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https://www.readbyqxmd.com/read/27905550/deep-sequencing-of-transcriptome-profiling-of-gstm2-knock-down-in-swine-testis-cells
#1
Yuqi Lv, Yi Jin, Yongqiang Zhou, Jianjun Jin, Zhenfa Ma, Zhuqing Ren
Glutathione-S-transferases mu 2 (GSTM2), a kind of important Phase II antioxidant enzyme of eukaryotes, is degraded by nonsense mediated mRNA decay due to a C27T substitution in the fifth exon of pigs. As a reproductive performance-related gene, GSTM2 is involved in embryo implantation, whereas, functional deficiency of GSTM2 induces pre- or post-natal death in piglets potentially. To have some insight into the role of GSTM2 in embryo development, high throughput RNA sequencing is performed using the swine testis cells (ST) with the deletion of GSTM2...
December 1, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27905398/structure-of-the-rbm7-zcchc8-core-of-the-next-complex-reveals-connections-to-splicing-factors
#2
Sebastian Falk, Ksenia Finogenova, Mireille Melko, Christian Benda, Søren Lykke-Andersen, Torben Heick Jensen, Elena Conti
The eukaryotic RNA exosome participates extensively in RNA processing and degradation. In human cells, three accessory factors (RBM7, ZCCHC8 and hMTR4) interact to form the nuclear exosome targeting (NEXT) complex, which directs a subset of non-coding RNAs for exosomal degradation. Here we elucidate how RBM7 is incorporated in the NEXT complex. We identify a proline-rich segment of ZCCHC8 as the interaction site for the RNA-recognition motif (RRM) of RBM7 and present the crystal structure of the corresponding complex at 2...
December 1, 2016: Nature Communications
https://www.readbyqxmd.com/read/27903898/transfer-rna-is-highly-unstable-during-early-amino-acid-starvation-in-escherichia-coli
#3
Sine Lo Svenningsen, Mette Kongstad, Thomas Søndergaard Stenum, Ana J Muñoz-Gómez, Michael A Sørensen
Due to its long half-life compared to messenger RNA, bacterial transfer RNA is known as stable RNA. Here, we show that tRNAs become highly unstable as part of Escherichia coli's response to amino acid starvation. Degradation of the majority of cellular tRNA occurs within twenty minutes of the onset of starvation for each of several amino acids. Both the non-cognate and cognate tRNA for the amino acid that the cell is starving for are degraded, and both charged and uncharged tRNA species are affected. The alarmone ppGpp orchestrates the stringent response to amino acid starvation...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27902874/spodoptera-litura-autophagy-related-protein-1-interacts-with-autophagy-related-protein-5-and-enhances-its-degradation
#4
N Zhang, Y Yang, H Lu, Y Xiang, X Huang, R Hu, Z Chen, W Yuan, R Peng, J Peng, H Ai, K Liu
It is known that the autophagy-related protein 1 (ATG1) plays critical roles in the regulation of autophagy in mammals and yeast, whereas the function of ATG1 in lepidopteran insects is not well elucidated. Here Spodoptera litura ATG1 (SlATG1) and its interactions with other ATG proteins were characterized. Alternative splicing of SlAtg1 produced at least four transcript variants. Over-expression and RNA interference knockdown of SlAtg1 demonstrated that SlATG1 enhanced autophagy. SlATG1A-Green fluorescent protein (GFP) tagged localized in the cytoplasm and formed some punctuate dots, which were colocalized with red fluorescent protein mCherry tagged Spodoptera exigua ATG5 (SeATG5)...
November 30, 2016: Insect Molecular Biology
https://www.readbyqxmd.com/read/27902378/neuronal-retrograde-transport-of-borna-disease-virus-occurs-in-signaling-endosomes
#5
Caroline M Charlier, Solène Debaisieux, Charlotte Foret, Anne Thouard, Giampetro Schiavo, Daniel Gonzalez-Dunia, Cécile Evelyne Malnou
Long-range axonal retrograde transport is a key mechanism for the cellular dissemination of neuro-invasive viruses, such as Borna Disease Virus (BDV), for which entry and egress sites are usually distant from the nucleus, where viral replication takes place. Although BDV is known to disseminate very efficiently in neurons, both in vivo and in primary cultures, the modalities of its axonal transport are still poorly characterized. In this work, we combined different methodological approaches, such as confocal microscopy and biochemical purification of endosomes, to study BDV retrograde transport...
November 8, 2016: Journal of General Virology
https://www.readbyqxmd.com/read/27901124/analysis-of-chikungunya-virus-proteins-reveals-that-non-structural-proteins-nsp2-and-nsp3-exhibit-rna-interference-rnai-suppressor-activity
#6
Kalika Mathur, Abhishek Anand, Sunil Kumar Dubey, Neeti Sanan-Mishra, Raj K Bhatnagar, Sujatha Sunil
RNAi pathway is an antiviral defence mechanism employed by insects that result in degradation of viral RNA thereby curbing infection. Several viruses including flaviviruses encode viral suppressors of RNAi (VSRs) to counteract the antiviral RNAi pathway. Till date, no VSR has been reported in alphaviruses. The present study was undertaken to evaluate chikungunya virus (CHIKV) proteins for RNAi suppressor activity. We systematically analyzed all nine CHIKV proteins for RNAi suppressor activity using Sf21 RNAi sensor cell line based assay...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27901120/complete-genome-sequence-and-transcriptomic-analysis-of-a-novel-marine-strain-bacillus-weihaiensis-reveals-the-mechanism-of-brown-algae-degradation
#7
Yueming Zhu, Peng Chen, Yunjuan Bao, Yan Men, Yan Zeng, Jiangang Yang, Jibin Sun, Yuanxia Sun
A novel marine strain representing efficient degradation ability toward brown algae was isolated, identified, and assigned to Bacillus weihaiensis Alg07. The alga-associated marine bacteria promote the nutrient cycle and perform important functions in the marine ecosystem. The de novo sequencing of the B. weihaiensis Alg07 genome was carried out. Results of gene annotation and carbohydrate-active enzyme analysis showed that the strain harbored enzymes that can completely degrade alginate and laminarin, which are the specific polysaccharides of brown algae...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27899881/transcriptomics-of-environmental-enrichment-reveals-a-role-for-retinoic-acid-signaling-in-addiction
#8
Yafang Zhang, Fanping Kong, Elizabeth J Crofton, Steven N Dragosljvich, Mala Sinha, Dingge Li, Xiuzhen Fan, Shyny Koshy, Jonathan D Hommel, Heidi M Spratt, Bruce A Luxon, Thomas A Green
There exists much variability in susceptibility/resilience to addiction in humans. The environmental enrichment paradigm is a rat model of resilience to addiction-like behavior, and understanding the molecular mechanisms underlying this protective phenotype may lead to novel targets for pharmacotherapeutics to treat cocaine addiction. We investigated the differential regulation of transcript levels using RNA sequencing of the rat nucleus accumbens after environmental enrichment/isolation and cocaine/saline self-administration...
2016: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/27899618/rna-seq-mixology-designing-realistic-control-experiments-to-compare-protocols-and-analysis-methods
#9
Aliaksei Z Holik, Charity W Law, Ruijie Liu, Zeya Wang, Wenyi Wang, Jaeil Ahn, Marie-Liesse Asselin-Labat, Gordon K Smyth, Matthew E Ritchie
Carefully designed control experiments provide a gold standard for benchmarking different genomics research tools. A shortcoming of many gene expression control studies is that replication involves profiling the same reference RNA sample multiple times. This leads to low, pure technical noise that is atypical of regular studies. To achieve a more realistic noise structure, we generated a RNA-sequencing mixture experiment using two cell lines of the same cancer type. Variability was added by extracting RNA from independent cell cultures and degrading particular samples...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899565/the-rrp6-c-terminal-domain-binds-rna-and-activates-the-nuclear-rna-exosome
#10
Elizabeth V Wasmuth, Christopher D Lima
The eukaryotic RNA exosome is an essential, multi-subunit complex that catalyzes RNA turnover, maturation, and quality control processes. Its non-catalytic donut-shaped core includes 9 subunits that associate with the 3' to 5' exoribonucleases Rrp6, and Rrp44/Dis3, a subunit that also catalyzes endoribonuclease activity. Although recent structures and biochemical studies of RNA bound exosomes from S. cerevisiae revealed that the Exo9 central channel guides RNA to either Rrp6 or Rrp44 using partially overlapping and mutually exclusive paths, several issues related to RNA recruitment remain...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27897407/activin-a-induces-skeletal-muscle-catabolism-via-p38%C3%AE-mitogen-activated-protein-kinase
#11
Hui Ding, Guohua Zhang, Ka Wai Thomas Sin, Zhelong Liu, Ren-Kuo Lin, Min Li, Yi-Ping Li
BACKGROUND: Activation of type IIB activin receptor (ActRIIB) in skeletal muscle leads to muscle atrophy because of increased muscle protein degradation. However, the intracellular signalling mechanism that mediates ActRIIB-activated muscle catabolism is poorly defined. METHODS: We investigated the role of p38β mitogen-activated protein kinases (MAPK) in mediating ActRIIB ligand activin A-activated muscle catabolic pathways in C2C12 myotubes and in mice with perturbation of this kinase pharmacologically and genetically...
September 16, 2016: Journal of Cachexia, Sarcopenia and Muscle
https://www.readbyqxmd.com/read/27895152/spatio-temporal-uncoupling-of-mirna-mediated-translational-repression-and-target-rna-degradation-controls-mirnp-recycling-in-mammalian-cells
#12
Mainak Bose, Bahnisikha Barman, Avijit Goswami, Suvendra N Bhattacharyya
miRNA-mediated repression control expression of more than half of protein coding genes in metazoan animals. Translation repression is associated with target mRNA degradation initiated by decapping and deadenylation of the repressed mRNAs. Earlier evidence suggest Endoplasmic Reticulum (ER) as the site where miRNPs interact with their targets before the translation repression sets in but the subcellular location of subsequent degradation of miRNA-repressed messages is largely unidentified. Here, we explore the subcellular distribution of essential components of degradation machineries of miRNA-targeted mRNAs...
November 28, 2016: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/27892983/association-of-mutations-in-tbk1-with-sporadic-and-familial-amyotrophic-lateral-sclerosis-and-frontotemporal-dementia
#13
Axel Freischmidt, Kathrin Müller, Albert C Ludolph, Jochen H Weishaupt, Peter M Andersen
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are related neurodegenerative syndromes that occur sporadically or have been associated with mostly dominant inheritance of mutations in more than 30 genes. A critical issue is whether all reported mutations are disease causing or are coincidental findings. In this review we analyze the pathogenicity of nonsynonymous variants in the newly discovered gene encoding TANK-binding kinase 1 (TBK1). The available data suggest that mutations in TBK1 that cause a 50% reduction of TBK1 protein levels are pathogenic...
November 21, 2016: JAMA Neurology
https://www.readbyqxmd.com/read/27889570/inhibitor-of-apoptosis-protein-1-regulates-tumor-necrosis-factor-mediated-destruction-of-intestinal-epithelial-cells
#14
Thomas Grabinger, Konstantin J Bode, Janine Demgenski, Carina Seitz, M Eugenia Delgado, Feodora Kostadinova, Cindy Reinhold, Nima Etemadi, Sabine Wilhelm, Matthias Schweinlin, Kay Hänggi, Janin Knop, Christof Hauck, Heike Walles, John Silke, Harald Wajant, Ueli Nachbur, W Wei-Lynn Wong, Thomas Brunner
BACKGROUND AND AIMS: Tumor necrosis factor (TNF) is a cytokine that promotes inflammation and contributes to pathogenesis of inflammatory bowel diseases. Unlike other cells and tissues, intestinal epithelial cells undergo rapid cell death upon exposure to TNF, by unclear mechanisms. We investigated the roles of inhibitor of apoptosis proteins (IAPs) in the regulation of TNF-induced cell death in the intestinal epithelium of mice and intestinal organoids. METHODS: RNA from cell lines and tissues and analyzed by quantitative PCR, protein levels were analyzed by immunoblot assays...
November 23, 2016: Gastroenterology
https://www.readbyqxmd.com/read/27886165/induction-of-tumor-apoptosis-through-a-circular-rna-enhancing-foxo3-activity
#15
William W Du, Ling Fang, Weining Yang, Nan Wu, Faryal Mehwish Awan, Zhenguo Yang, Burton B Yang
Circular RNAs are a class of non-coding RNAs that are receiving extensive attention. Despite reports showing circular RNAs acting as microRNA sponges, the biological functions of circular RNAs remain largely unknown. We show that in patient tumor samples and in a panel of cancer cells, circ-Foxo3 was minimally expressed. Interestingly, during cancer cell apoptosis, the expression of circ-Foxo3 was found to be significantly increased. We found that silencing endogenous circ-Foxo3 enhanced cell viability, whereas ectopic expression of circ-Foxo3 triggered stress-induced apoptosis and inhibited the growth of tumor xenografts...
November 25, 2016: Cell Death and Differentiation
https://www.readbyqxmd.com/read/27886048/interactions-between-the-hiv-1-unspliced-mrna-and-host-mrna-decay-machineries
#16
REVIEW
Daniela Toro-Ascuy, Bárbara Rojas-Araya, Fernando Valiente-Echeverría, Ricardo Soto-Rifo
The human immunodeficiency virus type-1 (HIV-1) unspliced transcript is used both as mRNA for the synthesis of structural proteins and as the packaged genome. Given the presence of retained introns and instability AU-rich sequences, this viral transcript is normally retained and degraded in the nucleus of host cells unless the viral protein REV is present. As such, the stability of the HIV-1 unspliced mRNA must be particularly controlled in the nucleus and the cytoplasm in order to ensure proper levels of this viral mRNA for translation and viral particle formation...
November 23, 2016: Viruses
https://www.readbyqxmd.com/read/27884102/gene-expression-profile-of-intramuscular-muscle-in-nellore-cattle-with-extreme-values-of-fatty-acid
#17
Mariana P Berton, Larissa F S Fonseca, Daniela F J Gimenez, Bruno L Utembergue, Aline S M Cesar, Luiz L Coutinho, Marcos Vinicius A de Lemos, Carolyn Aboujaoude, Angélica S C Pereira, Rafael M de O Silva, Nedenia B Stafuzza, Fabieli L B Feitosa, Hermenegildo L J Chiaia, Bianca F Olivieri, Elisa Peripolli, Rafael L Tonussi, Daniel M Gordo, Rafael Espigolan, Adrielle M Ferrinho, Lenise F Mueller, Lucia G de Albuquerque, Henrique N de Oliveira, Susan Duckett, Fernando Baldi
BACKGROUND: Fatty acid type in beef can be detrimental to human health and has received considerable attention in recent years. The aim of this study was to identify differentially expressed genes in longissimus thoracis muscle of 48 Nellore young bulls with extreme phenotypes for fatty acid composition of intramuscular fat by RNA-seq technique. RESULTS: Differential expression analyses between animals with extreme phenotype for fatty acid composition showed a total of 13 differentially expressed genes for myristic (C14:0), 35 for palmitic (C16:0), 187 for stearic (C18:0), 371 for oleic (C18:1, cis-9), 24 for conjugated linoleic (C18:2 cis-9, trans11, CLA), 89 for linoleic (C18:2 cis-9,12 n6), and 110 genes for α-linolenic (C18:3 n3) fatty acids...
November 25, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27882132/silencing-of-wnt5a-prevents-interleukin-1%C3%AE-induced-collagen-type-ii-degradation-in-rat-chondrocytes
#18
Shiping Shi, Zhentao Man, Wei Li, Shui Sun, Wei Zhang
Osteoarthritis (OA) is a joint disease, and few treatments to date have been able to delay OA progression. The degradation of collagen type II (COL2) in the cartilage matrix is an important initiating factor for OA progression; the upregulation of Wnt5a protein activates COL2 degradation. In the present study, small interfering RNA of Wnt-5a was delivered by a lentiviral vector (LV-Wnt5a-RNAi) to silence Wnt-5a mRNA and prevent COL2 degradation. To determine the function of LV-Wnt5a-RNAi, the OA chondrocyte model (OA-like chondrocytes) were constructed using interleukin (IL)-1β...
November 2016: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/27881650/mechanism-of-enhanced-hiv-restriction-by-virion-coencapsidated-cytidine-deaminases-apobec3f-and-apobec3g
#19
Anjuman Ara, Robin P Love, Tyson B Follack, Khawaja A Ahmed, Madison B Adolph, Linda Chelico
: The APOBEC3 (A3) enzymes, A3G and A3F, are coordinately expressed in CD4+ T cells and can become coencapsidated into HIV-1 virions, primarily in the absence of the viral infectivity factor (Vif). A3F and A3G are deoxycytidine deaminases that inhibit HIV-1 replication by inducing guanine to adenine hypermutation through deamination of cytosine to form uracil in (-)DNA. The effect of the simultaneous presence of both A3G and A3F on HIV-1 restriction ability is not clear. Here, we used a single cycle infectivity assay and biochemical analyses to determine if coencapsidated A3G and A3F differ in their restriction capacity than A3G or A3F alone...
November 23, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27881476/lin28a-uses-distinct-mechanisms-of-binding-to-rna-and-affects-positively-and-negatively-mirna-levels
#20
Jakub Stanislaw Nowak, Fruzsina Hobor, Angela Downie Ruiz Velasco, Nila Roy Choudhury, Gregory Heikel, Alastair Kerr, Andres Ramos, Gracjan Michlewski
Lin28a inhibits the biogenesis of let-7 miRNAs by triggering the polyuridylation and degradation of their precursors by terminal uridylyltransferases TUT4/7 and 3'-5' exoribonuclease Dis3l2, respectively. Previously, we showed that Lin28a also controls the production of neuro-specific miRNA-9 via a polyuridylation-independent mechanism. Here we reveal that the sequences and structural characteristics of pre-let-7 and pre-miRNA-9 are eliciting two distinct modes of binding to Lin28a. We present evidence that Dis3l2 controls miRNA-9 production...
November 23, 2016: RNA
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