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Subcellular RNA

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https://www.readbyqxmd.com/read/28520934/the-smap1-2-proteins-of-the-crenarchaeon-sulfolobus-solfataricus-interact-with-the-exosome-and-stimulate-a-rich-tailing-of-transcripts
#1
Birgit Märtens, Linlin Hou, Fabian Amman, Michael T Wolfinger, Elena Evguenieva-Hackenberg, Udo Bläsi
The conserved Sm and Sm-like proteins are involved in different aspects of RNA metabolism. Here, we explored the interactome of SmAP1 and SmAP2 of the crenarchaeon Sulfolobus solfataricus (Sso) to shed light on their physiological function(s). Both, SmAP1 and SmAP2 co-purified with several proteins involved in RNA-processing/modification, translation and protein turnover as well as with components of the exosome involved in 3΄ to 5΄ degradation of RNA. In follow-up studies a direct interaction with the poly(A) binding and accessory exosomal subunit DnaG was demonstrated...
May 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28500073/fc%C3%AE-riiia-signaling-modulates-endosomal-tlr-responses-in-human-cd4-t-cells
#2
Anil K Chauhan
Recognition of Ab-opsonized pathogens by immune cells triggers both TLR and Fc receptor signaling. Fc receptors endocytose modified nucleic acids bound to Abs and deliver them to endosomes, where they are recognized by nucleic acid-sensing TLRs (NA-TLRs). We show that in CD4(+) T cells, NA-TLRs, TLR3, TLR8, and TLR9 are upregulated by FcγRIIIa-pSyk cosignaling and localize with FcγRIIIa on the cell surface. TLR9 accumulates on the cell surface, where it recognizes CpG oligonucleotide 2006. Subcellular location of NA-TLRs is a key determinant in discriminating self versus viral nucleic acid...
May 12, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28498920/copy-number-variation-of-functional-rbmy1-is-associated-with-sperm-motility-an-azoospermia-factor-linked-candidate-for-asthenozoospermia
#3
Yuanlong Yan, Xiling Yang, Yunqiang Liu, Ying Shen, Wenling Tu, Qiang Dong, Dong Yang, Yongyi Ma, Yuan Yang
STUDY QUESTION: What is the influence of copy number variation (CNV) in functional RNA binding motif protein Y-linked family 1 (RBMY1) on spermatogenic phenotypes? SUMMARY ANSWER: The RBMY1 functional copy dosage is positively correlated with sperm motility, and dosage insufficiency is an independent risk factor for asthenozoospermia. WHAT IS KNOWN ALREADY: RBMY1, a multi-copy gene expressed exclusively in the adult testis, is one of the most important candidates for male infertility in the azoospermia factor (AZF) region of the Y-chromosome...
May 12, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28490361/adducin-family-proteins-possess-different-nuclear-export-potentials
#4
Chia-Mei Liu, Wen-Hsin Hsu, Wan-Yi Lin, Hong-Chen Chen
BACKGROUND: The adducin (ADD) family proteins, namely ADD1, ADD2, and ADD3, are actin-binding proteins that play important roles in the stabilization of membrane cytoskeleton and cell-cell junctions. All the ADD proteins contain a highly conserved bipartite nuclear localization signal (NLS) at the carboxyl termini, but only ADD1 can localize to the nucleus. The reason for this discrepancy is not clear. METHODS: To avoid the potential effect of cell-cell junctions on the distribution of ADD proteins, HA epitope-tagged ADD proteins and mutants were transiently expressed in NIH3T3 fibroblasts and their distribution in the cytoplasm and nucleus was examined by immunofluorescence staining...
May 10, 2017: Journal of Biomedical Science
https://www.readbyqxmd.com/read/28479380/crispr-groundbreaking-technology-for-rna-guided-genome-engineering
#5
EDITORIAL
Le Cong
Years of advances in high-throughput biotechnologies exemplified by nucleic acid sequencing and single-molecular imaging have led to our increasing capacity to interrogate genomes down to nucleotide accuracy with single-cell or even subcellular resolution, thereby gaining high-dimensional information on the genetic variants and epigenetic states associated with physiological and pathological processes. To achieve a causal understanding the exquisite biology encoded in our genome, researchers in the past decades have sought to develop companion genome engineering tools...
May 4, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28472810/the-long-non-coding-rna-crnde-promotes-colorectal-carcinoma-progression-by-competitively-binding-mir-217-with-tcf7l2-and-enhancing-the-wnt-%C3%AE-catenin-signaling-pathway
#6
Bo Yu, Xuan Ye, Qiong Du, Bin Zhu, Qing Zhai, Xin-Xiang Li
BACKGROUND/AIMS: The long non-coding RNA colorectal neoplasia differentially expressed (CRNDE) contributes to the proliferation and migration of tumors. However, its molecular mechanism underlying gastric cancer remains unknown. In the present study, we investigated whether CRNDE was involved in the development of colorectal cancer via the binding of microRNA (miR)-217 with transcription factor 7-like 2 (TCF7L2) to enhance the Wnt signaling pathway. METHODS: Quantitative polymerase chain reaction was used to detect CRNDE, miR-217 and TCF7L2 in colorectal cancer tissues and cells...
May 4, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28461312/knockdown-of-host-antioxidant-defense-genes-enhances-the-effect-of-glucantime-on-intracellular-leishmania-braziliensis-in-human-macrophages
#7
Jair Téllez, Ibeth Romero, Maurilio José Soares, Mario Steindel, Alvaro José Romanha
Leishmaniasis is a neglected tropical disease affecting millions of people worldwide and represents a major public health problem. Information on protein expression patterns and functional roles within the context of Leishmania-infected human monocyte-derived macrophages (MDMs) under drug treatment conditions are essential to understand the role of these cells in leishmaniasis treatment. We analyzed functional changes in expression of human MDM genes and proteins during in vitro infection by Leishmania braziliensis and treatment with Glucantime (Sb(V)) using quantitative polymerase chain reaction (qPCR) arrays, western blotting, confocal microscopy and short-interfering RNA (siRNA) human gene-inhibition assays...
May 1, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28453527/altered-nucleocytoplasmic-proteome-and-transcriptome-distributions-in-an-in-vitro-model-of-amyotrophic-lateral-sclerosis
#8
Jee-Eun Kim, Yoon Ho Hong, Jin Young Kim, Gye Sun Jeon, Jung Hee Jung, Byung-Nam Yoon, Sung-Yeon Son, Kwang-Woo Lee, Jong-Il Kim, Jung-Joon Sung
Aberrant nucleocytoplasmic localization of proteins has been implicated in many neurodegenerative diseases. Evidence suggests that cytoplasmic mislocalization of nuclear proteins such as transactive response DNA-binding protein 43 (TDP-43) and fused in sarcoma (FUS) may be associated with neurotoxicity in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration. This study investigated the changes in nucleocytoplasmic distributions of the proteome and transcriptome in an in vitro model of ALS...
2017: PloS One
https://www.readbyqxmd.com/read/28452949/generation-and-applications-of-a-dna-aptamer-against-gremlin-1
#9
Qian Li, Yongwei Huo, Yonghong Guo, Xiaoyan Zheng, Wengang Sun, Zhiming Hao
Gremlin-1, a highly conserved glycosylated and phosphorylated secretory protein, plays important roles in diverse biological processes including early embryonic development, fibrosis, tumorigenesis, and renal pathophysiology. Aptamers, which are RNA or DNA single-stranded oligonucleotides capable of binding specifically to different targets ranging from small organics to whole cells, have potential applications in targeted imaging, diagnosis and therapy. In this study, we obtained a DNA aptamer against Gremlin-1 (G-ap49) using in vitro Systematic Evolution of Ligands by Exponential Enrichment (SELEX)...
April 28, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28450395/binding-of-dead-box-helicase-dhh1-to-the-5-utr-of-ash1-mrna-represses-localized-translation-of-ash1-in-yeast-cells
#10
Qianjun Zhang, Xiuhua Meng, Delin Li, Shaoyin Chen, Jianmin Luo, Linjie Zhu, Robert H Singer, Wei Gu
Local translation of specific mRNAs is regulated by dynamic changes in their subcellular localization, and these changes are due to complex mechanisms controlling cytoplasmic mRNA transport. The budding yeast Saccharomyces cerevisiae is well suited to studying these mechanisms because many of its transcripts are transported from the mother cell to the budding daughter cell. Here, we investigated the translational control of ASH1 mRNA after transport and localization. We show that although ASH1 transcripts were translated after they reached the bud-tip, some mRNAs were bound by the RNA-binding protein Puf6 and were non-polysomal...
April 27, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28443075/grim-19-restricts-hcv-replication-by-attenuating-intracellular-lipid-accumulation
#11
Jung-Hee Kim, Pil S Sung, Eun B Lee, Wonhee Hur, Dong J Park, Eui-Cheol Shin, Marc P Windisch, Seung K Yoon
Gene-associated with retinoid-interferon-induced mortality 19 (GRIM-19) targets multiple signaling pathways involved in cell death and growth. However, the role of GRIM-19 in the pathogenesis of hepatitis virus infections remains unexplored. Here, we investigated the restrictive effects of GRIM-19 on the replication of hepatitis C virus (HCV). We found that GRIM-19 protein levels were reduced in HCV-infected Huh7 cells and Huh7 cells harboring HCV replicons. Moreover, ectopically expressed GRIM-19 caused a reduction in both intracellular viral RNA levels and secreted viruses in HCVcc-infected cell cultures...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28423324/resolving-subcellular-mirna-trafficking-and-turnover-at-single-molecule-resolution
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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