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https://www.readbyqxmd.com/read/29040648/molecular-basis-for-asymmetry-sensing-of-sirnas-by-the-drosophila-loqs-pd-dcr-2-complex-in-rna-interference
#1
Jan-Niklas Tants, Stephanie Fesser, Thomas Kern, Ralf Stehle, Arie Geerlof, Christoph Wunderlich, Michael Juen, Christoph Hartlmüller, Romy Böttcher, Stefan Kunzelmann, Oliver Lange, Christoph Kreutz, Klaus Förstemann, Michael Sattler
RNA interference defends against RNA viruses and retro-elements within an organism's genome. It is triggered by duplex siRNAs, of which one strand is selected to confer sequence-specificity to the RNA induced silencing complex (RISC). In Drosophila, Dicer-2 (Dcr-2) and the double-stranded RNA binding domain (dsRBD) protein R2D2 form the RISC loading complex (RLC) and select one strand of exogenous siRNAs according to the relative thermodynamic stability of base-pairing at either end. Through genome editing we demonstrate that Loqs-PD, the Drosophila homolog of human TAR RNA binding protein (TRBP) and a paralog of R2D2, forms an alternative RLC with Dcr-2 that is required for strand choice of endogenous siRNAs in S2 cells...
October 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29030847/single-molecule-analysis-for-risc-assembly-and-target-cleavage
#2
Hiroshi M Sasaki, Hisashi Tadakuma, Yukihide Tomari
RNA-induced silencing complex (RISC) is a small RNA-protein complex that mediates silencing of complementary target RNAs. Biochemistry has been successfully used to characterize the molecular mechanism of RISC assembly and function for nearly two decades. However, further dissection of intermediate states during the reactions has been warranted to fill in the gaps in our understanding of RNA silencing mechanisms. Single-molecule analysis with total internal reflection fluorescence (TIRF) microscopy is a powerful imaging-based approach to interrogate complex formation and dynamics at the individual molecule level with high sensitivity...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29030846/reconstitution-of-rna-interference-machinery
#3
Shintaro Iwasaki, Yukihide Tomari
Small RNAs, including small interfering RNAs (siRNAs) and microRNAs (miRNAs), silence protein expression from target mRNAs bearing their complementary sequences, via the formation of the effector complex called RNA-induced silencing complex (RISC). Although the mechanism of RISC assembly has been studied for nearly two decades, the detailed mechanism has still remained unclear in part due to the lack of a pure reconstitution system. Recently, we identified all the core proteins necessary for RISC assembly in flies and successfully recapitulated the assembly of catalytically active RISC with eight recombinant proteins...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29030839/quantification-of-mirnas-co-immunoprecipitated-with-argonaute-proteins-using-sybr-green-based-qrt-pcr
#4
Hong-Duc Phan, Junan Li, Ming Poi, Kotaro Nakanishi
MicroRNAs (miRNAs) are small non-coding RNAs that trigger post-transcriptional gene silencing. These RNAs need to be associated with the Argonaute proteins to be functional. This assembly begins with loading of a miRNA duplex, followed by the ejection of one of the strands (passenger). The remaining strand (guide) together with the Argonaute protein forms a ribonucleoprotein effector complex (the RNA-induced silencing complex, RISC). Mutation on the Argonaute protein, if affecting either step of the RISC assembly, impacts the function of miRNAs...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29029897/worldwide-trends-in-body-mass-index-underweight-overweight-and-obesity-from-1975-to-2016-a-pooled-analysis-of-2416-population-based-measurement-studies-in-128%C3%A2-9-million-children-adolescents-and-adults
#5
(no author information available yet)
BACKGROUND: Underweight, overweight, and obesity in childhood and adolescence are associated with adverse health consequences throughout the life-course. Our aim was to estimate worldwide trends in mean body-mass index (BMI) and a comprehensive set of BMI categories that cover underweight to obesity in children and adolescents, and to compare trends with those of adults. METHODS: We pooled 2416 population-based studies with measurements of height and weight on 128·9 million participants aged 5 years and older, including 31·5 million aged 5-19 years...
October 10, 2017: Lancet
https://www.readbyqxmd.com/read/29017520/the-nuclear-receptor-er%C3%AE-engages-ago2-in-regulation-of-gene-transcription-rna-splicing-and-risc-loading
#6
Roberta Tarallo, Giorgio Giurato, Giuseppina Bruno, Maria Ravo, Francesca Rizzo, Annamaria Salvati, Luca Ricciardi, Giovanna Marchese, Angela Cordella, Teresa Rocco, Valerio Gigantino, Biancamaria Pierri, Giovanni Cimmino, Luciano Milanesi, Concetta Ambrosino, Tuula A Nyman, Giovanni Nassa, Alessandro Weisz
BACKGROUND: The RNA-binding protein Argonaute 2 (AGO2) is a key effector of RNA-silencing pathways It exerts a pivotal role in microRNA maturation and activity and can modulate chromatin remodeling, transcriptional gene regulation and RNA splicing. Estrogen receptor beta (ERβ) is endowed with oncosuppressive activities, antagonizing hormone-induced carcinogenesis and inhibiting growth and oncogenic functions in luminal-like breast cancers (BCs), where its expression correlates with a better prognosis of the disease...
October 6, 2017: Genome Biology
https://www.readbyqxmd.com/read/28986804/rnai-mediated-knockdown-of-protein-expression
#7
Volker Baumann, Cornelia Lorenzer, Michael Thell, Anna-Maria Winkler, Johannes Winkler
RNA interference is an essential method for studying genomic functions of single genes by loss-of-function experiments. Short interfering siRNAs are efficiently transfected into cultured cells to enable RISC-mediated mRNA cleavage and inhibition of translation in a sequence-specific manner. RNAi enables knockdown of single genes and screening for specific cellular processes or outcomes. In this chapter, we describe a detailed universal protocol for lipoplex-mediated siRNA transfection for cell cultures and cell lysis for subsequent RNA or protein analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28981809/impact-of-enhanced-metabolic-stability-on-pharmacokinetics-and-pharmacodynamics-of-galnac-sirna-conjugates
#8
Jayaprakash K Nair, Husain Attarwala, Alfica Sehgal, Qianfan Wang, Krishna Aluri, Xuemei Zhang, Minggeng Gao, Ju Liu, Ramesh Indrakanti, Sally Schofield, Philip Kretschmer, Christopher R Brown, Swati Gupta, Jennifer L S Willoughby, Julie A Boshar, Vasant Jadhav, Klaus Charisse, Tracy Zimmermann, Kevin Fitzgerald, Muthiah Manoharan, Kallanthottathil G Rajeev, Akin Akinc, Renta Hutabarat, Martin A Maier
Covalent attachment of a synthetic triantennary N-acetylagalactosamine (GalNAc) ligand to chemically modified siRNA has enabled asialoglycoprotein (ASGPR)-mediated targeted delivery of therapeutically active siRNAs to hepatocytes in vivo. This approach has become transformative for the delivery of RNAi therapeutics as well as other classes of investigational oligonucleotide therapeutics to the liver. For efficient functional delivery of intact drug into the desired subcellular compartment, however, it is critical that the nucleic acids are stabilized against nucleolytic degradation...
September 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28977639/biochemical-and-single-molecule-analyses-of-the-rna-silencing-suppressing-activity-of-crpv-1a
#9
Mariko Watanabe, Hiro-Oki Iwakawa, Hisashi Tadakuma, Yukihide Tomari
Viruses often encode viral silencing suppressors (VSSs) to counteract the hosts' RNA silencing activity. The cricket paralysis virus 1A protein (CrPV-1A) is a unique VSS that binds to a specific Argonaute protein (Ago)-the core of the RNA-induced silencing complex (RISC)-in insects to suppress its target cleavage reaction. However, the precise molecular mechanism of CrPV-1A action remains unclear. Here we utilized biochemical and single-molecule imaging approaches to analyze the effect of CrPV-1A during target recognition and cleavage by Drosophila Ago2-RISC...
August 24, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28973449/expression-of-short-hairpin-rnas-using-the-compact-architecture-of-retroviral-microrna-genes
#10
James M Burke, Rodney P Kincaid, Francesca Aloisio, Nicole Welch, Christopher S Sullivan
Short hairpin RNAs (shRNAs) are effective in generating stable repression of gene expression. RNA polymerase III (RNAP III) type III promoters (U6 or H1) are typically used to drive shRNA expression. While useful for some knockdown applications, the robust expression of U6/H1-driven shRNAs can induce toxicity and generate heterogeneous small RNAs with undesirable off-target effects. Additionally, typical U6/H1 promoters encompass the majority of the ∼270 base pairs (bp) of vector space required for shRNA expression...
September 29, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28971854/in-vitro-reconstitution-of-chaperone-mediated-human-risc-assembly
#11
Ken Naruse, Eriko Matsuura-Suzuki, Mariko Watanabe, Shintaro Iwasaki, Yukihide Tomari
To silence target mRNAs, small RNAs and Argonaute (Ago) proteins need to be assembled into RNA-induced silencing complexes (RISCs). Although the assembly of Drosophila melanogaster RISC was recently reconstituted by Ago2, the Dicer-2/R2D2 heterodimer, and 5 chaperone proteins, the absence of a reconstitution system for mammalian RISC assembly has posed analytical challenges. Here we describe reconstitution of human RISC assembly using Ago2 and 5 recombinant chaperone proteins: Hsp90β, Hsc70, Hop, Dnaja2, and p23...
October 2, 2017: RNA
https://www.readbyqxmd.com/read/28961149/psychometric-validation-of-the-10-item-connor-davidson-resilience-scale
#12
John Ehrich, Angela Mornane, Tim Powern
Resilience is the personality trait of having positive dispositions which enable individuals to cope with stressful situations. Hence, a reliable resilience scale can provide useful information on understanding and treating individuals suffering from stress and trauma. The 10-item Connor-Davidson Resiliance Scale (CD-RISC-10) is a candidate scale. However, very little psychometric research has been conducted on this scale and, moreover, psychometric analyses to date have not been conclusive. To attain further evidence of the scale's psychometric properties, we tested the CD-RISC-10 on 288 adult Education major students at an Australian University using both traditional (factor analyses) and modern (Rasch) measurement approaches...
2017: Journal of Applied Measurement
https://www.readbyqxmd.com/read/28959421/regulation-and-imaging-of-gene-expression-via-an-rna-interference-antagonistic-biomimetic-probe
#13
Kai Zhang, Xue-Jiao Yang, Wei Zhao, Ming-Chen Xu, Jing-Juan Xu, Hong-Yuan Chen
Regulation of gene expression is highly important in the area of cell biology. In this work a novel convenient and versatile strategy is reported which permits both gene regulation and imaging in living cells. An oligonucleotide-based biomimetic probe was designed to target an RNA-induced silencing complex (RISC) and served as an agent for the modulation of c-Myc protein expression in living cells through regulating the RNA interference (RNAi) pathway. In this probe, a DNA strand (Strand1) serving as the frame was immobilized on a AuNP with a thiol group at the 5' end...
July 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28959243/rnase-h-as-gene-modifier-driver-of-evolution-and-antiviral-defense
#14
REVIEW
Karin Moelling, Felix Broecker, Giancarlo Russo, Shinichi Sunagawa
Retroviral infections are 'mini-symbiotic' events supplying recipient cells with sequences for viral replication, including the reverse transcriptase (RT) and ribonuclease H (RNase H). These proteins and other viral or cellular sequences can provide novel cellular functions including immune defense mechanisms. Their high error rate renders RT-RNases H drivers of evolutionary innovation. Integrated retroviruses and the related transposable elements (TEs) have existed for at least 150 million years, constitute up to 80% of eukaryotic genomes and are also present in prokaryotes...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28930465/single-molecule-based-white-light-emissive-organic-solids-with-molecular-packing-dependent-thermally-activated-delayed-fluorescence
#15
Yuewei Zhang, Yang Miao, Xiaoxian Song, Yu Gao, Zuolun Zhang, Kaiqi Ye, Yue Wang
White-light-emitting single molecules have attracted broad attention because of their great potential for use in flat-panel displays and future light sources. We report a unique molecule of 3-(diphenylamino)-9H-xanthen-9-one (3-DPH-XO), which was found to exhibit bright white-light emission in the solid state caused by the spontaneous formation of a mixture with different polymorphs. Single-crystal analyses demonstrate that noncovalent interactions (such as π···π stacking, hydrogen bonding, and C-H···π interactions) induce different stacking arrangements (polymorphs A, B, and C) with different photophysical properties in a molecular solid...
September 21, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28925592/defining-a-microrna-mrna-interaction-map-for-calcineurin-inhibitor-induced-nephrotoxicity
#16
Christopher J Benway, John Iacomini
Calcineurin inhibitors induce nephrotoxicity through poorly understood mechanisms thereby limiting their use in transplantation and other diseases. Here we define a microRNA (miRNA)-messenger RNA (mRNA) interaction map that facilitates exploration into the role of miRNAs in cyclosporine-induced nephrotoxicity (CIN) and the gene pathways they regulate. Using photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP), we isolated RNAs associated with Argonaute 2 in the RNA-Induced Silencing Complex (RISC) of cyclosporine A (CsA) treated and control human proximal tubule cells and identified mRNAs undergoing active targeting by miRNAs...
September 19, 2017: American Journal of Transplantation
https://www.readbyqxmd.com/read/28923700/venous-thromboembolism-risk-in-patients-with-locoregional-urothelial-tract-tumors
#17
Jorge D Ramos, Jonathan T Wingate, Roman Gulati, Elizabeth R Plimack, Lauren C Harshman, Thomas Powles, Simon J Crabb, Guenter Niegisch, Joaquim Bellmunt, Sylvain Ladoire, Ugo De Giorgi, Syed Hussain, Ajjai S Alva, Jack Baniel, Neeraj Agarwal, Jonathan E Rosenberg, Ulka N Vaishampayan, Matthew D Galsky, Evan Y Yu
BACKGROUND: Venous thromboembolism (VTE) is common in cancer patients, but there is limited data on patients with urothelial tract tumors (UTT). We previously identified several associative factors for increased VTE rates in patients with metastatic UTT. In this study, we assessed the frequency, associative factors, and impact on survival of VTE in patients with locoregional UTT. METHODS: Patients with locoregional bladder, upper urinary tract, or urethral cancer were included in this multi-center study from 29 academic institutions...
August 24, 2017: Clinical Genitourinary Cancer
https://www.readbyqxmd.com/read/28918018/locked-nucleic-acid-gapmers-and-conjugates-potently-silence-adam33-an-asthma-associated-metalloprotease-with-nuclear-localized-mrna
#18
Hannah M Pendergraff, Pranathi Meda Krishnamurthy, Alexandre J Debacker, Michael P Moazami, Vivek K Sharma, Liisa Niitsoo, Yong Yu, Yen Nee Tan, Hans Michael Haitchi, Jonathan K Watts
Two mechanisms dominate the clinical pipeline for oligonucleotide-based gene silencing, namely, the antisense approach that recruits RNase H to cleave target RNA and the RNAi approach that recruits the RISC complex to cleave target RNA. Multiple chemical designs can be used to elicit each pathway. We compare the silencing of the asthma susceptibility gene ADAM33 in MRC-5 lung fibroblasts using four classes of gene silencing agents, two that use each mechanism: traditional duplex small interfering RNAs (siRNAs), single-stranded small interfering RNAs (ss-siRNAs), locked nucleic acid (LNA) gapmer antisense oligonucleotides (ASOs), and novel hexadecyloxypropyl conjugates of the ASOs...
September 15, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28905147/evaluation-and-control-of-mirna-like-off-target-repression-for-rna-interference
#19
REVIEW
Heeyoung Seok, Haejeong Lee, Eun-Sook Jang, Sung Wook Chi
RNA interference (RNAi) has been widely adopted to repress specific gene expression and is easily achieved by designing small interfering RNAs (siRNAs) with perfect sequence complementarity to the intended target mRNAs. Although siRNAs direct Argonaute (Ago), a core component of the RNA-induced silencing complex (RISC), to recognize and silence target mRNAs, they also inevitably function as microRNAs (miRNAs) and suppress hundreds of off-targets. Such miRNA-like off-target repression is potentially detrimental, resulting in unwanted toxicity and phenotypes...
September 13, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28877994/cadherin-complexes-recruit-mrnas-and-risc-to-regulate-epithelial-cell-signaling
#20
Antonis Kourtidis, Brian Necela, Wan-Hsin Lin, Ruifeng Lu, Ryan W Feathers, Yan W Asmann, E Aubrey Thompson, Panos Z Anastasiadis
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 cell signaling...
October 2, 2017: Journal of Cell Biology
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