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https://www.readbyqxmd.com/read/29045748/conserved-asymmetry-underpins-homodimerization-of-dicer-associated-double-stranded-rna-binding-proteins
#1
Alex Heyam, Claire E Coupland, Clément Dégut, Ruth A Haley, Nicola J Baxter, Leonhard Jakob, Pedro M Aguiar, Gunter Meister, Michael P Williamson, Dimitris Lagos, Michael J Plevin
Double-stranded RNA-binding domains (dsRBDs) are commonly found in modular proteins that interact with RNA. Two varieties of dsRBD exist: canonical Type A dsRBDs interact with dsRNA, while non-canonical Type B dsRBDs lack RNA-binding residues and instead interact with other proteins. In higher eukaryotes, the microRNA biogenesis enzyme Dicer forms a 1:1 association with a dsRNA-binding protein (dsRBP). Human Dicer associates with HIV TAR RNA-binding protein (TRBP) or protein activator of PKR (PACT), while Drosophila Dicer-1 associates with Loquacious (Loqs)...
October 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29042235/splicing-factors-as-regulators-of-mirna-biogenesis-links-to-human-disease
#2
REVIEW
Madara Ratnadiwakara, Monika Mohenska, Minna-Liisa Anko
MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression post-transcriptionally by fine-tuning mRNA levels and translation during development and in adult tissues. miRNAs are transcribed as parts of longer precursors that undergo multiple processing steps before the mature miRNAs reach their target mRNAs in the cytoplasm. In addition to Drosha/DGCR8 and Dicer that are the essential components of the miRNA processing pathway, a range of other RNA binding proteins have recently been implicated in miRNA biogenesis...
October 14, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/29040648/molecular-basis-for-asymmetry-sensing-of-sirnas-by-the-drosophila-loqs-pd-dcr-2-complex-in-rna-interference
#3
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/29039012/method-for-the-large-scale-identification-of-phasirnas-in-brachypodium-distachyon
#4
Kun Yang, Xiaopeng Wen, Gaurav Sablok
Postranscriptional regulation has been widely shown to be regulated by several classes of small non-coding RNAs; most abundantly, microRNAs, which have been shown to be the first dominant class and has been widely characterized as post-transcriptional regulators. In addition to microRNAs, triggered by miRNAs, transcripts called as PHAS (or TAS) generate abundant class of small RNAs in 21-nt manner, which is a pattern formed by DICER-LIKE 4 (DCL4) processing. Although PHAS can be identified by aligning transcripts to reported PHAS in other species, the most sensitive and accurate way to discovery them is by mapping of the smallRNAs taking into account the transcript coordinates...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29036355/design-and-implementation-of-a-synthetic-pre-mir-switch-for-controlling-mirna-biogenesis-in-mammals
#5
Janina Atanasov, Florian Groher, Julia E Weigand, Beatrix Suess
Synthetic RNA-based systems have increasingly been used for the regulation of eukaryotic gene expression. Due to their structural properties, riboregulators provide a convenient basis for the development of ligand-dependent controllable systems. Here, we demonstrate reversible conditional control of miRNA biogenesis with an aptamer domain as a sensing unit connected to a natural miRNA precursor for the first time. For the design of the pre-miR switch, we replaced the natural terminal loop with the TetR aptamer...
September 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036314/mirnovo-genome-free-prediction-of-micrornas-from-small-rna-sequencing-data-and-single-cells-using-decision-forests
#6
Dimitrios M Vitsios, Elissavet Kentepozidou, Leonor Quintais, Elia Benito-Gutiérrez, Stijn van Dongen, Matthew P Davis, Anton J Enright
The discovery of microRNAs (miRNAs) remains an important problem, particularly given the growth of high-throughput sequencing, cell sorting and single cell biology. While a large number of miRNAs have already been annotated, there may well be large numbers of miRNAs that are expressed in very particular cell types and remain elusive. Sequencing allows us to quickly and accurately identify the expression of known miRNAs from small RNA-Seq data. The biogenesis of miRNAs leads to very specific characteristics observed in their sequences...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29032448/effect-of-single-residue-bulges-on-rna-double-helical-structures-crystallographic-database-analysis-and-molecular-dynamics-simulation-studies
#7
Angana Ray, Ankita Agarwal, Dhananjay Bhattacharyya
Asymmetric bulge loop motifs are widely dispersed in all types of functional RNAs. They are frequently occurring structural motifs in folded RNA structures and appear commonly in pre-microRNA and ribosomes, where they are involved in specific RNA-RNA and RNA-protein interactions. It is therefore necessary to understand such motifs from a structural point of view. We analyzed all available RNA structures and identified quite a few fragments of double helices that contain bulges. We found that these discontinuities often introduce kinks into the double helices, which also affects the stacking overlap between the base pairs across the irregularity...
October 14, 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/29031552/agrp-knockdown-blocks-long-term-appetitive-but-not-consummatory-feeding-behaviors-in-siberian-hamsters
#8
REVIEW
M Alex Thomas, Vy Tran, Vitaly Ryu, Bingzhong Xue, Timothy J Bartness
Arcuate hypothalamus-derived agouti-related protein (AgRP) and neuropeptide Y (NPY) are critical for maintaining energy homeostasis. Fasting markedly upregulates AgRP/NPY expression and circulating ghrelin, and exogenous ghrelin treatment robustly increases acute food foraging and food intake, and chronic food hoarding behaviors in Siberian hamsters. We previously demonstrated that 3rd ventricular AgRP injection robustly stimulates acute and chronic food hoarding, largely independent of food foraging and intake...
October 12, 2017: Physiology & Behavior
https://www.readbyqxmd.com/read/29030844/kinetic-analysis-of-small-silencing-rna-production-by%C3%A2-human-and-drosophila-dicer-enzymes-in-vitro
#9
Susan E Liao, Ryuya Fukunaga
Dicer enzymes produce small silencing RNAs such as microRNAs (miRNAs) and small interfering RNAs (siRNAs), which then are loaded into Argonaute proteins and act as sequence-specific guides. A powerful tool to understand the molecular mechanism of small silencing RNA production by Dicers is an in vitro RNA processing assay using recombinant Dicer proteins. Such biochemical analyses have elucidated the substrate specificities and kinetics of Dicers, the mechanism by which the length of small RNAs produced by Dicers is determined, and the effects of Dicer-partner proteins and endogenous small molecules such as ATP and inorganic phosphate on small RNA production by Dicers, among others...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29021386/suppression-of-microrna-activity-in-kidney-collecting-ducts-induces-partial-loss-of-epithelial-phenotype-and-renal-fibrosis
#10
Sachin Hajarnis, Matanel Yheskel, Darren Williams, Thomas Brefort, Bob Glaudemans, Huguette Debaix, Michel Baum, Olivier Devuyst, Vishal Patel
microRNAs (miRNAs) are sequence-specific inhibitors of post-transcriptional gene expression. The physiologic function of these noncoding RNAs in postnatal renal tubules still remains unclear. Surprisingly, they appear to be dispensable for mammalian proximal tubule (PT) function. Here, we examined the effects of miRNA suppression in collecting ducts (CDs). To conclusively evaluate the role of miRNAs, we generated three mouse models with CD-specific inactivation of key miRNA pathway genes Dicer, Dgcr8, and the entire Argonaute gene family (Ago1, 2, 3, and 4)...
October 11, 2017: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/29016810/mir-30c-5p-regulates-macrophage-mediated-inflammation-and-pro-atherosclerosis-pathways
#11
Giulio Ceolotto, Alessandra Giannella, Mattia Albiero, Maniselvan Kuppusamy, Claudia Radu, Paolo Simioni, Katia Garlaschelli, Andrea Baragetti, Alberico Luigi Catapano, Elisabetta Iori, Gian Paolo Fadini, Angelo Avogaro, Saula Vigili de Kreutzenberg
Aims: Atherosclerosis is an inflammatory disease wherein cholesterol-loaded macrophages play a major role. MicroRNAs and microparticles propagate inflammatory pathways and are involved in cardiovascular disease. We aimed to screen and validate circulating microRNAs correlated with atherosclerosis development in humans, and to dissect the molecular mechanisms associated with atherogenesis using in vitro and in vivo approaches. Methods and results: A panel of 179 secreted microRNAs was screened in plasma samples of patients with and without atherosclerosis, and validated cross-sectionally and prospectively in patients followed for up to 11 years...
August 14, 2017: Cardiovascular Research
https://www.readbyqxmd.com/read/28988987/a-dgcr8-independent-stable-microrna-expression-strategy-reveals-important-functions-of-mir-290-and-mir-183-182-families-in-mouse-embryonic-stem-cells
#12
Xi-Wen Wang, Jing Hao, Wen-Ting Guo, Le-Qi Liao, Si-Yue Huang, Xiangpeng Guo, Xichen Bao, Miguel A Esteban, Yangming Wang
Dgcr8 knockout cells provide a great means to understand the function of microRNAs (miRNAs) in vitro and in vivo. Current strategies to study miRNA function in Dgcr8 knockout cells depend on transient transfection of chemically synthesized miRNA mimics, which is costly and not suitable for long-term study and genetic selection of miRNA function. Here, we developed a cost-effective DGCR8-independent stable miRNA expression (DISME) strategy based on a short hairpin RNA vector that can be precisely processed by DICER...
September 28, 2017: Stem Cell Reports
https://www.readbyqxmd.com/read/28985428/an-rna-editing-dsrna-binding-independent-gene-regulatory-mechanism-of-adars-and-its-clinical-implication-in-cancer
#13
Lihua Qi, Yangyang Song, Tim Hon Man Chan, Henry Yang, Chi Ho Lin, Daryl Jin Tai Tay, HuiQi Hong, Sze Jing Tang, Kar Tong Tan, Xi Xiao Huang, Jaymie Siqi Lin, Vanessa Hui En Ng, Julien Jean Pierre Maury, Daniel G Tenen, Leilei Chen
Adenosine-to-inosine (A-to-I) RNA editing, catalyzed by Adenosine DeAminases acting on double-stranded RNA(dsRNA) (ADAR), occurs predominantly in the 3΄ untranslated regions (3΄UTRs) of spliced mRNA. Here we uncover an unanticipated link between ADARs (ADAR1 and ADAR2) and the expression of target genes undergoing extensive 3΄UTR editing. Using METTL7A (Methyltransferase Like 7A), a novel tumor suppressor gene with multiple editing sites at its 3΄UTR, we demonstrate that its expression could be repressed by ADARs beyond their RNA editing and double-stranded RNA (dsRNA) binding functions...
July 29, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28982684/direct-and-efficient-transfection-of-mouse-neural-stem-cells-and-mature-neurons-by-in-vivo-mrna-electroporation
#14
Stéphane Bugeon, Antoine de Chevigny, Camille Boutin, Natalie Coré, Stefan Wild, Andreas Bosio, Harold Cremer, Christophe Beclin
In vivo brain electroporation of DNA expression vectors is a widely used method for lineage and gene function studies in the developing and postnatal brain. However, transfection efficiency of DNA is limited and adult brain tissue is refractory to electroporation. Here we present a systematic study of mRNA as a vector for acute genetic manipulation in the developing and adult brain. We demonstrate that mRNA electroporation is far more efficient than DNA and leads to faster and more homogeneous protein expression in vivo Importantly, mRNA electroporation allows the manipulation of neural stem cells and postmitotic neurons in the adult brain with minimal invasive procedures...
October 5, 2017: Development
https://www.readbyqxmd.com/read/28981840/the-sirna-suppressor-rtl1-is-redox-regulated-through-glutathionylation-of-a-conserved-cysteine-in-the-double-stranded-rna-binding-domain
#15
Cyril Charbonnel, Adnan K Niazi, Emilie Elvira-Matelot, Elzbieta Nowak, Matthias Zytnicki, Anne de Bures, Edouard Jobet, Alisson Opsomer, Nahid Shamandi, Marcin Nowotny, Christine Carapito, Jean-Philippe Reichheld, Hervé Vaucheret, Julio Sáez-Vásquez
RNase III enzymes cleave double stranded (ds)RNA. This is an essential step for regulating the processing of mRNA, rRNA, snoRNA and other small RNAs, including siRNA and miRNA. Arabidopsis thaliana encodes nine RNase III: four DICER-LIKE (DCL) and five RNASE THREE LIKE (RTL). To better understand the molecular functions of RNase III in plants we developed a biochemical assay using RTL1 as a model. We show that RTL1 does not degrade dsRNA randomly, but recognizes specific duplex sequences to direct accurate cleavage...
September 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28979249/differential-characteristics-of-viral-sirnas-between-leaves-and-roots-of-wheat-plants-naturally-infected-with-wheat-yellow-mosaic-virus-a-soil-borne-virus
#16
Linying Li, Ida Bagus Andika, Yu Xu, Yan Zhang, Xiangqi Xin, Lifeng Hu, Zongtao Sun, Gaojie Hong, Yang Chen, Fei Yan, Jian Yang, Junmin Li, Jianping Chen
RNA silencing is an important innate antiviral defense in plants. Soil-borne plant viruses naturally infect roots via soil-inhabiting vectors, but it is unclear how antiviral RNA silencing responds to virus infection in this particular tissue. In this study, viral small interfering RNA (siRNA) profiles from leaves and roots of wheat plants naturally infected with a soil-borne virus, wheat yellow mosaic virus (WYMV, genus Bymovirus), were analyzed by deep sequencing. WYMV siRNAs were much more abundant in roots than leaves, which was positively correlated with the accumulation of viral RNA...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28978012/dicer-protein-levels-elevated-by-mild-hyperthermia-promote-a-pro-survival-phenotype
#17
Anand S Devasthanam, Thomas B Tomasi
Cellular exposure to mild stress (39.5°C - 41.5°C) induces thermotolerance, rendering cells resistant to a subsequent heat shock (>42°C) insult. We found that mild hyperthermia at 39.5°C leads to elevations in dicer, a protein well-known for its role in microRNA processing and for its role in cellular stress responses. However, whether elevated dicer protein levels play a role in sustaining a thermotolerant phenotype has, to our knowledge, not been reported. Here we demonstrate that elevated dicer protein is linked to a thermotolerant phenotype in the cervical carcinoma cell line HeLa and in murine embryonic fibroblasts (MEF), and demonstrate that dicer plays a role in mediating PKR and eIF2α phosphorylation...
September 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28977573/dicer-independent-processing-of-small-rna-duplexes-mechanistic-insights-and-applications
#18
Elena Herrera-Carrillo, Ben Berkhout
MicroRNAs (miRNAs) play a pivotal role in the regulation of cellular gene expression via the conserved RNA interference (RNAi) mechanism. Biogenesis of the unusual miR-451 does not require Dicer. This molecule is instead processed by the Argonaute 2 (Ago2) enzyme. Similarly, unconventional short hairpin RNA (shRNA) molecules have been designed as miR-451 mimics that rely exclusively on Ago2 for maturation. We will review recent progress made in the understanding of this alternative processing route. Next, we describe different Dicer-independent shRNA designs that have been developed and discuss their therapeutic advantages and disadvantages...
August 31, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28971854/in-vitro-reconstitution-of-chaperone-mediated-human-risc-assembly
#19
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/28964256/a-novel-mechanism-of-lncrna-and-mirna-interaction-ccat2-regulates-mir-145-expression-by-suppressing-its-maturation-process-in-colon-cancer-cells
#20
Yingjie Yu, Pratima Nangia-Makker, Lulu Farhana, Adhip P N Majumdar
BACKGROUND: Although both long and micro RNAs are emerging as important functional components in colorectal cancer (CRC) progression and metastasis, the mechanism of their interaction remains poorly understood. CCAT2 (Colon cancer-associated transcript-2), a long noncoding RNA (lncRNA), has been reported to be over-expressed in CRC and is found to promote tumor growth. miRNAs, a class of naturally occurring short RNAs negatively control the expression of target genes by cleaving mRNA or through translation repression...
September 30, 2017: Molecular Cancer
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