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Subcellular RNA

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https://www.readbyqxmd.com/read/28423324/resolving-subcellular-mirna-trafficking-and-turnover-at-single-molecule-resolution
#1
Sethuramasundaram Pitchiaya, Laurie A Heinicke, Jun I Park, Elizabeth L Cameron, Nils G Walter
Regulation of microRNA (miRNA) localization and stability is critical for their extensive cytoplasmic RNA silencing activity and emerging nuclear functions. Here, we have developed single-molecule fluorescence-based tools to assess the subcellular trafficking, integrity, and activity of miRNAs. We find that seed-matched RNA targets protect miRNAs against degradation and enhance their nuclear retention. While target-stabilized, functional, cytoplasmic miRNAs reside in high-molecular-weight complexes, nuclear miRNAs, as well as cytoplasmic miRNAs targeted by complementary anti-miRNAs, are sequestered stably within significantly lower-molecular-weight complexes and rendered repression incompetent...
April 18, 2017: Cell Reports
https://www.readbyqxmd.com/read/28412294/visualization-of-hepatitis-e-virus-rna-and-proteins-in-the-human-liver
#2
Daniela Lenggenhager, Jérôme Gouttenoire, Mohsen Malehmir, Marion Bawohl, Hanna Honcharova-Biletska, Susanne Kreutzer, David Semela, Jörg Neuweiler, Sandra Hürlimann, Patrick Aepli, Montserrat Fraga, Roland Sahli, Luigi Terracciano, Laura Rubbia-Brandt, Beat Müllhaupt, Christine Sempoux, Darius Moradpour, Achim Weber
BACKGROUND: / Aims: Although hepatitis E constitutes a substantial disease burden worldwide, surprisingly little is known about the localization of hepatitis E virus (HEV) in the human liver. We therefore aimed to visualize HEV RNA and proteins in situ. METHODS: A panel of 12 different antibodies against HEV open reading frame (ORF) 1-3 proteins was evaluated for immunohistochemistry (IHC) and two probes for in situ hybridization (ISH) in formalin-fixed, paraffin-embedded (FFPE) Huh-7 cells transfected with HEV ORF1-3 expression vectors...
April 12, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28386015/lncatlas-database-for-subcellular-localisation-of-long-noncoding-rnas
#3
David Mas-Ponte, Joana Carlevaro-Fita, Emilio Palumbo, Toni Hermoso Pulido, Roderic Guigo, Rory Johnson
The subcellular localisation of long noncoding RNAs (lncRNAs) holds valuable clues to their molecular function. However, measuring localisation of newly-discovered lncRNAs involves time-consuming and costly experimental methods. We have created "LncATLAS", a comprehensive resource of lncRNA localisation in human cells based on RNA-sequencing datasets. Altogether, 6,768 GENCODE-annotated lncRNAs are represented across various compartments of 15 cell lines. We introduce "Relative concentration index" (RCI) as a useful measure of localisation derived from ensemble RNAseq measurements...
April 6, 2017: RNA
https://www.readbyqxmd.com/read/28381696/sterile-inflammation-and-degradation-systems-in-heart-failure
#4
Kazuhiko Nishida, Kinya Otsu
In most patients with chronic heart failure (HF), levels of circulating cytokines are elevated and the elevated cytokine levels correlate with the severity of HF and prognosis. Various stresses induce subcellular component abnormalities, such as mitochondrial damage. Damaged mitochondria induce accumulation of reactive oxygen species and apoptogenic proteins, and subcellular inflammation. The vicious cycle of subcellular component abnormalities, inflammatory cell infiltration and neurohumoral activation induces cardiomyocyte injury and death, and cardiac fibrosis, resulting in cardiac dysfunction and HF...
April 5, 2017: Circulation Journal: Official Journal of the Japanese Circulation Society
https://www.readbyqxmd.com/read/28381466/intracellular-angiotensin-ii-interacts-with-nuclear-angiotensin-receptors-in-cardiac-fibroblasts-and-regulates-rna-synthesis-cell-proliferation-and-collagen-secretion
#5
Artavazd Tadevosyan, Jiening Xiao, Sirirat Surinkaew, Patrice Naud, Clémence Merlen, Masahide Harada, Xiaoyan Qi, David Chatenet, Alain Fournier, Bruce G Allen, Stanley Nattel
BACKGROUND: Cardiac fibroblasts play important functional and pathophysiological roles. Intracellular ("intracrine") angiotensin-II (Ang-II) signaling regulates intercellular communication, excitability, and gene expression in cardiomyocytes; however, the existence and role of intracrine Ang-II signaling in cardiac fibroblasts is unstudied. Here, we evaluated the localization of Ang-II receptors on atrial fibroblast nuclei and associated intracrine effects of potential functional significance...
April 5, 2017: Journal of the American Heart Association
https://www.readbyqxmd.com/read/28367995/a-furoviral-replicase-recruits-host-hsp70-to-membranes-for-viral-rna-replication
#6
Jian Yang, Fen Zhang, Nian-Jun Cai, Ne Wu, Xuan Chen, Jing Li, Xiang-Feng Meng, Tong-Quan Zhu, Jian-Ping Chen, Heng-Mu Zhang
Many host factors have been identified to be involved in viral infection. However, although furoviruses cause important diseases of cereals worldwide, no host factors have yet been identified that interact with furoviral genes or participate in the viral infection cycle. In this study, both TaHSP70 and NbHSP70 were up-regulated in Chinese wheat mosaic furovirus (CWMV)-infected plants. Their overexpression and inhibition were correlated with the accumulation of viral genomic RNAs, suggesting that the HSP70 genes could be necessary for CWMV infection...
April 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28349430/rna-fish-to-study-regulatory-rna-at-the-site-of-transcription
#7
Marta Soler, Raquel Boque-Sastre, Sonia Guil
The increasing role of all types of regulatory RNAs in the orchestration of cellular programs has enhanced the development of a variety of techniques that allow its precise detection, quantification, and functional scrutiny. Recent advances in imaging and fluoresecent in situ hybridization (FISH) methods have enabled the utilization of user-friendly protocols that provide highly sensitive and accurate detection of ribonucleic acid molecules at both the single cell and subcellular levels. We herein describe the approach originally developed by Stellaris(®), in which the target RNA molecule is fluoresecently labeled with multiple tiled complementary probes each carrying a fluorophore, thus improving sensitivity and reducing the chance of false positives...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28324503/visualization-of-human-telomerase-localization-by-fluorescence-microscopy-techniques
#8
Eladio Abreu, Rebecca M Terns, Michael P Terns
Human telomerase is a ribonucleoprotein (RNP) that synthesizes DNA repeats at the ends of chromosomes and maintains telomere length and genome stability. The enzyme is comprised of telomerase RNA (hTR) (which provides the template for telomere addition) and several protein subunits including telomerase reverse transcriptase (hTERT) (the catalytic component). Intracellular trafficking of the enzyme has emerged as an important factor in the regulation of telomerase activity. Telomerase trafficking between nuclear Cajal bodies (proposed sites of telomerase biogenesis and regulation) and telomeres (sites of action) is regulated by the cell cycle in concordance with telomere synthesis during S phase...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28320287/subcellular-localization-and-detection-of-tobacco-mosaic-virus-orf6-protein-by-immunoelectron-microscopy
#9
T N Erokhina, E A Lazareva, K R Richert-Pöggeler, E V Sheval, A G Solovyev, S Y Morozov
Members of the genus Tobamovirus represent one of the best-characterized groups of plant positive, single stranded RNA viruses. Previous studies have shown that genomes of some tobamoviruses contain not only genes coding for coat protein, movement protein, and the cistron coding for different domains of RNA-polymerase, but also a gene, named ORF6, coding for a poorly conserved small protein. The amino acid sequences of ORF6 proteins encoded by different tobamoviruses are highly divergent. The potential role of ORF6 proteins in replication of tobamoviruses still needs to be elucidated...
January 2017: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/28300784/the-molecular-basis-of-toxins-interactions-with-intracellular-signaling-via-discrete-portals
#10
REVIEW
Adi Lahiani, Ephraim Yavin, Philip Lazarovici
An understanding of the molecular mechanisms by which microbial, plant or animal-secreted toxins exert their action provides the most important element for assessment of human health risks and opens new insights into therapies addressing a plethora of pathologies, ranging from neurological disorders to cancer, using toxinomimetic agents. Recently, molecular and cellular biology dissecting tools have provided a wealth of information on the action of these diverse toxins, yet, an integrated framework to explain their selective toxicity is still lacking...
March 16, 2017: Toxins
https://www.readbyqxmd.com/read/28300211/als-along-the-axons-expression-of-coding-and-noncoding-rna-differs-in-axons-of-als-models
#11
Nimrod Rotem, Iddo Magen, Ariel Ionescu, Noga Gershoni-Emek, Topaz Altman, Christopher J Costa, Tal Gradus, Metsada Pasmanik-Chor, Dianna E Willis, Iddo Z Ben-Dov, Eran Hornstein, Eran Perlson
Amyotrophic lateral sclerosis (ALS) is a multifactorial lethal motor neuron disease with no known treatment. Although the basic mechanism of its degenerative pathogenesis remains poorly understood, a subcellular spatial alteration in RNA metabolism is thought to play a key role. The nature of these RNAs remains elusive, and a comprehensive characterization of the axonal RNAs involved in maintaining neuronal health has yet to be described. Here, using cultured spinal cord (SC) neurons grown using a compartmented platform followed by next-generation sequencing (NGS) technology, we find that RNA expression differs between the somatic and axonal compartments of the neuron, for both mRNA and microRNA (miRNA)...
March 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28296067/rna-binding-proteins-of-the-nxf-nuclear-export-factor-family-and-their-connection-with-the-cytoskeleton
#12
REVIEW
L A Mamon, V R Ginanova, S F Kliver, A O Yakimova, A A Atsapkina, E V Golubkova
The mutual relationship between mRNA and the cytoskeleton can be seen from two points of view. On the one hand, the cytoskeleton is necessary for mRNA trafficking and anchoring to subcellular domains. On the other hand, cytoskeletal growth and rearrangement require the translation of mRNAs that are connected to the cytoskeleton. β-actin mRNA localization may influence dynamic changes in the actin cytoskeleton. In the cytoplasm, long-lived mRNAs exist in the form of RNP (ribonucleoprotein) complexes, where they interact with RNA-binding proteins, including NXF (Nuclear eXport Factor)...
March 13, 2017: Cytoskeleton
https://www.readbyqxmd.com/read/28283797/influence-of-nrf2-activators-on-subcellular-skeletal-muscle-protein-and-dna-synthesis-rates-after-6%C3%A2-weeks-of-milk-protein-feeding-in-older-adults
#13
Adam R Konopka, Jaime L Laurin, Robert V Musci, Christopher A Wolff, Justin J Reid, Laurie M Biela, Qian Zhang, Fredrick F Peelor, Christopher L Melby, Karyn L Hamilton, Benjamin F Miller
In older adults, chronic oxidative and inflammatory stresses are associated with an impaired increase in skeletal muscle protein synthesis after acute anabolic stimuli. Conjugated linoleic acid (CLA) and Protandim have been shown to activate nuclear factor erythroid-derived 2-like 2 (Nrf2), a transcription factor for the antioxidant response element and anti-inflammatory pathways. This study tested the hypothesis that compared to a placebo control (CON), CLA and Protandim would increase skeletal muscle subcellular protein (myofibrillar, mitochondrial, cytoplasmic) and DNA synthesis in older adults after 6 weeks of milk protein feeding...
March 10, 2017: GeroScience
https://www.readbyqxmd.com/read/28281199/unraveling-new-functions-of-superoxide-dismutase-using-yeast-model-system-beyond-its-conventional-role-in-superoxide-radical-scavenging
#14
REVIEW
Woo-Hyun Chung
To deal with chemically reactive oxygen molecules constantly threatening aerobic life, cells are readily equipped with elaborate biological antioxidant systems. Superoxide dismutase is a metalloenzyme catalytically eliminating superoxide radical as a first-line defense mechanism against oxidative stress. Multiple different SOD isoforms have been developed throughout evolution to play distinct roles in separate subcellular compartments. SOD is not essential for viability of most aerobic organisms and intriguingly found even in strictly anaerobic bacteria...
March 9, 2017: Journal of Microbiology / the Microbiological Society of Korea
https://www.readbyqxmd.com/read/28276020/localizing-mrnas-encoding-mitochondrial-proteins-in-yeast-by-fluorescence-microscopy-and-subcellular-fractionation
#15
Dmitry Zabezhinsky, Hannah Sperber, Jeffrey E Gerst
Mitochondria are thought to have evolved from ancestral proteobacteria and, as a result of symbiosis, became an indispensable organelle in all eukaryotic cells. Mitochondria perform essential functions that provide the cell with ATP, amino acids, phospholipids, and both heme and iron-sulfur clusters. However, only 1% of mitochondrial proteins are encoded by the mitochondrial genome, while the remaining 99% are encoded in the nucleus. This raises a logistical challenge to the cell, as these nuclear-encoded proteins have to be translated, delivered to the mitochondrial surface, and translocated to its various compartments...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28265061/amyotrophic-lateral-sclerosis-linked-mutations-increase-the-viscosity-of-liquid-like-tdp-43-rnp-granules-in-neurons
#16
Pallavi P Gopal, Jeffrey J Nirschl, Eva Klinman, Erika L F Holzbaur
Ribonucleoprotein (RNP) granules are enriched in specific RNAs and RNA-binding proteins (RBPs) and mediate critical cellular processes. Purified RBPs form liquid droplets in vitro through liquid-liquid phase separation and liquid-like non-membrane-bound structures in cells. Mutations in the human RBPs TAR-DNA binding protein 43 (TDP-43) and RNA-binding protein FUS cause amyotrophic lateral sclerosis (ALS), but the biophysical properties of these proteins have not yet been studied in neurons. Here, we show that TDP-43 RNP granules in axons of rodent primary cortical neurons display liquid-like properties, including fusion with rapid relaxation to circular shape, shear stress-induced deformation, and rapid fluorescence recovery after photobleaching...
March 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28264987/nuclear-retention-of-the-lncrna-snhg1-by-doxorubicin-attenuates-hnrnpc-p53-protein-interactions
#17
Yuan Shen, Shanshan Liu, Jiao Fan, Yinghua Jin, Baolei Tian, Xiaofei Zheng, Hanjiang Fu
The protein p53 plays a crucial role in the regulation of cellular responses to diverse stresses. Thus, a major priority in cell biology is to define the mechanisms that regulate p53 activity in response to stresses or maintain it at basal levels under normal conditions. Moreover, further investigation is required to establish whether RNA participates in regulating p53's interaction with other proteins. Here, by conducting systematic experiments, we discovered a p53 interactor-hnRNPC-that directly binds to p53, destabilizes it, and prevents its activation under normal conditions...
April 2017: EMBO Reports
https://www.readbyqxmd.com/read/28258033/rnp-transport-in-cell-biology-the-long-and-winding-road
#18
REVIEW
Carolina Eliscovich, Robert H Singer
Regulation of gene expression is key determinant to cell structure and function. RNA localization, where specific mRNAs are transported to subcellular regions and then translated, is highly conserved in eukaryotes ranging from yeast to extremely specialized and polarized cells such as neurons. Messenger RNA and associated proteins (mRNP) move from the site of transcription in the nucleus to their final destination in the cytoplasm both passively through diffusion and actively via directed transport. Dysfunction of RNA localization, transport and translation machinery can lead to pathology...
February 28, 2017: Current Opinion in Cell Biology
https://www.readbyqxmd.com/read/28256719/rna-whole-mount-in-situ-hybridization-proximity-ligation-assay-rish-pla-an-assay-for-detecting-rna-protein-complexes-in-intact-cells
#19
Ioannis M Roussis, Fiona A Myers, Garry P Scarlett
Techniques for studying RNA-protein interactions have lagged behind those for DNA-protein interactions as a consequence of the complexities associated with working with RNA. This unit describes a method for the adaptation of the In Situ Hybridization-Proximity Ligation Assay (ISH-PLA) to the study of RNA regulation (rISH-PLA). The rISH-PLA assay allows the identification of a given RNA-protein complex at subcellular and single-cell resolution, thus avoiding the lack of spatial resolution and sensitivity associated with assaying heterogeneous cell populations from which conventional RNA-protein interaction detection techniques suffer...
March 3, 2017: Current Protocols in Cell Biology
https://www.readbyqxmd.com/read/28256001/expression-subcellular-localisation-and-possible-roles-of-dipeptidyl-peptidase-9-dpp9-in-murine-macrophages
#20
Emilija Zapletal, Barbara Cupic, Jelka Gabrilovac
Dipeptidyl peptidase 9 (DPP9) is a peptidase of the DPPIV gene family, and its role in immune responses has been reported. In this study, we compared the messenger RNA expression profile of DPP9 to that of the related DPP8 and DPPIV in murine haematopoietic and lymphatic tissues. A similar order of expression levels was observed for all 3 peptidases: peritoneal macrophages < bone marrow < spleen ≤ lymph nodes. Also, we examined the subcellular localisation of DPP9 and its possible role(s) in J774 cell line of macrophage origin...
March 2017: Cell Biochemistry and Function
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