) associate with Argonaute (AGO) proteins in effector complexes, termed RNA-induced silencing complexes (RISCs), which regulate complementary transcripts by translation inhibition and/or RNA degradation. In the unicellular algaChlamydomonas, several metazoans, and land plants, emerging evidence indicates that polyribosome-associated transcripts can be translationally repressed by RISCs without substantial messenger RNA (mRNA) destabilization. However, the mechanism of translation inhibition in a polyribosomal context is not understood. Here we show thatChlamydomonasVIG1, an or

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Pare, Justin M., Paul LaPointe, and Tom C. Hobman. "Hsp90 cochaperones p23 and FKBP4 physically interact with hAgo2 and activate RNA interference–mediated silencing in mammalian cells." Molecular Biology of the Cell 24, no. 15 (2013): 2303–10. http://dx.doi.org/10.1091/mbc.e12-12-0892.

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Argonaute proteins and small RNAs together form the RNA-induced silencing complex (RISC), the central effector of RNA interference (RNAi). The molecular chaperone Hsp90 is required for the critical step of loading small RNAs onto Argonaute proteins. Here we show that the Hsp90 cochaperones Cdc37, Aha1, FKBP4, and p23 are required for efficient RNAi. Whereas FKBP4 and p23 form a stable complex with hAgo2, the function of Cdc37 in RNAi appears to be indirect and may indicate that two or more Hsp90 complexes are involved. Our data also suggest that p23 and FKBP4 interact with hAgo2 before small R

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Buck, Amy H., and Mark Blaxter. "Functional diversification of Argonautes in nematodes: an expanding universe." Biochemical Society Transactions 41, no. 4 (2013): 881–86. http://dx.doi.org/10.1042/bst20130086.

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In the last decade, many diverse RNAi (RNA interference) pathways have been discovered that mediate gene silencing at epigenetic, transcriptional and post-transcriptional levels. The diversity of RNAi pathways is inherently linked to the evolution of Ago (Argonaute) proteins, the central protein component of RISCs (RNA-induced silencing complexes). An increasing number of diverse Agos have been identified in different species. The functions of most of these proteins are not yet known, but they are generally assumed to play roles in development, genome stability and/or protection against viruse

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Rajgor, Dipen, Jason A. Mellad, Daniel Soong, Jerome B. Rattner, Marvin J. Fritzler, and Catherine M. Shanahan. "Mammalian microtubule P-body dynamics are mediated by nesprin-1." Journal of Cell Biology 205, no. 4 (2014): 457–75. http://dx.doi.org/10.1083/jcb.201306076.

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Nesprins are a multi-isomeric family of spectrin-repeat (SR) proteins, predominantly known as nuclear envelope scaffolds. However, isoforms that function beyond the nuclear envelope remain poorly examined. Here, we characterize p50Nesp1, a 50-kD isoform that localizes to processing bodies (PBs), where it acts as a microtubule-associated protein capable of linking mRNP complexes to microtubules. Overexpression of dominant-negative p50Nesp1 caused Rck/p54, but not GW182, displacement from microtubules, resulting in reduced PB movement and cross talk with stress granules (SGs). These cells disass

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Pokornowska, Maria, Marek C. Milewski, Kinga Ciechanowska, et al. "The RNA–RNA base pairing potential of human Dicer and Ago2 proteins." Cellular and Molecular Life Sciences 77, no. 16 (2019): 3231–44. http://dx.doi.org/10.1007/s00018-019-03344-6.

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Abstract The ribonuclease Dicer produces microRNAs (miRNAs) and small interfering RNAs that are handed over to Ago proteins to control gene expression by targeting complementary sequences within transcripts. Interestingly, a growing number of reports have demonstrated that the activity of Dicer may extend beyond the biogenesis of small regulatory RNAs. Among them, a report from our latest studies revealed that human Dicer facilitates base pairing of complementary sequences present in two nucleic acids, thus acting as a nucleic acid annealer. Accordingly, in this manuscript, we address how RNA

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DeBeauchamp, Jennifer L., Arian Moses, Victoria J. P. Noffsinger, et al. "Chp1-Tas3 Interaction Is Required To Recruit RITS to Fission Yeast Centromeres and for Maintenance of Centromeric Heterochromatin." Molecular and Cellular Biology 28, no. 7 (2008): 2154–66. http://dx.doi.org/10.1128/mcb.01637-07.

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ABSTRACT The maintenance of centromeric heterochromatin in fission yeast relies on the RNA interference-dependent complexes RITS (RNA-induced transcriptional silencing complex) and RDRC (RNA-directed RNA polymerase complex), which cooperate in a positive feedback loop to recruit high levels of histone H3 K9 methyltransferase activity to centromeres and to promote the assembly and maintenance of centromeric heterochromatin. However, it is unclear how these complexes are targeted to chromatin. RITS comprises Chp1, which binds K9-methylated histone H3; Ago1, which binds short interfering (siRNAs)

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Cheng, De-Jie, Xiao-Jie Xu, Zhi-Yong Yan, et al. "The chloroplast ribosomal protein large subunit 1 interacts with viral polymerase and promotes virus infection." Plant Physiology 187, no. 1 (2021): 174–86. http://dx.doi.org/10.1093/plphys/kiab249.

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Abstract Chloroplasts play an indispensable role in the arms race between plant viruses and hosts. Chloroplast proteins are often recruited by plant viruses to support viral replication and movement. However, the mechanism by which chloroplast proteins regulate potyvirus infection remains largely unknown. In this study, we observed that Nicotiana benthamiana ribosomal protein large subunit 1 (NbRPL1), a chloroplast ribosomal protein, localized to the chloroplasts via its N-terminal 61 amino acids (transit peptide), and interacted with tobacco vein banding mosaic virus (TVBMV) nuclear inclusion

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Mazza, Mariarosa, Hassan Ahmad, Marilena Hadjidemetriou, et al. "Hampering brain tumor proliferation and migration using peptide nanofiber:siPLK1/MMP2 complexes." Nanomedicine 14, no. 24 (2019): 3127–42. http://dx.doi.org/10.2217/nnm-2019-0298.

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Aim: To develop a nonviral tool for the delivery of siRNA to brain tumor cells using peptide nanofibers (PNFs). Materials & methods: Uptake of PNFs was evaluated by confocal microscopy and flow cytometry. Gene silencing was determined by RT-qPCR and cell invasion assay. Results: PNFs enter phagocytic (BV-2) and nonphagocytic (U-87 MG) cells via endocytosis and passive translocation. si PLK1 delivered using PNFs reduced the expression of polo-like kinase 1 mRNA and induced cell death in a panel of immortalized and glioblastoma-derived stem cells. Moreover, targeting MMP2 using PNF:si MMP2 r

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van der Vaart, Aniek, Molly Godfrey, Vincent Portegijs, and Sander van den Heuvel. "Dose-dependent functions of SWI/SNF BAF in permitting and inhibiting cell proliferation in vivo." Science Advances 6, no. 21 (2020): eaay3823. http://dx.doi.org/10.1126/sciadv.aay3823.

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SWI/SNF (switch/sucrose nonfermenting) complexes regulate transcription through chromatin remodeling and opposing gene silencing by Polycomb group (PcG) proteins. Genes encoding SWI/SNF components are critical for normal development and frequently mutated in human cancer. We characterized the in vivo contributions of SWI/SNF and PcG complexes to proliferation-differentiation decisions, making use of the reproducible development of the nematode Caenorhabditis elegans. RNA interference, lineage-specific gene knockout, and targeted degradation of SWI/SNF BAF components induced either overprolifer

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Dalmadi, Ágnes, Péter Gyula, Jeannette Bálint, György Szittya, and Zoltán Havelda. "AGO-unbound cytosolic pool of mature miRNAs in plant cells reveals a novel regulatory step at AGO1 loading." Nucleic Acids Research 47, no. 18 (2019): 9803–17. http://dx.doi.org/10.1093/nar/gkz690.

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Abstract RNA interference (RNAi) is mediated by small, 20-24-nt-long, non-coding regulatory (s)RNAs such as micro (mi) and small interfering (si) RNAs via the action of ARGONAUTE (AGO) proteins. High-throughput sequencing of size-separated sRNA pools of plant crude extracts revealed that the majority of the canonical miRNAs were associated with high molecular weight RNA-induced silencing complexes co-migrating with AGO1 (HMW RISC). In contrast, the majority of 24-nt-long siRNAs were found in association with low molecular weight complexes co-migrating with AGO4 (LMW RISC). Intriguingly, we ide

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Moradimotlagh, Atieh, Harsimran Kaur Brar, Stella Chen, et al. "Characterization of Argonaute-containing protein complexes in Leishmania-infected human macrophages." PLOS ONE 19, no. 5 (2024): e0303686. http://dx.doi.org/10.1371/journal.pone.0303686.

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The intracellular protozoan parasite Leishmania causes leishmaniasis in humans, leading to serious illness and death in tropical and subtropical areas worldwide. Unfortunately, due to the unavailability of approved vaccines for humans and the limited efficacy of available drugs, leishmaniasis is on the rise. A comprehensive understanding of host-pathogen interactions at the molecular level could pave the way to counter leishmaniasis. There is growing evidence that several intracellular pathogens target RNA interference (RNAi) pathways in host cells to facilitate their persistence. The core ele

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Helderman, Tieme, Laurens Deurhof, André Bertran, et al. "An Isoform of the Eukaryotic Translation Elongation Factor 1A (eEF1a) Acts as a Pro-Viral Factor Required for Tomato Spotted Wilt Virus Disease in Nicotiana benthamiana." Viruses 13, no. 11 (2021): 2190. http://dx.doi.org/10.3390/v13112190.

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The tripartite genome of the negative-stranded RNA virus Tomato spotted wilt orthotospovirus (TSWV) is assembled, together with two viral proteins, the nucleocapsid protein and the RNA-dependent RNA polymerase, into infectious ribonucleoprotein complexes (RNPs). These two viral proteins are, together, essential for viral replication and transcription, yet our knowledge on the host factors supporting these two processes remains limited. To fill this knowledge gap, the protein composition of viral RNPs collected from TSWV-infected Nicotiana benthamiana plants, and of those collected from a recon

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Lidak, Tomas, Nikol Baloghova, Vladimir Korinek, et al. "CRL4-DCAF12 Ubiquitin Ligase Controls MOV10 RNA Helicase during Spermatogenesis and T Cell Activation." International Journal of Molecular Sciences 22, no. 10 (2021): 5394. http://dx.doi.org/10.3390/ijms22105394.

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Multisubunit cullin-RING ubiquitin ligase 4 (CRL4)-DCAF12 recognizes the C-terminal degron containing acidic amino acid residues. However, its physiological roles and substrates are largely unknown. Purification of CRL4-DCAF12 complexes revealed a wide range of potential substrates, including MOV10, an “ancient” RNA-induced silencing complex (RISC) complex RNA helicase. We show that DCAF12 controls the MOV10 protein level via its C-terminal motif in a proteasome- and CRL-dependent manner. Next, we generated Dcaf12 knockout mice and demonstrated that the DCAF12-mediated degradation of MOV10 is

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Hwang, Hun-Way, Erik A. Wentzel, and Joshua T. Mendell. "Cell–cell contact globally activates microRNA biogenesis." Proceedings of the National Academy of Sciences 106, no. 17 (2009): 7016–21. http://dx.doi.org/10.1073/pnas.0811523106.

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MicroRNAs (miRNAs) are 18- to 24-nt RNA molecules that regulate messenger RNAs (mRNAs). Posttranscriptional mechanisms regulate miRNA abundance during development as well as in cancer cells where miRNAs frequently exhibit dysregulated expression. The molecular mechanisms that govern the global efficiency of miRNA biogenesis in these settings remain incompletely understood, and experimental systems for the biochemical dissection of these pathways are currently lacking. Here, we demonstrate that miRNAs are subject to dynamic posttranscriptional regulation in widely used cell culture systems. As

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Hudy, Dorota, and Joanna Rzeszowska-Wolny. "Expression of miRNA-Targeted and Not-Targeted Reporter Genes Shows Mutual Influence and Intercellular Specificity." International Journal of Molecular Sciences 23, no. 23 (2022): 15059. http://dx.doi.org/10.3390/ijms232315059.

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The regulation of translation by RNA-induced silencing complexes (RISCs) composed of Argonaute proteins and micro-RNAs is well established; however, the mechanisms underlying specific cellular responses to miRNAs and how specific complexes arise are not completely clear. To explore these questions, we performed experiments with Renilla and firefly luciferase reporter genes transfected in a psiCHECK-2 plasmid into human HCT116 or Me45 cells, where only the Renilla gene contained sequences targeted by microRNAs (miRNAs) in the 3′UTR. The effects of targeting were miRNA-specific; miRNA-21-5p caus

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Yoshii, Atsushi, Takumi Shimizu, Akiko Yoshida, et al. "NTH201, a Novel Class II KNOTTED1-Like Protein, Facilitates the Cell-to-Cell Movement of Tobacco mosaic virus in Tobacco." Molecular Plant-Microbe Interactions® 21, no. 5 (2008): 586–96. http://dx.doi.org/10.1094/mpmi-21-5-0586.

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NTH201, a novel class II KNOTTED1-like protein gene, was cloned from tobacco (Nicotiana tabacum cv. Xanthi) and its role in Tobacco mosaic virus (TMV) infection was analyzed. Virus-induced gene silencing of NTH201 caused a delay in viral RNA accumulation as well as virus spread in infected tobacco plants. Overexpression of the gene in a transgenic tobacco plant (N. tabacum cv. Xanthi nc) infected by TMV showed larger local lesions than those of the nontransgenic plant. NTH201 exhibited no intercellular trafficking ability but did exhibit colocalization with movement protein (MP) at the plasmod

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Fedorin, Dmitry N., Anna E. Khomutova, and Alexander T. Eprintsev. "Electrophoretic method and assessing the formation of an RNA-interfering complex with miR775A in corn leaves under the conditions of normoxia and hypoxia." Сорбционные и хроматографические процессы 24, no. 2 (2024): 289–98. http://dx.doi.org/10.17308/sorpchrom.2024.24/12137.

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Oxidative processes in cells, in particular mitochondrial respiration, are most sensitive to a lack of oxygen, therefore, it requires cell metabolism coordination. MicroRNAs are one of the tools of the molecular epigenetic regulation. These are a class of non-coding small RNA molecules (20-22 nt) that are able to regulate target genes expression at the post-transcriptional level by inhibiting the translation or cleavage of their mRNAs. It is known that microRNAs can act by RNA interference or can bind to an RNA-induced transcriptional silencing (RITS) complex. The study of the role of microRNA

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Luo, Chaohu, Zhan Qi Wang, Xianan Liu, Liling Zhao, Xueping Zhou, and Yan Xie. "Identification and Analysis of Potential Genes Regulated by an Alphasatellite (TYLCCNA) that Contribute to Host Resistance against Tomato Yellow Leaf Curl China Virus and Its Betasatellite (TYLCCNV/TYLCCNB) Infection in Nicotiana benthamiana." Viruses 11, no. 5 (2019): 442. http://dx.doi.org/10.3390/v11050442.

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Recently, begomovirus/betasatellite disease complexes were found to be associated with alphasatellites, and their presence modulated disease symptoms and/or viral DNA accumulation in infected plants. However, the biological functions of alphasatellites during begomovirus/betasatellite infections remain unclear. Tomato yellow leaf curl China virus (TYLCCNV) associated with a betasatellite (TYLCCNB) is a widespread monopartite begomovirus in China. In the Yunnan province of China, the TYLCCNV/TYLCCNB disease complex is found in association with an alphasatellite (TYLCCNA). In this study, in orde

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Spada, Maria, Claudio Pugliesi, Marco Fambrini, Diego Palpacelli, Andrea Caneo, and Susanna Pecchia. "Spray-Induced Gene Silencing (SIGS): Nanocarrier-Mediated dsRNA Delivery Improves RNAi Efficiency in the Management of Lettuce Gray Mold Caused by Botrytis cinerea." Agronomy 15, no. 1 (2025): 194. https://doi.org/10.3390/agronomy15010194.

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The plant pathogenic fungus Botrytis cinerea causes significant losses in agricultural production and it is rather difficult to control due to its broad host range and environmental persistence. The management of gray mold disease is still mainly based on the use of chemicals, which could have harmful effects not only due to impacts on the environment and human health, but also because they favor the development of fungicide-resistant strains. In this scenario, the strategy of RNA interference (RNAi) is being widely considered, and Spray-Induced Gene Silencing (SIGS) is gaining interest as a v

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Nuke Ardiyan, Yustina, and Johana Puspasari Dwi Pratiwi. "Biogenesis and Function of miRNAs and Their Role in Cancer." Jurnal Impresi Indonesia 3, no. 6 (2024): 404–10. http://dx.doi.org/10.58344/jii.v3i6.4974.

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MicroRNA (miRNA) is a small RNA molecule that regulates post-transcriptional gene expression. miRNA combines with the RNA-induced silencing complex (RISC) and carries out its function in controlling translation. The formation of miRNA involves enzymes and proteins that cut it in its processing as well as protein complexes in the cytoplasm that make the miRNA mature. Several changes, for example deletion or overexpression, can occur in miRNAs, causing cancer growth. The aim of this study was to investigate the process of miRNA biogenesis as well as analyze how changes in miRNA expression can af

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Nair-Menon, Joyce, Amanda C. Daulagala, Dean M. Connor, et al. "Predominant Distribution of the RNAi Machinery at Apical Adherens Junctions in Colonic Epithelia Is Disrupted in Cancer." International Journal of Molecular Sciences 21, no. 7 (2020): 2559. http://dx.doi.org/10.3390/ijms21072559.

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The RNA interference (RNAi) machinery is an essential component of the cell, regulating miRNA biogenesis and function. RNAi complexes were thought to localize either in the nucleus, such as the microprocessor, or in the cytoplasm, such as the RNA-induced silencing complex (RISC). We recently revealed that the core microprocessor components DROSHA and DGCR8, as well as the main components of RISC, including Ago2, also associate with the apical adherens junctions of well-differentiated cultured epithelial cells. Here, we demonstrate that the localization of the core RNAi components is specific a

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Fislová, Tatiana, Benjamin Thomas, Katy M. Graef, and Ervin Fodor. "Association of the Influenza Virus RNA Polymerase Subunit PB2 with the Host Chaperonin CCT." Journal of Virology 84, no. 17 (2010): 8691–99. http://dx.doi.org/10.1128/jvi.00813-10.

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ABSTRACT The RNA polymerase of influenza A virus is a host range determinant and virulence factor. In particular, the PB2 subunit of the RNA polymerase has been implicated as a crucial factor that affects cell tropism as well as virulence in animal models. These findings suggest that host factors associating with the PB2 protein may play an important role during viral replication. In order to identify host factors that associate with the PB2 protein, we purified recombinant PB2 from transiently transfected mammalian cells and identified copurifying host proteins by mass spectrometry. We found

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La Rocca, Gaspare, Scott H. Olejniczak, Alvaro J. González, et al. "In vivo, Argonaute-bound microRNAs exist predominantly in a reservoir of low molecular weight complexes not associated with mRNA." Proceedings of the National Academy of Sciences 112, no. 3 (2015): 767–72. http://dx.doi.org/10.1073/pnas.1424217112.

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MicroRNAs repress mRNA translation by guiding Argonaute proteins to partially complementary binding sites, primarily within the 3′ untranslated region (UTR) of target mRNAs. In cell lines, Argonaute-bound microRNAs exist mainly in high molecular weight RNA-induced silencing complexes (HMW-RISC) associated with target mRNA. Here we demonstrate that most adult tissues contain reservoirs of microRNAs in low molecular weight RISC (LMW-RISC) not bound to mRNA, suggesting that these microRNAs are not actively engaged in target repression. Consistent with this observation, the majority of individual

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Ryu, Masao, Takashi Yurube, Yoshiki Takeoka, et al. "Gene-Silencing Therapeutic Approaches Targeting PI3K/Akt/mTOR Signaling in Degenerative Intervertebral Disk Cells: An In Vitro Comparative Study Between RNA Interference and CRISPR–Cas9." Cells 13, no. 23 (2024): 2030. https://doi.org/10.3390/cells13232030.

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The mammalian target of rapamycin (mTOR), a serine/threonine kinase, promotes cell growth and inhibits autophagy. The following two complexes contain mTOR: mTORC1 with the regulatory associated protein of mTOR (RAPTOR) and mTORC2 with the rapamycin-insensitive companion of mTOR (RICTOR). The phosphatidylinositol 3-kinase (PI3K)/Akt/mTOR signaling pathway is important in the intervertebral disk, which is the largest avascular, hypoxic, low-nutrient organ in the body. To examine gene-silencing therapeutic approaches targeting PI3K/Akt/mTOR signaling in degenerative disk cells, an in vitro compar

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