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https://www.readbyqxmd.com/read/28781168/rna-docking-and-local-translation-regulate-site-specific-axon-remodeling-in%C3%A2-vivo
#1
Hovy Ho-Wai Wong, Julie Qiaojin Lin, Florian Ströhl, Cláudio Gouveia Roque, Jean-Michel Cioni, Roberta Cagnetta, Benita Turner-Bridger, Romain F Laine, William A Harris, Clemens F Kaminski, Christine E Holt
Nascent proteins can be positioned rapidly at precise subcellular locations by local protein synthesis (LPS) to facilitate localized growth responses. Axon arbor architecture, a major determinant of synaptic connectivity, is shaped by localized growth responses, but it is unknown whether LPS influences these responses in vivo. Using high-resolution live imaging, we examined the spatiotemporal dynamics of RNA and LPS in retinal axons during arborization in vivo. Endogenous RNA tracking reveals that RNA granules dock at sites of branch emergence and invade stabilized branches...
August 2, 2017: Neuron
https://www.readbyqxmd.com/read/28780716/epigenetics-a-potential-key-mechanism-involved-in-the-pathogenesis-of-cardiorenal-syndromes
#2
REVIEW
Grazia Maria Virzì, Anna Clementi, Alessandra Brocca, Massimo de Cal, Claudio Ronco
Epigenetics is defined as the heritable changes in gene expression patterns which are not directly encoded by modifications in the nucleotide DNA sequence of the genome, including higher order chromatin organization, DNA methylation, cytosine modifications, covalent histone tail modifications, and short non-coding RNA molecules. Recently, much attention has been paid to the role and the function of epigenetics and epimutations in the cellular and subcellular pathways and in the regulation of genes in the setting of both kidney and cardiovascular disease...
August 5, 2017: Journal of Nephrology
https://www.readbyqxmd.com/read/28766296/methods-for-extraction-of-rna-proteins-or-protein-complexes-from-subcellular-compartments-of-eukaryotic-cells
#3
Kyu-Hyeon Yeom, Andrey Damianov
Eukaryotic organelles or subcellular compartments can be selectively isolated based on their physical density and their stability in the presence of nonionic detergents. This chapter describes a protocol for the preparation of cytoplasm, nucleoplasm, and chromatin, in addition to isolation of RNA and proteins from these fractions. Proteins and protein complexes stably associated with chromatin and other high molecular weight nuclear components can be extracted under non-denaturing conditions by enzymatic digestion of RNA and DNA...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28763035/a-motif-in-the-f-homomorph-of-rabbit-haemorrhagic-disease-virus-polymerase-is-important-for-the-subcellular-localisation-of-the-protein-and-its-ability-to-induce-redistribution-of-golgi-membranes
#4
Nadya Urakova, Andrew C Warden, Peter A White, Tanja Strive, Michael Frese
Rabbit haemorrhagic disease virus (RHDV) is a calicivirus that infects and frequently kills rabbits. Previously, we showed that the RHDV RNA-dependent RNA polymerase (RdRp) is associated with distinct, but yet uncharacterised subcellular structures and is capable of inducing a redistribution of Golgi membranes. In this study, we identified a partially hidden hydrophobic motif that determines the subcellular localisation of recombinant RHDV RdRp in transfected cells. This novel motif, 189LLWGCDVGVAVCAAAVFHNICY210, is located within the F homomorph, between the conserved F3 and A motifs of the core RdRp domain...
August 1, 2017: Viruses
https://www.readbyqxmd.com/read/28761359/nuclear-ddx3-expression-predicts-poor-outcome-in-colorectal-and-breast-cancer
#5
Marise R Heerma van Voss, Farhad Vesuna, Guus M Bol, Jan Meeldijk, Ana Raman, G Johan Offerhaus, Horst Buerger, Arvind H Patel, Elsken van der Wall, Paul J van Diest, Venu Raman
PURPOSE: DEAD box protein 3 (DDX3) is an RNA helicase with oncogenic properties that shuttles between the cytoplasm and nucleus. The majority of DDX3 is found in the cytoplasm, but a subset of tumors has distinct nuclear DDX3 localization of yet unknown biological significance. This study aimed to evaluate the significance of and mechanisms behind nuclear DDX3 expression in colorectal and breast cancer. METHODS: Expression of nuclear DDX3 and the nuclear exporter chromosome region maintenance 1 (CRM1) was evaluated by immunohistochemistry in 304 colorectal and 292 breast cancer patient samples...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28761138/an-atypical-strictosidine-synthase-osstrl2-plays-key-roles-in-anther-development-and-pollen-wall-formation-in-rice
#6
Ting Zou, Shuangcheng Li, Mingxing Liu, Tao Wang, Qiao Xiao, Dan Chen, Qiao Li, Yanling Liang, Jun Zhu, Yueyang Liang, Qiming Deng, Shiquan Wang, Aiping Zheng, Lingxia Wang, Ping Li
Strictosidine synthase (STR) plays an important role in the biosynthesis of terpenoid indole alkaloids (TIAs) and is expressed in a range of active meristematic tissues of higher plants. STR proteins are involved in different physiological and biochemical pathways. However, the function of STR proteins in rice development remains poorly understood. In this study, we identified 21 possible STR-like (OsSTRL) family members in rice genome and found that only one gene, OsSTRL2, exhibited a pre-emergency specific florescence expression pattern...
July 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28759634/the-role-of-co-opted-escrt-proteins-and-lipid-factors-in-protection-of-tombusviral-double-stranded-rna-replication-intermediate-against-reconstituted-rnai-in-yeast
#7
Nikolay Kovalev, Jun-Ichi Inaba, Zhenghe Li, Peter D Nagy
Reconstituted antiviral defense pathway in surrogate host yeast is used as an intracellular probe to further our understanding of virus-host interactions and the role of co-opted host factors in formation of membrane-bound viral replicase complexes in protection of the viral RNA against ribonucleases. The inhibitory effect of the RNA interference (RNAi) machinery of S. castellii, which only consists of the two-component DCR1 and AGO1 genes, was measured against tomato bushy stunt virus (TBSV) in wild type and mutant yeasts...
July 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28751858/distinct-localization-of-snap47-protein-in-gabaergic-and-glutamatergic-neurons-in-the-mouse-and-the-rat-hippocampus
#8
Agnieszka Münster-Wandowski, Heike Heilmann, Felix Bolduan, Thorsten Trimbuch, Yuchio Yanagawa, Imre Vida
Synaptosomal-associated protein of 47 kDa (SNAP47) isoform is an atypical member of the SNAP family, which does not contribute directly to exocytosis and synaptic vesicle (SV) recycling. Initial characterization of SNAP47 revealed a widespread expression in nervous tissue, but little is known about its cellular and subcellular localization in hippocampal neurons. Therefore, in the present study we applied multiple-immunofluorescence labeling, immuno-electron microscopy and in situ hybridization (ISH) and analyzed the localization of SNAP47 in pre- and postsynaptic compartments of glutamatergic and GABAergic neurons in the mouse and rat hippocampus...
2017: Frontiers in Neuroanatomy
https://www.readbyqxmd.com/read/28699864/the-predominant-circular-form-of-avocado-sunblotch-viroid-accumulates-in-planta-as-a-free-rna-adopting-a-rod-shaped-secondary-structure-unprotected-by-tightly-bound-host-proteins
#9
Amparo López-Carrasco, Ricardo Flores
Avocado sunblotch viroid (ASBVd), the type member of the family Avsunviroidae, replicates and accumulates in chloroplasts. Whether this minimal non-protein-coding circular RNA of 246-250 nt exists in vivo as a free nucleic acid or closely associated with host proteins remains unknown. To tackle this issue, the secondary structures of the monomeric circular (mc) (+) and (-) strands of ASBVd have been examined in silico by searching those of minimal free energy, and in vitro at single-nucleotide resolution by selective 2'-hydroxyl acylation analysed by primer extension (SHAPE)...
July 12, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28693611/dual-function-of-the-nuclear-export-signal-of-the-borna-disease-virus-nucleoprotein-in-nuclear-export-activity-and-binding-to-viral-phosphoprotein
#10
Mako Yanai, Madoka Sakai, Akiko Makino, Keizo Tomonaga
BACKGROUND: Borna disease virus (BoDV), which has a negative-sense, single-stranded RNA genome, causes persistent infection in the cell nucleus. The nuclear export signal (NES) of the viral nucleoprotein (N) consisting of leucine at positions 128 and 131 and isoleucine at positions 133 and 136 overlaps with one of two predicted binding sites for the viral phosphoprotein (P). A previous study demonstrated that higher expression of BoDV-P inhibits nuclear export of N; however, the function of N NES in the interaction with P remains unclear...
July 11, 2017: Virology Journal
https://www.readbyqxmd.com/read/28677426/dkk1-promotes-migration-and-invasion-of-non-small-cell-lung-cancer-via-%C3%AE-catenin-signaling-pathway
#11
Jing Zhang, Xintong Zhang, Xiaoting Zhao, Mei Jiang, Meng Gu, Ziyu Wang, Wentao Yue
Disregulation of dickkopf-related protein 1 (DKK1) has been reported in a variety of human cancers. However, how DKK1 functions in Non-small cell lung cancer has not been revealed. In the current study, DKK1 was knocked out by the lentivirus-mediated short hairpin RNA interference approach in H1299 and 95C non-small cell lung cancer cell lines. Subsequently, the migration and invasion ability were assessed by wound-healing and transwell assays. In addition, epithelial-mesenchymal transition markers and β-catenin were examined by Western blot analysis...
July 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28672168/regulating-cellular-trace-metal-economy-in-algae
#12
REVIEW
Crysten E Blaby-Haas, Sabeeha S Merchant
As indispensable protein cofactors, Fe, Mn, Cu and Zn are at the center of multifaceted acclimation mechanisms that have evolved to ensure extracellular supply meets intracellular demand. Starting with selective transport at the plasma membrane and ending in protein metalation, metal homeostasis in algae involves regulated trafficking of metal ions across membranes, intracellular compartmentalization by proteins and organelles, and metal-sparing/recycling mechanisms to optimize metal-use efficiency. Overlaid on these processes are additional circuits that respond to the metabolic state as well as to the prior metal status of the cell...
June 30, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28668588/optimized-fish-methods-for-visualizing-rna-localization-properties-in-drosophila-and-human-tissues-and-cultured-cells
#13
Cédric Diot, Ashley Chin, Eric Lécuyer
Eukaryotic gene expression is orchestrated by a large number of regulatory steps to modulate the synthesis, maturation and fate of various families of protein-coding and non-coding RNA molecules. Defining a given RNA molecule subcellular localization is thus of considerable importance for gleaning its function(s) and for elucidating post-transcriptional gene regulation pathways. For decades, fluorescent In Situ hybridization (FISH) has constituted the gold-standard technique for assessing RNA expression and distribution properties in cultured cells, tissue specimens, and whole mount organisms...
June 28, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28663102/rnase-h1-dependent-antisense-oligonucleotides-are-robustly-active-in-directing-rna-cleavage-in-both-the-cytoplasm-and-the-nucleus
#14
Xue-Hai Liang, Hong Sun, Joshua G Nichols, Stanley T Crooke
RNase H1-dependent antisense oligonucleotides (ASOs) are active in reducing levels of both cytoplasmic mRNAs and nuclear retained RNAs. Although ASO activity in the nucleus has been well demonstrated, the cytoplasmic activity of ASOs is less clear. Using kinetic and subcellular fractionation studies, we evaluated ASO activity in the cytoplasm. Upon transfection, ASOs targeting exonic regions rapidly reduced cytoplasmically enriched mRNAs, whereas an intron-targeting ASO that only degrades the nuclear pre-mRNA reduced mRNA levels at a slower rate, similar to normal mRNA decay...
June 26, 2017: Molecular Therapy: the Journal of the American Society of Gene Therapy
https://www.readbyqxmd.com/read/28653874/invalidation-of-mitophagy-by-fbp1-mediated-repression-promotes-apoptosis-in-breast-cancer
#15
Yifeng Liu, Yulin Jiang, Nian Wang, Qianni Jin, Feihu Ji, Changli Zhong, Zhiqiang Zhang, Junhong Yang, Xiangsen Ye, Tingmei Chen
Fructose-1,6-bisphosphatase 1, a rate-limiting enzyme in gluconeogenesis, was recently shown to be a tumor suppressor. However, the functions of fructose-1,6-bisphosphatase 1 in the regulation of mitophagy and apoptosis remain unknown. Here, we investigated the effects of fructose-1,6-bisphosphatase 1 on mitophagy and apoptosis as well as their underlying mechanisms in breast cancer cells. In this work, the messenger RNA and protein expression of various molecules were determined by quantitative realtime polymerase chain reaction and western blot, respectively...
June 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28651607/the-long-non-coding-rna-bc200-bcyrn1-is-critical-for-cancer-cell-survival-and-proliferation
#16
Evan P Booy, Ewan Ks McRae, Amit Koul, Francis Lin, Sean A McKenna
BACKGROUND: BC200 is a long non-coding RNA expressed at high levels in the brain and elevated in a variety of tumour types. BC200 has a hypothesized role in translational regulation; however, to date the functional role of BC200 in both normal and diseased states remains poorly characterized. METHODS: Detailed BC200 expression analyses were performed in tumor cell lines, primary and non-tumorigenic cultured breast and lung cells, and a panel of normal human tissues by quantitative real-time PCR and confirmed by northern blot...
June 26, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28637691/settling-the-m-6-a-debate-methylation-of-mature-mrna-is-not-dynamic-but-accelerates-turnover
#17
REVIEW
Nicolle A Rosa-Mercado, Johanna B Withers, Joan A Steitz
Post-transcriptional modification of RNA nucleosides has been implicated as a pivotal regulator of mRNA biology. In this issue of Genes & Development, Ke and colleagues (pp. 990-1006) provide insights into the temporal and spatial distribution of N(6)-methyladenosine (m(6)A) in RNA transcripts by analyzing different subcellular fractions. Using a recently developed biochemical approach for detecting m(6)A, the researchers show that m(6)A methylations are enriched in exons and are added to transcripts prior to splicing...
May 15, 2017: Genes & Development
https://www.readbyqxmd.com/read/28635588/genome-sequence-variation-in-the-constricta-strain-dramatically-alters-the-protein-interaction-and-localization-map-of-potato-yellow-dwarf-virus
#18
Chanyong Jang, Renyuan Wang, Joseph Wells, Fabian Leon, Mark Farman, John Hammond, Michael M Goodin
The genome sequence of the constricta strain of Potato yellow dwarf virus (CYDV) was determined to be 12 792 nt long and organized into seven ORFs with the gene order 3'-N-X-P-Y-M-G-L-5', which encodes the nucleocapsid, phospho, movement, matrix, glyco, and RNA-dependent RNA polymerase proteins, respectively, except for X, which is of unknown function. Cloned ORFs for each gene, except L, were used to construct a protein interaction and localization map (PILM) for this virus, which shares greater than 80 % amino acid similarity in all ORFs except X and P with the sanguinolenta strain of this species (SYDV)...
June 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28634384/alternative-splicing-regulates-distinct-subcellular-localization-of-epithelial-splicing-regulatory-protein-1-esrp1-isoforms
#19
Yueqin Yang, Russ P Carstens
Epithelial-Splicing-Regulatory-Protein 1 (Esrp1) is a cell-type specific RNA-binding protein (RBP) that is essential for mammalian development through maintenance of epithelial cell properties including barrier function. Esrp1 also regulates splicing during the epithelial to mesenchymal transition (EMT). It contains three highly conserved RNA recognition motifs (RRMs) in the absence of other clearly defined protein domains. Esrp1 itself is also alternatively spliced to produce multiple protein isoforms. Here we determined that two competing alternative 5' splice sites in exon 12 yield Esrp1 isoforms with differential nucleocytoplasmic localization...
June 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28630007/rna-localization-making-its-way-to-the-center-stage
#20
REVIEW
Ashley Chin, Eric Lécuyer
Cells are highly organized entities that rely on intricate addressing mechanisms to sort their constituent molecules to precise subcellular locations. These processes are crucial for cells to maintain their proper organization and carry out specialized functions in the body, consequently genetic perturbations that clog up these addressing systems can contribute to disease aetiology. The trafficking of RNA molecules represents an important layer in the control of cellular organization, a process that is both highly prevalent and for which features of the regulatory machineries have been deeply conserved evolutionarily...
June 16, 2017: Biochimica et Biophysica Acta
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