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https://www.readbyqxmd.com/read/28331089/diversity-distribution-and-evolution-of-tomato-viruses-in-china-uncovered-by-small-rna-sequencing
#1
Chenxi Xu, Xuepeng Sun, Angela Taylor, Chen Jiao, Yimin Xu, Xiaofeng Cai, Xiaoli Wang, Chenhui Ge, Guanghui Pan, Quanxi Wang, Zhangjun Fei, Quanhua Wang
Tomato is a major vegetable crop that has tremendous popularity. However, viral disease is still a major factor limiting tomato production. Here we report the tomato virome identified through sequencing small RNAs of 170 field-grown samples collected in China. A total of 22 viruses were identified including both well-documented and newly detected viruses. The tomato viral community is dominated by a few species, and they exhibit polymorphisms and recombination in the genomes with coldspots and hotspots. Most samples were co-infected by multiple viruses and the majority of identified viruses are positive-sense single-stranded RNA viruses...
March 22, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28325872/small-rna-mediated-repair-of-uv-induced-dna-lesions-by-the-dna-damage-binding-protein-2-and-argonaute-1
#2
Catherine Schalk, Valérie Cognat, Stéfanie Graindorge, Timothée Vincent, Olivier Voinnet, Jean Molinier
As photosynthetic organisms, plants need to prevent irreversible UV-induced DNA lesions. Through an unbiased, genome-wide approach, we have uncovered a previously unrecognized interplay between Global Genome Repair and small interfering RNAs (siRNAs) in the recognition of DNA photoproducts, prevalently in intergenic regions. Genetic and biochemical approaches indicate that, upon UV irradiation, the DNA DAMAGE-BINDING PROTEIN 2 (DDB2) and ARGONAUTE 1 (AGO1) of Arabidopsis thaliana form a chromatin-bound complex together with 21-nt siRNAs, which likely facilitates recognition of DNA damages in an RNA/DNA complementary strand-specific manner...
March 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28319084/structural-and-mechanistic-insights-into-an-archaeal-dna-guided-argonaute-protein
#3
Sarah Willkomm, Christine A Oellig, Adrian Zander, Tobias Restle, Ronan Keegan, Dina Grohmann, Sabine Schneider
Argonaute (Ago) proteins in eukaryotes are known as key players in post-transcriptional gene silencing(1), while recent studies on prokaryotic Agos hint at their role in the protection against invading DNA(2,3). Here, we present crystal structures of the apo enzyme and a binary Ago-guide complex of the archaeal Methanocaldococcus jannaschii (Mj) Ago. Binding of a guide DNA leads to large structural rearrangements. This includes the structural transformation of a hinge region containing a switch helix, which has been shown for human Ago2 to be critical for the dynamic target search process(4-6)...
March 20, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28270624/abscisic-acid-induces-resistance-against-bamboo-mosaic-virus-through-argonaute-2-and-3
#4
Mazen Alazem, Meng-Hsun He, Peter Moffett, Na-Sheng Lin
Plant resistance to pathogens is tuned by defense-related hormones. Of which, ABA is well documented to moderate resistance against fungi and bacteria. However, ABA's contribution to resistance against viruses is pleiotropic. ABA affects callose deposition at plasmodesmata (therefore hindering the viral cell-to-cell movement), but here we show that when callose synthase is downregulated, ABA still induces resistance against Bamboo mosaic virus (BaMV) infection. By examining the potential connections between the ABA and RNA silencing pathway in Arabidopsis, we showed that ABA regulates the expression of almost the whole Argonaute (AGO) gene family, of which some are required for plant resistance against BaMV...
March 7, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28239561/regulation-of-cardiac-cacnb2-by-microrna-499-potential-role-in-atrial-fibrillation
#5
Tian-You Ling, Xiao-Li Wang, Qiang Chai, Tong Lu, John M Stulak, Lyle D Joyce, Richard C Daly, Kevin L Greason, Li-Qun Wu, Win-Kuang Shen, Yong-Mei Cha, Hon-Chi Lee
The L-type calcium channel (LTCC) is one of the major ion channels that are known to be associated with the electrical remodeling of atrial fibrillation (AF). In AF, there is significant downregulation of the LTCC, but the underlying mechanism for such downregulation is not clear. We have previously reported that microRNA-499 (miR-499) is significantly upregulated in patients with permanent AF and that KCNN3, the gene that encodes the small-conductance calcium-activated potassium channel 3 (SK3), is a target of miR-499...
June 2017: BBA Clinical
https://www.readbyqxmd.com/read/28130299/identification-and-functional-analysis-of-dicer-and-argonaute-genes-involved-in-rna-interference-in-the-entomopathogenic-fungus-metarhizium-robertsii
#6
Huimin Meng, Zhangxun Wang, Yulong Wang, Hong Zhu, Bo Huang
RNA interference (RNAi) is a gene silencing mechanism that plays an important role in gene regulation in a number of eukaryotic organisms. Two core components, Dicer and Argonaute, are central in the RNAi machinery. However, the physiological roles of Dicer and Argonaute in the entomopathogenic fungus Metarhizium robertsii remained unclear. Here, the roles of genes encoding Dicers (Mrdcl1 and Mrdcl2) and Argonautes (Mrago1 and Mrago2) in M.robertsii were investigated. The results showed that the Dicer protein MrDCL2 and Argonaute protein MrAGO1 are the major components of the RNAi process occurring in M...
January 27, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27928938/sequence-and-structure-based-analysis-of-proteins-involved-in-mirna-biogenesis
#7
Chhaya Sharma, Debasisa Mohanty
miRNA biogenesis is a multistage process for the generation of a mature miRNA and involves several different proteins. In this work, we have carried out both sequence- and 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 that are determinants of their function. Our analysis reveals that in animals the miRNA biogenesis pathway first originated in molluscs...
January 4, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/27918527/induction-and-suppression-of-antiviral-rna-interference-by-influenza-a-virus-in-mammalian-cells
#8
Yang Li, Megha Basavappa, Jinfeng Lu, Shuwei Dong, D Alexander Cronkite, John T Prior, Hans-Christian Reinecker, Paul Hertzog, Yanhong Han, Wan-Xiang Li, Sihem Cheloufi, Fedor V Karginov, Shou-Wei Ding, Kate L Jeffrey
Influenza A virus (IAV) causes annual epidemics and occasional pandemics, and is one of the best-characterized human RNA viral pathogens(1). However, a physiologically relevant role for the RNA interference (RNAi) suppressor activity of the IAV non-structural protein 1 (NS1), reported over a decade ago(2), remains unknown(3). Plant and insect viruses have evolved diverse virulence proteins to suppress RNAi as their hosts produce virus-derived small interfering RNAs (siRNAs) that direct specific antiviral defence(4-7) by an RNAi mechanism dependent on the slicing activity of Argonaute proteins (AGOs)(8,9)...
December 5, 2016: Nature Microbiology
https://www.readbyqxmd.com/read/27893851/expression-and-regulation-of-piwil-proteins-and-piwi-interacting-rnas-in-rheumatoid-arthritis
#9
Lenka Pleštilová, Michel Neidhart, Giancarlo Russo, Mojca Frank-Bertoncelj, Caroline Ospelt, Adrian Ciurea, Christoph Kolling, Renate E Gay, Beat A Michel, Jiří Vencovský, Steffen Gay, Astrid Jüngel
OBJECTIVE: The PIWIL (P-element induced wimpy testis like protein) subfamily of argonaute proteins is essential for Piwi-interacting RNA (piRNA) biogenesis and their function to silence transposons during germ-line development. Here we explored their presence and regulation in rheumatoid arthritis (RA). METHODS: The expression of PIWIL genes in RA and osteoarthritis (OA) synovial tissues and synovial fibroblasts (SF) was analysed by Real-time PCR, immunofluorescence and Western blot...
2016: PloS One
https://www.readbyqxmd.com/read/27871067/the-lncrna-snhg5-mir-32-axis-regulates-gastric-cancer-cell-proliferation-and-migration-by-targeting-klf4
#10
Lianmei Zhao, Taotao Han, Yanshuang Li, Jiazeng Sun, Shang Zhang, Yanxin Liu, Baoen Shan, Dexian Zheng, Juan Shi
Long noncoding RNAs (lncRNAs) are emerging as important regulators in cellular processes, including the development, proliferation, and migration of cancer cells. We have demonstrated in a prior study that small nucleolar RNA host gene 5 (SNHG5) is dysregulated in gastric cancer (GC). To further explore the underlying mechanisms of SNGH5 function in the development of GC, in this study, we screened the microRNAs interacting with SNHG5 and elucidated their roles in GC. We showed that SNHG5 contains a putative miR-32-binding site and that deletion of this site abolishes the responsiveness to miR-32...
November 21, 2016: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/27813706/global-genome-repair-factors-controls-dna-methylation-patterns-in-arabidopsis
#11
Catherine Schalk, Jean Molinier
As obligate photosynthetic organisms plants are particularly exposed to the damaging effects of excess light and ultraviolet wavelengths, which can impact genome and epigenome dynamics by inducing DNA sequence and chromatin alterations. DNA DAMAGE-BINDING PROTEIN 2 (DDB2) is the main factor involved in the recognition of UV-induced DNA lesions during Global Genome Repair (GGR) in mammals and in plants. (1) In a recent study we reported that, in Arabidopsis, loss of DDB2 function alters DNA methylation patterns at many repeat loci and protein coding genes...
December 2016: Plant Signaling & Behavior
https://www.readbyqxmd.com/read/27716257/characterization-of-virus-derived-small-interfering-rnas-in-apple-stem-grooving-virus-infected-in-vitro-cultured-pyrus-pyrifolia-shoot-tips-in-response-to-high-temperature-treatment
#12
Juan Liu, XueJiao Zhang, YueKun Yang, Ni Hong, GuoPing Wang, Aiming Wang, LiPing Wang
BACKGROUND: Heat treatment (known as thermotherapy) together with in vitro culture of shoot meristem tips is a commonly used technology to obtain virus-free germplasm for the effective control of virus diseases in fruit trees. RNA silencing as an antiviral defense mechanism has been implicated in this process. To understand if high temperature-mediated acceleration of the host antiviral gene silencing system in the meristem tip facilitates virus-derived small interfering RNAs (vsiRNA) accumulation to reduce the viral RNA titer in the fruit tree meristem tip cells, we used the Apple stem grooving virus (ASGV)-Pyrus pyrifolia pathosystem to explore the possible roles of vsiRNA in thermotherapy...
October 6, 2016: Virology Journal
https://www.readbyqxmd.com/read/27693359/crystal-structure-of-silkworm-piwi-clade-argonaute-siwi-bound-to-pirna
#13
Naoki Matsumoto, Hiroshi Nishimasu, Kazuhiro Sakakibara, Kazumichi M Nishida, Takamasa Hirano, Ryuichiro Ishitani, Haruhiko Siomi, Mikiko C Siomi, Osamu Nureki
PIWI-clade Argonaute proteins associate with PIWI-interacting RNAs (piRNAs) and silence transposable elements in animal gonads. Here, we report the crystal structure of a silkworm PIWI-clade Argonaute, Siwi, bound to the endogenous piRNA, at 2.4 Å resolution. Siwi adopts a bilobed architecture consisting of N-PAZ and MID-PIWI lobes, in which the 5' and 3' ends of the bound piRNA are anchored by the MID-PIWI and PAZ domains, respectively. A structural comparison of Siwi with AGO-clade Argonautes reveals notable differences in their nucleic-acid-binding channels, likely reflecting the distinct lengths of their guide RNAs and their mechanistic differences in guide RNA loading and cleavage product release...
October 6, 2016: Cell
https://www.readbyqxmd.com/read/27685626/mirna-558-promotes-gastric-cancer-progression-through-attenuating-smad4-mediated-repression-of-heparanase-expression
#14
Liduan Zheng, Wanju Jiao, Huajie Song, Hongxia Qu, Dan Li, Hong Mei, Yajun Chen, Feng Yang, Huanhuan Li, Kai Huang, Qiangsong Tong
Previous studies have indicated that as the only mammalian endo-β-D-glucuronidase, heparanase (HPSE) is up-regulated and associated with poor prognosis in gastric cancer, while the underlying mechanisms still remain to be determined. Herein, through integrative analysis of public datasets, we found microRNA-558 (miR-558) and SMAD family member 4 (Smad4) as the crucial transcription regulators of HPSE expression in gastric cancer, with their adjacent target sites within the promoter of HPSE. We identified that endogenous miR-558 activated the transcription and expression of HPSE in gastric cancer cell lines...
2016: Cell Death & Disease
https://www.readbyqxmd.com/read/27650800/the-effect-of-renal-dysfunction-and-haemodialysis-on-circulating-liver-specific-mir-122
#15
Laura Rivoli, A D Bastiaan Vliegenthart, Carmelita M J de Potter, Job J M H van Bragt, Nikolaos Tzoumas, Peter Gallacher, Tariq E Farrah, Neeraj Dhaun, James W Dear
AIMS: microRNA-122 (miR-122) is a hepatotoxicity biomarker with utility in the management of paracetamol overdose and in drug development. Renal dysfunction and haemodialysis have been associated with a reduction in circulating microRNA. The objective of this study was to determine their effect on miR-122. METHODS: Blood samples were collected from 17 patients with end-stage renal disease (ESRD) on haemodialysis, 22 healthy controls, 30 patients with chronic kidney disease (CKD) and 15 patients post-kidney transplantation...
March 2017: British Journal of Clinical Pharmacology
https://www.readbyqxmd.com/read/27531226/dna-damage-binding-protein-2-ddb2-shapes-the-dna-methylation-landscape
#16
Catherine Schalk, Stephanie Drevensek, Amira Kramdi, Mohamed Kassam, Ikhlak Ahmed, Valerie Cognat, Stefanie Graindorge, Marc Bergdoll, Nicolas Baumberger, Dimitri Heintz, Chris Bowler, Pascal Genschik, Fredy Barneche, Vincent Colot, Jean Molinier
In eukaryotes, DNA repair pathways help to maintain genome integrity and epigenomic patterns. However, the factors at the nexus of DNA repair and chromatin modification/remodeling remain poorly characterized. Here, we uncover a previously unrecognized interplay between the DNA repair factor DNA DAMAGE-BINDING PROTEIN 2 (DDB2) and the DNA methylation machinery in Arabidopsis thaliana. Loss-of-function mutation in DDB2 leads to genome-wide DNA methylation alterations. Genetic and biochemical evidence indicate that at many repeat loci, DDB2 influences de novo DNA methylation by interacting with ARGONAUTE 4 (AGO4) and by controlling the local abundance of 24-nt short interfering RNAs (siRNAs)...
August 16, 2016: Plant Cell
https://www.readbyqxmd.com/read/27510362/an-agrobacterium-delivered-crispr-cas9-system-for-high-frequency-targeted-mutagenesis-in-maize
#17
Si Nian Char, Anjanasree K Neelakandan, Hartinio Nahampun, Bronwyn Frame, Marcy Main, Martin H Spalding, Philip W Becraft, Blake C Meyers, Virginia Walbot, Kan Wang, Bing Yang
CRISPR/Cas9 is a powerful genome editing tool in many organisms, including a number of monocots and dicots. Although the design and application of CRISPR/Cas9 is simpler compared to other nuclease-based genome editing tools, optimization requires the consideration of the DNA delivery and tissue regeneration methods for a particular species to achieve accuracy and efficiency. Here, we describe a public sector system, ISU Maize CRISPR, utilizing Agrobacterium-delivered CRISPR/Cas9 for high-frequency targeted mutagenesis in maize...
February 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/27412786/an-mirna-mediated-therapy-for-sca6-blocks-ires-driven-translation-of-the-cacna1a-second-cistron
#18
Yu Miyazaki, Xiaofei Du, Shin-Ichi Muramatsu, Christopher M Gomez
Spinocerebellar ataxia type 6 (SCA6) is a dominantly inherited neurodegenerative disease characterized by slowly progressive ataxia and Purkinje cell degeneration. SCA6 is caused by a polyglutamine repeat expansion within a second CACNA1A gene product, α1ACT. α1ACT expression is under the control of an internal ribosomal entry site (IRES) present within the CACNA1A coding region. Whereas SCA6 allele knock-in mice show indistinguishable phenotypes from wild-type littermates, expression of SCA6-associated α1ACT (α1ACTSCA6) driven by a Purkinje cell-specific promoter in mice produces slowly progressive ataxia and cerebellar atrophy...
July 13, 2016: Science Translational Medicine
https://www.readbyqxmd.com/read/27399870/terminal-duplex-stability-and-nucleotide-identity-differentially-control-sirna-loading-and-activity-in-rna-interference
#19
Phillip A Angart, Rebecca J Carlson, Kwasi Adu-Berchie, S Patrick Walton
Efficient short interfering RNA (siRNA)-mediated gene silencing requires selection of a sequence that is complementary to the intended target and possesses sequence and structural features that encourage favorable functional interactions with the RNA interference (RNAi) pathway proteins. In this study, we investigated how terminal sequence and structural characteristics of siRNAs contribute to siRNA strand loading and silencing activity and how these characteristics ultimately result in a functionally asymmetric duplex in cultured HeLa cells...
October 2016: Nucleic Acid Therapeutics
https://www.readbyqxmd.com/read/27387838/structure-guided-control-of-sirna-off-target-effects
#20
Scott R Suter, Jessica Sheu-Gruttadauria, Nicole T Schirle, Rachel Valenzuela, Alexi A Ball-Jones, Kazumitsu Onizuka, Ian J MacRae, Peter A Beal
Short interfering RNAs (siRNAs) are promising therapeutics that make use of the RNA interference (RNAi) pathway, but liabilities arising from the native RNA structure necessitate chemical modification for drug development. Advances in the structural characterization of components of the human RNAi pathway have enabled structure-guided optimization of siRNA properties. Here we report the 2.3 Å resolution crystal structure of human Argonaute 2 (hAgo2), a key nuclease in the RNAi pathway, bound to an siRNA guide strand bearing an unnatural triazolyl nucleotide at position 1 (g1)...
July 20, 2016: Journal of the American Chemical Society
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