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Chantal Brosseau, Mohamed El Oirdi, Ayooluwa Adurogbangba, Xiaofang Ma, Peter Moffett
In plants, RNA silencing regulates gene expression through the action of Dicer-like (DCL) and Argonaute (AGO) proteins via micro RNAs and RNA-dependent DNA methylation (RdDM). In addition, RNA silencing functions as an anti-viral defense mechanism by targeting virus-derived double stranded RNA. Plants encode multiple AGO proteins with specialized functions, including AGO4-like proteins, which effect RdDM and AGO2, AGO5 and AGO1, which have antiviral activities. We show here that AGO4 is also required for defense against Plantago asiatica mosaic potexvirus (PlAMV), most likely independent of RdDM components such as DCL3, Pol IV and Pol V...
October 20, 2016: Molecular Plant-microbe Interactions: MPMI
Zhen-Hua Chen, Wen-Tao Wang, Wei Huang, Ke Fang, Yu-Meng Sun, Shu-Rong Liu, Xue-Qun Luo, Yue-Qin Chen
Increasing evidence has indicated that long noncoding RNAs (lncRNAs) are of great importance in different cell contexts. However, only a very small number of lncRNAs have been experimentally validated and functionally annotated during human hematopoiesis. Here, we report an lncRNA, HOTAIRM1, which is associated with myeloid differentiation and has pivotal roles in the degradation of oncoprotein PML-RARA and in myeloid cell differentiation by regulating autophagy pathways. We first revealed that HOTAIRM1 has different variants that are expressed at different levels in cells and that the expression pattern of HOTAIRM1 is closely related to that of the PML-RARA oncoprotein in acute promyelocytic leukemia (APL) patients...
October 14, 2016: Cell Death and Differentiation
Pierre-Yves Mantel, Daisy Hjelmqvist, Michael Walch, Solange Kharoubi-Hess, Sandra Nilsson, Deepali Ravel, Marina Ribeiro, Christof Grüring, Siyuan Ma, Prasad Padmanabhan, Alexander Trachtenberg, Johan Ankarklev, Nicolas M Brancucci, Curtis Huttenhower, Manoj T Duraisingh, Ionita Ghiran, Winston P Kuo, Luis Filgueira, Roberta Martinelli, Matthias Marti
Malaria remains one of the greatest public health challenges worldwide, particularly in sub-Saharan Africa. The clinical outcome of individuals infected with Plasmodium falciparum parasites depends on many factors including host systemic inflammatory responses, parasite sequestration in tissues and vascular dysfunction. Production of pro-inflammatory cytokines and chemokines promotes endothelial activation as well as recruitment and infiltration of inflammatory cells, which in turn triggers further endothelial cell activation and parasite sequestration...
October 10, 2016: Nature Communications
Levente Kontra, Tibor Csorba, Mario Tavazza, Alessandra Lucioli, Raffaela Tavazza, Simon Moxon, Viktória Tisza, Anna Medzihradszky, Massimo Turina, József Burgyán
RNA silencing is one of the main defense mechanisms employed by plants to fight viruses. In change, viruses have evolved silencing suppressor proteins to neutralize antiviral silencing. Since the endogenous and antiviral functions of RNA silencing pathway rely on common components, it was suggested that viral suppressors interfere with endogenous silencing pathway contributing to viral symptom development. In this work, we aimed to understand the effects of the tombusviral p19 suppressor on endogenous and antiviral silencing during genuine virus infection...
October 2016: PLoS Pathogens
Mengmeng Deng, Junwei Hou, Jun Hu, Shuo Wang, Mi Chen, Lizhao Chen, Ying Ju, Changfei Li, Songdong Meng
Hepatitis B virus (HBV) infection induces hepatocarcinogenesis and malignant progression, yet global effects of the redundant viral mRNAs produced during infection are unexplored. Here, microRNA (miRNA) target prediction and whole genome expression analysis revealed that HBV pre-C/C mRNA leads to upregulation of multiple let-7a targeted genes. A let-7a complementary region from nt 86 to 108 in the HBV genome was then identified in HBV pre-C/C, pre-S, and S mRNAs. The let-7a sequestration effect by HBV mRNAs was observed under transfection and virus infection, which is dependent on the let-7a response sequence...
September 29, 2016: Cancer Letters
Gesche K Gerresheim, Nadia Dünnes, Anika Nieder-Röhrmann, Lyudmila A Shalamova, Markus Fricke, Ivo Hofacker, Christian Höner Zu Siederdissen, Manja Marz, Michael Niepmann
We have analyzed the binding of the liver-specific microRNA-122 (miR-122) to three conserved target sites of hepatitis C virus (HCV) RNA, two in the non-structural protein 5B (NS5B) coding region and one in the 3' untranslated region (3'UTR). miR-122 binding efficiency strongly depends on target site accessibility under conditions when the range of flanking sequences available for the formation of local RNA secondary structures changes. Our results indicate that the particular sequence feature that contributes most to the correlation between target site accessibility and binding strength varies between different target sites...
September 27, 2016: Cellular and Molecular Life Sciences: CMLS
Chris Wang, Pratyush Gupta, Lucile Fressigne, Gabriel D Bossé, Xin Wang, Martin J Simard, Dave Hansen
MiRNAs post-transcriptionally regulate gene expression by recruiting the miRNA-induced silencing complex (miRISC) to target mRNAs. However, the mechanisms by which miRISC components are maintained at appropriate levels for proper function are largely unknown. Here, we demonstrate that Caenorhabditis elegans TEG-1 regulates the stability of two miRISC effectors, VIG-1 and ALG-1, which in turn affects the abundance of miRNAs in various families. We demonstrate that TEG-1 physically interacts with VIG-1, and complexes with mature let-7 miRNA...
September 19, 2016: Nucleic Acids Research
Vladimir S Trubetskoy, Jacob B Griffin, Anthony L Nicholas, Eric M Nord, Zhao Xu, Ryan M Peterson, Christine I Wooddell, David B Rozema, Darren H Wakefield, David L Lewis, Steven B Kanner
The RNA interference (RNAi)-based therapeutic ARC-520 for chronic hepatitis B virus (HBV) infection consists of a melittin-derived peptide conjugated to N-acetylgalactosamine for hepatocyte targeting and endosomal escape, and cholesterol-conjugated RNAi triggers, which together result in HBV gene silencing. To characterize the kinetics of RNAi trigger delivery and 5'-phosphorylation of guide strands correlating with gene knockdown, we employed a peptide-nucleic acid (PNA) hybridization assay. A fluorescent sense strand PNA probe binding to RNAi duplex guide strands was coupled with anion exchange high performance liquid chromatography to quantitate guide strands and metabolites...
September 19, 2016: Nucleic Acids Research
Daniel Rodríguez-Leal, Amanda Castillo-Cobián, Isaac Rodríguez-Arévalo, Jean-Philippe Vielle-Calzada
Small RNA (sRNA)-mediated gene silencing represents a conserved regulatory mechanism controlling a wide diversity of developmental processes through interactions of sRNAs with proteins of the ARGONAUTE (AGO) family. On the basis of a large phylogenetic analysis that includes 206 AGO genes belonging to 23 plant species, AGO genes group into four clades corresponding to the phylogenetic distribution proposed for the ten family members of Arabidopsis thaliana. A primary analysis of the corresponding protein sequences resulted in 50 sequences of amino acids (blocks) conserved across their linear length...
2016: Frontiers in Plant Science
Delphine Carouge, Valerie Blanc, Sue E Knoblaugh, Robert J Hunter, Nicholas O Davidson, Joseph H Nadeau
Testicular tumors, the most common cancer in young men, arise from abnormalities in germ cells during fetal development. Unconventional inheritance for testicular germ cell tumor (TGCT) risk both in humans and mice implicates epigenetic mechanisms. Apolipoprotein B mRNA-editing enzyme complex 1 (APOBEC1) cytidine deaminase and Deadend-1, which are involved in C-to-U RNA editing and microRNA-dependent mRNA silencing, respectively, are potent epigenetic modifiers of TGCT susceptibility in the genetically predisposed 129/Sv inbred mouse strain...
September 13, 2016: Proceedings of the National Academy of Sciences of the United States of America
Jui-Hung Hung, Zhiping Weng
This protocol illustrates the steps of searching a sequence database with BLAST, which in essence performs pairwise alignment between the query sequence and each target sequence in the database. Steps for performing multiple sequence alignments with ClustalW are then described. Argonaute 2 (Ago2) is an essential component for small interfering RNA (siRNA)-directed RNA interference (RNAi) in fruit flies. This protocol uses Ago2 to demonstrate how to search for all Ago2 paralogs in the fly proteome using BLAST and to obtain a multiple sequence alignment of these sequences with ClustalW...
August 29, 2016: Cold Spring Harbor Protocols
Chunxia Du, Ziyang Shen, Rujin Zang, Hua Xie, Hongxing Li, Pingfa Chen, Bo Hang, Xiaoqun Xu, Weibing Tang, Yankai Xia
Hirschsprung disease (HSCR) is a genetic disorder of neural crest development. It is also believed that epigenetic changes plays a role in the progression of this disease. Here we show that the MIR143 host gene (MIR143HG), the precursor of miR-143 and miR-145, decreased cell proliferation and migration and forms a negative feedback loop with RBM24 in HSCR. As RBM24 mRNA is a target of miR-143, upregulation of RBM24 upon an increase in the level of MIR143HG could be attributed to sequestration of miR-143 by MIR143HG (sponge effect)...
August 23, 2016: Biochimica et Biophysica Acta
Huaping Li, Xiaorong Zhang, Feng Wang, Ling Zhou, Zhongwei Yin, Jiahui Fan, Xiang Nie, Peihua Wang, Xiang-Dong Fu, Chen Chen, Dao Wen Wang
BACKGROUND: Excessive reactive oxygen species generated in mitochondria has been implicated as a causal event in hypertensive cardiomyopathy. Multiple recent studies suggest that microRNAs (miRNAs) are able to translocate to mitochondria to modulate mitochondrial activities, but the medical significance of such a new miRNA function has remained unclear. Here, we characterized spontaneous hypertensive rats (SHRs) in comparison with Wistar rats, finding that micro RNA-21 (miR-21) was dramatically induced in SHRs relative to Wistar rats...
September 6, 2016: Circulation
Samuel H Lewis, Claire L Webster, Heli Salmela, Darren J Obbard
Argonaute2 (Ago2) is a rapidly evolving nuclease in the Drosophila melanogaster RNA interference (RNAi) pathway that targets viruses and transposable elements in somatic tissues. Here we reconstruct the history of Ago2 duplications across the D. obscura group and use patterns of gene expression to infer new functional specialization. We show that some duplications are old, shared by the entire species group, and that losses may be common, including previously undetected losses in the lineage leading to D. pseudoobscura We find that while the original (syntenic) gene copy has generally retained the ancestral ubiquitous expression pattern, most of the novel Ago2 paralogs have independently specialized to testis-specific expression...
October 2016: Genetics
Daniel Völler, Lisa Linck, Astrid Bruckmann, Judith Hauptmann, Rainer Deutzmann, Gunter Meister, Anja Katrin Bosserhoff
The members of the Argonaute (AGO) protein family are key players in miRNA-guided gene silencing. They enable the interaction between small RNAs and their respective target mRNA(s) and support the catalytic destruction of the gene transcript or recruit additional proteins for downstream gene silencing. The human AGO family consists of four AGO proteins (AGO1-AGO4), but only AGO2 harbors nuclease activity. In this study, we characterized the expression of the four AGO proteins in cancer cell lines and normal tissues with a new mass spectrometry approach called AGO-APP (AGO Affinity Purification by Peptides)...
2016: PloS One
Noor Faizah Che Harun, Hiroyasu Takemoto, Takahiro Nomoto, Keishiro Tomoda, Makoto Matsui, Nobuhiro Nishiyama
A new strategy for controlling gene silencing activity of siRNA in the cell was developed in the present study. siRNA was linearly conjugated with PNIPAAm, where coil-globule transition of the conjugated PNIPAAm allows thermoresponsive exposure of the vicinal siRNA molecule; a coil form of PNIPAAm (T < LCST) inhibits siRNA interaction with gene silencing-related proteins due to the steric hindrance effect, while a globule form of PNIPAAm (T > LCST) allows a ready access of siRNA to gene silencing pathway...
September 21, 2016: Bioconjugate Chemistry
Z Nikolić, D Savić Pavićević, N Vučić, S Cerović, V Vukotić, G Brajušković
PURPOSE: The purpose of this study is to evaluate the potential association between genetic variants in genes encoding the components of RNA-induced silencing complex and prostate cancer (PCa) risk. Genetic variants chosen for this study are rs3742330 in DICER1, rs4961280 in AGO2, rs784567 in TARBP2, rs7813 in GEMIN4 and rs197414 in GEMIN3. METHODS: The study involved 355 PCa patients, 360 patients with benign prostatic hyperplasia and 318 healthy controls. For individuals diagnosed with PCa, clinicopathological characteristics including serum prostate-specific antigen level at diagnosis, Gleason score (GS) and clinical stage were determined...
August 6, 2016: World Journal of Urology
Gerald J Prud'homme, Yelena Glinka, Zsuzsanna Lichner, George M Yousef
Extracellular miRNAs are increasingly studied as markers for specific diseases. They are released in biological fluids in a remarkably stable form, and may play a role in intercellular communication. They are thought to be protected against degradation by either encapsulation within microparticles, or by binding to proteins (mostly AGO2). The particulate forms may be internalized by endocytosis or membrane fusion, but the protein-bound forms require a receptor mechanism for their uptake. A major question is whether there are natural cell-membrane receptors that capture and internalize protein-bound functional miRNAs...
July 29, 2016: Oncotarget
A Turchinovich, H M Surowy, A G Tonevitsky, B Burwinkel
Despite a high sequence homology among four human RNAi-effectors Argonaute proteins and their coding sequences, the efficiency of ectopic overexpression of AGO3 and AGO4 coding sequences in human cells is greatly reduced as compared to AGO1 and AGO2. While investigating this phenomenon, we documented the existence of previously uncharacterized mechanism of gene expression regulation, which is manifested in greatly varying basal transcription levels from the RNApolII promoters depending on the promoter-proximal downstream sequences...
2016: Scientific Reports
Patrick Connerty, Sarah Bajan, Judit Remenyi, Frances V Fuller-Pace, Gyorgy Hutvagner
MicroRNAs (miRNAs) are short (21-23nt long) RNAs that post-transcriptionally regulate gene expression in plants and animals. They are key regulators in all biological processes. In mammalian cells miRNAs are loaded into one of the four members of the Argonaute (Ago) protein family to form the RNA-induced silencing complex (RISC). RISCs inhibit the translation of mRNAs that share sequence complementarity with their loaded miRNAs. miRNA processing and miRNA-mediated gene regulation are highly regulated processes and involve many RNA-binding proteins as auxiliary factors...
October 2016: Biochimica et Biophysica Acta
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