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RNA exosome

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https://www.readbyqxmd.com/read/28431250/nuclear-proximity-of-mtr4-to-rna-exosome-restricts-dna-mutational-asymmetry
#1
Junghyun Lim, Pankaj Kumar Giri, David Kazadi, Brice Laffleur, Wanwei Zhang, Veronika Grinstein, Evangelos Pefanis, Lewis M Brown, Erik Ladewig, Ophélie Martin, Yuling Chen, Raul Rabadan, François Boyer, Gerson Rothschild, Michel Cogné, Eric Pinaud, Haiteng Deng, Uttiya Basu
The distribution of sense and antisense strand DNA mutations on transcribed duplex DNA contributes to the development of immune and neural systems along with the progression of cancer. Because developmentally matured B cells undergo biologically programmed strand-specific DNA mutagenesis at focal DNA/RNA hybrid structures, they make a convenient system to investigate strand-specific mutagenesis mechanisms. We demonstrate that the sense and antisense strand DNA mutagenesis at the immunoglobulin heavy chain locus and some other regions of the B cell genome depends upon localized RNA processing protein complex formation in the nucleus...
April 20, 2017: Cell
https://www.readbyqxmd.com/read/28423032/complete-study-demonstrating-the-absence-of-rhabdovirus-in-a-distinct-sf9-cell-line
#2
Yoshifumi Hashimoto, Daniel Macri, Indresh Srivastava, Clifton McPherson, Rachael Felberbaum, Penny Post, Manon Cox
A putative novel rhabdovirus (SfRV) was previously identified in a Spodoptera frugiperda cell line (Sf9 cells [ATCC CRL-1711 lot 58078522]) by next generation sequencing and extensive bioinformatic analysis. We performed an extensive analysis of our Sf9 cell bank (ATCC CRL-1711 lot 5814 [Sf9L5814]) to determine whether this virus was already present in cells obtained from ATCC in 1987. Inverse PCR of DNA isolated from Sf9 L5814 cellular DNA revealed integration of SfRV sequences in the cellular genome. RT-PCR of total RNA showed a deletion of 320 nucleotides in the SfRV RNA that includes the transcriptional motifs for genes X and L...
2017: PloS One
https://www.readbyqxmd.com/read/28421898/targeting-the-nuclear-rna-exosome-poly-a-binding-proteins-enter-the-stage
#3
Nicola Meola, Torben Heick Jensen
Centrally positioned in nuclear RNA metabolism, the exosome deals with virtually all transcript types. This 3'-5' exo- and endo-nucleolytic degradation machine is guided to its RNA targets by adaptor proteins that enable substrate recognition. Recently, the discovery of the 'Poly(A) tail exosome targeting (PAXT)' connection as an exosome adaptor to human nuclear polyadenylated transcripts has relighted the interest of poly(A) binding proteins (PABPs) in both RNA productive and destructive processes.
April 19, 2017: RNA Biology
https://www.readbyqxmd.com/read/28411393/global-exosome-transcriptome-profiling-reveals-biomarkers-for-multiple-sclerosis
#4
Igor Selmaj, Maria Cichalewska, Magdalena Namiecinska, Grazyna Galazka, Wojciech Horzelski, Krzysztof W Selmaj, Marcin P Mycko
OBJECTIVE: Accumulating evidence supports a role for exosomes in immune regulation. In this study, we investigated the total circulating exosome transcriptome in relapsing-remitting multiple sclerosis patients (RRMS) and healthy controls (HC). METHODS: Next generation sequencing (NGS) was used to define the global RNA profile of serum exosomes in 19 RRMS patients (9 in relapse, 10 in remission) and 10 HC. We analyzed 5 million reads and over 50,000 transcripts per sample, including a detailed analysis of microRNA (miRNA) differentially expressed in RRMS...
April 15, 2017: Annals of Neurology
https://www.readbyqxmd.com/read/28411247/exosomal-microrna-transfer-into-macrophages-mediates-cellular-postconditioning
#5
Geoffrey de Couto, Romain Gallet, Linda Cambier, Ervin Jaghatspanyan, Nupur Makkar, James Frederick Dawkins, Benjamin P Berman, Eduardo Marbán
BACKGROUND: Cardiosphere-derived cells (CDCs) confer cardioprotection in acute myocardial infarction (MI) via distinctive macrophage (MΦ) polarization. Here we demonstrate that CDC-secreted exosomes (CDCexo) recapitulate the cardioprotective effects of CDC therapy known as cellular postconditioning. METHODS: Rats and pigs underwent MI induced by ischemia-reperfusion prior to intracoronary infusion of CDCexo, inert fibroblast exosomes (Fbexo; control), or vehicle. Two days later, infarct size was quantified...
April 14, 2017: Circulation
https://www.readbyqxmd.com/read/28407805/revelation-of-mrnas-and-proteins-in-porcine-milk-exosomes-by-transcriptomic-and-proteomic-analysis
#6
Ting Chen, Qian-Yun Xi, Jia-Jie Sun, Rui-Song Ye, Xiao Cheng, Rui-Ping Sun, Song-Bo Wang, Gang Shu, Li-Na Wang, Xiao-Tong Zhu, Qing-Yan Jiang, Yong-Liang Zhang
BACKGROUND: Milk is a complex liquid that provides nutrition to newborns. Recent reports demonstrated that milk is enriched in maternal-derived exosomes that are involved in fetal physiological and pathological conditions by transmission of exosomal mRNAs, miRNAs and proteins. Until now, there is no such research relevant to exosomal mRNAs and proteins in porcine milk, therefore, we have attempted to investigate porcine milk exosomal mRNAs and proteins using RNA-sequencing and proteomic analysis...
April 13, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/28401565/serum-and-exosomal-mir-122-and-mir-199a-as-a-biomarker-to-predict-therapeutic-efficacy-of-hepatitis-c-patients
#7
Xiaoyang Jiao, Zhicheng Fan, Huanzhu Chen, Ping He, Yazhen Li, Qiaoxin Zhang, Changwen Ke
AIM: MicroRNA (miRNA), which has been shown to correlate with liver functions, has been proposed as a new biomarker reflecting liver injury. The aim of the study was to investigate miRNA -122 (miR-122) and mir-RNA -199a (miR-199a) as a biomarker for predicting therapeutic efficacy in hepatitis C (HepC)patients. METHODS: 47 HepC 1b patients and 16 healthy subjects were enrolled in the study. Serum and exosomal mir-RNAs and other conventional biomarkers reflecting liver function were evaluated...
April 12, 2017: Journal of Medical Virology
https://www.readbyqxmd.com/read/28395182/sensitive-luminescent-reporter-viruses-reveal-appreciable-release-of-hepatitis-c-virus-ns5a-protein-into-the-extracellular-environment
#8
Nicholas S Eyre, Amanda L Aloia, Michael A Joyce, Monrat Chulanetra, D Lorne Tyrrell, Michael R Beard
The HCV NS5A protein is essential for viral RNA replication and virus particle assembly. To study the viral replication cycle and NS5A biology we generated an infectious HCV construct with a NanoLuciferase (NLuc) insertion within NS5A. Surprisingly, beyond its utility as a sensitive reporter of cytoplasmic viral RNA replication, we also observed strong luminescence in cell culture fluids. Further analysis using assembly-defective viruses and subgenomic replicons revealed that infectious virus production was not required for extracellular NS5A-NLuc activity but was associated with enrichment of extracellular NS5A-NLuc in intermediate-density fractions similar to those of exosomes and virus particles...
April 7, 2017: Virology
https://www.readbyqxmd.com/read/28393582/insights-into-the-human-brain-proteome-disclosing-the-biological-meaning-of-protein-networks-in-cerebrospinal-fluid
#9
Paulo Bastos, Rita Ferreira, Bruno Manadas, Paula I Moreira, Rui Vitorino
Cerebrospinal fluid (CSF) is an excellent source of biological information regarding the nervous system, once it is in close contact and accurately reflects alterations in this system. Several studies have analyzed differential protein profiles of CSF samples between healthy and diseased human subjects. However, the pathophysiological mechanisms and how CSF proteins relate to diseases are still poorly known. By applying bioinformatics tools, we attempted to provide new insights on the biological and functional meaning of proteomics data envisioning the identification of putative disease biomarkers...
April 10, 2017: Critical Reviews in Clinical Laboratory Sciences
https://www.readbyqxmd.com/read/28388413/circulating-immune-cells-mediate-a-systemic-rnai-based-adaptive-antiviral-response-in-drosophila
#10
Michel Tassetto, Mark Kunitomi, Raul Andino
Effective antiviral protection in multicellular organisms relies on both cell-autonomous and systemic immunity. Systemic immunity mediates the spread of antiviral signals from infection sites to distant uninfected tissues. In arthropods, RNA interference (RNAi) is responsible for antiviral defense. Here, we show that flies have a sophisticated systemic RNAi-based immunity mediated by macrophage-like haemocytes. Haemocytes take up dsRNA from infected cells and, through endogenous transposon reverse transcriptases, produce virus-derived complementary DNAs (vDNA)...
April 6, 2017: Cell
https://www.readbyqxmd.com/read/28388404/drosophilosophical-re-thinking-adaptive-immunity-in-the-fly
#11
Cara West, Neal Silverman
For decades, flies have been a model for innate immunity. In this issue of Cell, Tassetto et al. describe a mechanism for antiviral RNAi spreading that parallels mammalian adaptive immunity through reverse-transcribed vDNA circles and the systemic dissemination of small-RNA-containing exosomes.
April 6, 2017: Cell
https://www.readbyqxmd.com/read/28381156/characterization-of-exosomal-rnas-derived-from-human-gastric-cancer-cells-by-deep-sequencing
#12
Jia Ren, Quan Zhou, Hao Li, Jianfang Li, Li Pang, Liping Su, Qinlong Gu, Zhenggang Zhu, Bingya Liu
Exosomes secreted from the cell to the extracellular environment play an important role in intercellular communication. Next-generation sequencing technology, which has achieved great development recently, allows us to detect more complete data and gain even deeper analyses of RNA transcriptomes. In our research, we extracted exosomes from different gastric cancer cell lines and immortalized normal gastric mucosal epithelial cell line and examined the amounts of exosomal proteins and RNAs. Our data showed that the secreted amount of cancer cell-derived exosomes, which contain proteins and RNAs, was much higher than that of normal cell-derived exosomes...
April 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28372464/annals-express-degradation-of-serum-micrornas-during-transient-storage-of-serum-samples-at-4%C3%A2-c
#13
Toshiko Aiso, Shu Takigami, Akiko Yamaki, Hiroaki Ohnishi
BACKGROUND: Numerous studies demonstrate the potential of circulating microRNAs as non-invasive biomarkers of several diseases. Circulating microRNAs are much more stable than mRNAs and remain largely intact even after prolonged incubation at room temperature. However, recent reports show that microRNAs in serum or plasma samples have diverse stabilities. The aim of this pilot study is to evaluate the stabilities of miR-92a, miR-122, and miR-145 in serum during transient storage at 4°C before freezing...
January 1, 2017: Annals of Clinical Biochemistry
https://www.readbyqxmd.com/read/28361920/sedentary-lifestyle-related-exosomal-release-of-hotair-from-gluteal-femoral-fat-promotes-intestinal-cell-proliferation
#14
Xiaozhao Lu, Danna Bai, Xiangwei Liu, Chen Zhou, Guodong Yang
Pioneering epidemiological work has established strong association of sedentary lifestyle and obesity with the risk of colorectal cancer, while the detailed underlying mechanism remains unknown. Here we show that Hotair (HOX transcript antisense RNA) is a pro-adipogenic long non-coding RNA highly expressed in gluteal-femoral fat over other fat depots. Hotair knockout in adipose tissue results in gluteal-femoral fat defect. Squeeze of the gluteal-femoral fat induces intestinal proliferation in wildtype mice, while not in Hotair knockout mice...
March 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28358371/cell-based-therapy-using-mir-302-367-expressing-cells-represses-glioblastoma-growth
#15
Mohamed Fareh, Fabien Almairac, Laurent Turchi, Fanny Burel-Vandenbos, Philippe Paquis, Denys Fontaine, Sandra Lacas-Gervais, Marie-Pierre Junier, Hervé Chneiweiss, Thierry Virolle
Glioblastomas are incurable primary brain tumors that affect patients of all ages. The aggressiveness of this cancer has been attributed in part to the persistence of treatment-resistant glioblastoma stem-like cells. We have previously discovered the tumor-suppressor properties of the microRNA cluster miR-302-367, representing a potential treatment for glioblastoma. Here, we attempted to develop a cell-based therapy by taking advantage of the capability of glioma cells to secrete exosomes that enclose small RNA molecules...
March 30, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28355211/transcriptome-wide-analysis-of-alternative-routes-for-rna-substrates-into-the-exosome-complex
#16
Clémentine Delan-Forino, Claudia Schneider, David Tollervey
The RNA exosome complex functions in both the accurate processing and rapid degradation of many classes of RNA. Functional and structural analyses indicate that RNA can either be threaded through the central channel of the exosome or more directly access the active sites of the ribonucleases Rrp44 and Rrp6, but it was unclear how many substrates follow each pathway in vivo. We used CRAC (UV crosslinking and analysis of cDNA) in growing cells to identify transcriptome-wide interactions of RNAs with the major nuclear exosome-cofactor Mtr4 and with individual exosome subunits (Rrp6, Csl4, Rrp41 and Rrp44) along the threaded RNA path...
March 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28351885/loss-of-the-rna-helicase-skiv2l2-impairs-mitotic-progression-and-replication-dependent-histone-mrna-turnover-in-murine-cell-lines
#17
Alexis M Onderak, James T Anderson
RNA surveillance via the nuclear exosome requires cofactors such as the helicase SKIV2L2 to process and degrade certain noncoding RNAs. This research aimed to characterize the phenotype associated with RNAi knockdown of Skiv2l2 in two murine cancer cell lines: Neuro2A and P19. SKIV2L2 depletion in Neuro2A and P19 cells induced changes in gene expression indicative of cell differentiation and reduced cellular proliferation by thirty percent. Propidium iodide-based cell cycle analysis of Skiv2l2 knockdown cells revealed defective progression through G2/M phase and an accumulation of mitotic cells, suggesting SKIV2L2 contributes to mitotic progression...
March 28, 2017: RNA
https://www.readbyqxmd.com/read/28350871/oxygen-tension-regulates-the-mirna-profile-and-bioactivity-of-exosomes-released-from-extravillous-trophoblast-cells-liquid-biopsies-for-monitoring-complications-of-pregnancy
#18
Grace Truong, Dominic Guanzon, Vyjayanthi Kinhal, Omar Elfeky, Andrew Lai, Sherri Longo, Zarin Nuzhat, Carlos Palma, Katherin Scholz-Romero, Ramkumar Menon, Ben W Mol, Gregory E Rice, Carlos Salomon
Our understanding of how cells communicate has undergone a paradigm shift since the recent recognition of the role of exosomes in intercellular signaling. In this study, we investigated whether oxygen tension alters the exosome release and miRNA profile from extravillous trophoblast (EVT) cells, modifying their bioactivity on endothelial cells (EC). Furthermore, we have established the exosomal miRNA profile at early gestation in women who develop pre-eclampsia (PE) and spontaneous preterm birth (SPTB). HTR-8/SVneo cells were used as an EVT model...
2017: PloS One
https://www.readbyqxmd.com/read/28350318/overexpression-of-exosomal-cardioprotective-mirnas-mitigates-hypoxia-induced-h9c2-cells-apoptosis
#19
Jinwei Zhang, Jideng Ma, Keren Long, Wanling Qiu, Yujie Wang, Zihui Hu, Can Liu, Yi Luo, Anan Jiang, Long Jin, Qianzi Tang, Xun Wang, Xuewei Li, Mingzhou Li
Recent evidence suggests that hypoxia caused by acute myocardial infarction can induce cardiomyocyte apoptosis. Exosomes are signalling mediators that contribute to intercellular communication by transporting cytosolic components including miRNAs, mRNAs, and proteins. However, the systemic regulation and function of exosomal miRNAs in hypoxic cardiomyocytes are currently not well understood. Here, we used small RNA sequencing to investigate the effects of hypoxia stress on miRNAome of rat cardiomyoblast cells (H9c2) and corresponding exosomes...
March 28, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28341602/cytosolic-yb-1-and-nsun2-are-the-only-proteins-recognizing-specific-motifs-present-in-mrnas-enriched-in-exosomes
#20
Olga A Kossinova, Alexander V Gopanenko, Svetlana N Tamkovich, Olga A Krasheninina, Alexey E Tupikin, Elena Kiseleva, Darya D Yanshina, Alexey A Malygin, Alia G Ven'yaminova, Marsel R Kabilov, Galina G Karpova
Exosomes, membranous vesicles secreted by various cells, are involved in intercellular communication and carry vast repertoires of RNAs and proteins. Processes mediating RNA sorting into exosomes are currently poorly understood. Using bioinformatics approaches, three structural motifs ACCAGCCU, CAGUGAGC and UAAUCCCA have been discovered as enriched in exosomal mRNAs and long noncoding RNAs. Here, utilizing short RNA hairpins, each containing one of the motifs, in a pull-down assay of cytosolic extract of human embryonic kidney 293 (HEK293) cells, we prove that multifunctional RNA-binding protein YB-1 specifically interacts with all three motifs, whereas methyltransferase NSUN2 recognizes only the motif CAGUGAGC...
March 21, 2017: Biochimica et Biophysica Acta
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