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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
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
https://www.readbyqxmd.com/read/28624537/visualizing-rna-granule-transport-and-translation-in-living-neurons
#13
REVIEW
Karl E Bauer, Michael A Kiebler, Inmaculada Segura
In polarized cells, such as neurons, the synthesis of an mRNA does not ensure its proper cellular expression. Most mature transcripts require the association with RNA-binding proteins, resulting in the formation of RNA granules, which are then transported within the cytoplasm along the cytoskeleton and delivered to their proper subcellular locations, where they can be locally translated. Here we review current microscopy methods that have been developed to visualize RNA granule formation, transport and translation at the single cell level with a special emphasis on the MS2 and SunTag systems...
June 14, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28623268/ascorbate-induces-apoptosis-in-melanoma-cells-by-suppressing-clusterin-expression
#14
Sushmita Mustafi, David W Sant, Zhao-Jun Liu, Gaofeng Wang
Pharmacological levels of ascorbate have long been suggested as a potential treatment of cancer. However, we observed that EC50 of ascorbate was at a similar level for cultured healthy melanocytes and melanoma cells, suggesting a limit of pharmacological ascorbate in treating cancer. Loss of 5-hydroxymethylcytosine (5 hmC) is an epigenetic hallmark of cancer and ascorbate promotes 5 hmC generation by serving as a cofactor for TET methylcytosine dioxygenases. Our previous work demonstrated that ascorbate treatment at physiological level (100 μM) increased 5 hmC content in melanoma cells toward the level of healthy melanocytes...
June 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28621225/decreased-expression-of-mgmt-in-correlation-with-aberrant-dna-methylation-in-esophageal-cancer-patients-from-north-india
#15
Asad Ur Rehman, Snigdha Saikia, Mohammad Askandar Iqbal, Istaq Ahmad, Sadaf, Afzal Anees, P S Aravinda, Pramod Kumar Mishra, Suresh Hedau, Sundeep Singh Saluja, Subhash Medhi, Syed Akhtar Husain
O-6-methylguanine-DNA methyltransferase, DNA repair gene, has been found to be involved with the pathogenesis of the esophageal cancer. DNA hypermethylation and other factors have been suggested to downregulate O-6-methylguanine-DNA methyltransferase. In this communication, the methylation status of O-6-methylguanine-DNA methyltransferase gene and the corresponding O-6-methylguanine-DNA methyltransferase protein expression in esophageal cancer from North India has been studied. In all, 80 samples of tumor tissue along with adjacent normal tissue as controls were analyzed for messenger RNA level of O-6-methylguanine-DNA methyltransferase gene, protein expression, and subcellular localization...
June 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28611388/aberrant-plasticity-of-peripheral-sensory-axons-in-a-painful-neuropathy
#16
Takashi Hirai, Yatendra Mulpuri, Yanbing Cheng, Zheng Xia, Wei Li, Supanigar Ruangsri, Igor Spigelman, Ichiro Nishimura
Neuronal cells express considerable plasticity responding to environmental cues, in part, through subcellular mRNA regulation. Here we report on the extensive changes in distribution of mRNAs in the cell body and axon compartments of peripheral sensory neurons and the 3' untranslated region (3'UTR) landscapes after unilateral sciatic nerve entrapment (SNE) injury in rats. Neuronal cells dissociated from SNE-injured and contralateral L4 and L5 dorsal root ganglia were cultured in a compartmentalized system. Axonal and cell body RNA samples were separately subjected to high throughput RNA sequencing (RNA-Seq)...
June 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28591567/a-role-for-dystroglycan-in-the-pathophysiology-of-acute-leukemic-cells
#17
Lea Alonso-Rangel, Tizziani Benítez-Guerrero, Ivette Martínez-Vieyra, Bulmaro Cisneros, Adolfo Martínez-Tovar, Steve J Winder, Doris Cerecedo
AIMS: Previous reports have demonstrated that alterations or reduced expression of Dystroglycan (Dg) complex (αDg and βDg subunits) are related to progression and severity of neoplastic solid tissues. Therefore we determined the expression pattern and subcellular distribution of Dg complex in Acute Myeloid Leukemia (AML) primary blasts (M1, M2, and M3 phenotypes), as well as HL-60 and Kasumi-1 leukemia cell lines. Additionally, we evaluated the relative expression of the main enzymes controlling α-Dg glycosylation to ascertain the post-translational modifications in the leukemia cell phenotype...
August 1, 2017: Life Sciences
https://www.readbyqxmd.com/read/28589356/characterization-of-the-b-cell-transcriptome-bound-by-rna-binding-proteins-with-iclip
#18
Manuel D Díaz-Muñoz, Elisa Monzón-Casanova, Martin Turner
Posttranscriptional regulation of gene expression shapes the B cell transcriptome and controls messenger RNA (mRNA) translation into protein. Recent reports have highlighted the importance of RNA binding proteins (RBPs) for mRNA splicing, subcellular location, stability, and translation during B lymphocyte development, activation, and differentiation. Here we describe individual-nucleotide resolution UV cross-linking and immunoprecipitation (iCLIP) in primary lymphocytes, a method that maps RNA-protein interactions in a genome-wide scale allowing mechanistic analysis of RBP function...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28586434/the-arabidopsis-cys2-his2-zinc-finger-transcription-factor-zat18-is-a-positive-regulator-of-plant-tolerance-to-drought-stress
#19
Mingzhu Yin, Yanping Wang, Lihua Zhang, Jinzhu Li, Wenli Quan, Li Yang, Qingfeng Wang, Zhulong Chan
Environmental stress poses a global threat to plant growth and reproduction, especially drought stress. Zinc finger proteins comprise a family of transcription factors that play essential roles in response to various abiotic stresses. Here, we found that ZAT18 (At3g53600), a nuclear C2H2 zinc finger protein, was transcriptionally induced by dehydration stress. Overexpression (OE) of ZAT18 in Arabidopsis improved drought tolerance while mutation of ZAT18 resulted in decreased plant tolerance to drought stress...
June 6, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28579748/functional-characterization-of-rs2229094-t-c-polymorphism-in-the-tumor-necrosis-factor-locus-and-lymphotoxin-alpha-expression-in-human-retina-the-retina-4-project
#20
Salvador Pastor-Idoate, Irene Rodríguez-Hernández, Jimena Rojas, Lucia Gonzalez-Buendia, Santiago Delgado-Tirado, Jose Carlos López, Rogelio González-Sarmiento, Jose C Pastor
PURPOSE: The objective of this study is to determine the expression and localization of lymphotoxin alpha (LTA) in human retinas and the functionality of one of its polymorphisms rs2229094 (C13R) (T>C), previously associated with proliferative vitreoretinopathy (PVR) development. MATERIALS AND METHODS: Total RNA from three healthy human retinas were extracted and subjected to reverse transcription-polymerase chain reaction (RT-PCR) analysis, using flanking primers of LTA cDNA...
2017: Clinical Ophthalmology
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