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RNA metabolism

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https://www.readbyqxmd.com/read/29792949/srnaome-and-transcriptome-analysis-provide-insight-into-chilling-response-of-cowpea-pods
#1
Jinhua Zuo, Yunxiang Wang, Benzhong Zhu, Yunbo Luo, Qing Wang, Lipu Gao
Cowpea is an important horticultural crop in tropical and subtropical areas of Asia, Africa, and Latin America, as well as parts of southern Europe and Central and South America. Chilling injury is a common physiological hazard of cowpea in cold chain logistics which reduce the cowpea pod's nutritional quality and product value. However, the molecular mechanism involved in chilling injury remains unclear in cowpea pods. RNA-Seq and sRNA-Seq technologies were employed to decipher the miRNAs and mRNAs expression profiles and their regulatory networks in cowpea pods involved in chilling stress...
May 21, 2018: Gene
https://www.readbyqxmd.com/read/29792948/comparative-transcriptome-analysis-reveals-significant-differences-in-gene-expression-between-appressoria-and-hyphae-in-colletotrichum-gloeosporioides
#2
Meiyu Wang, Zongshan Zhou, Jianyuan Wu, Zhirui Ji, Junxiang Zhang
Fruit rot caused mainly by Colletotrichum gloeosporioides is a major cause of pre- and/or post-harvest diseases, which seriously constrains production, marketing, and export of fruits. To infect the host, this fungus evolves a specialized infection structure called the appressorium. Extensive past studies have characterized many appressorium-related genes in C. gloeosporioides, separately. However, a comprehensive understanding of the genes contributing to appressorium formation is far from complete. Here, global changes in gene expression were analyzed between appressoria and hyphae using RNA-Seq...
May 21, 2018: Gene
https://www.readbyqxmd.com/read/29792884/pharmacological-inhibition-of-dna-methylation-attenuates-pressure-overload-induced-cardiac-hypertrophy-in-rats
#3
Justus Stenzig, Yvonne Schneeberger, Alexandra Löser, Barbara S Peters, Andreas Schaefer, Rong-Rong Zhao, Shi Ling Ng, Grit Höppner, Birgit Geertz, Marc N Hirt, Wilson Tan, Eleanor Wong, Hermann Reichenspurner, Roger S-Y Foo, Thomas Eschenhagen
BACKGROUND: Heart failure is associated with altered gene expression and DNA methylation. De novo DNA methylation is associated with gene silencing, but its role in cardiac pathology remains incompletely understood. We hypothesized that inhibition of DNA methyltransferases (DNMT) might prevent the deregulation of gene expression and the deterioration of cardiac function under pressure overload (PO). To test this hypothesis, we evaluated a DNMT inhibitor in PO in rats and analysed DNA methylation in cardiomyocytes...
May 21, 2018: Journal of Molecular and Cellular Cardiology
https://www.readbyqxmd.com/read/29790663/a-distinctively-expressed-long-noncoding-rna-rp11-466i1-1-may-serve-as-a-prognostic-biomarker-in-hepatocellular-carcinoma
#4
Junyong Zhang, Di Zhang, Qi Zhao, Jianni Qi, Xiao Li, Chengyong Qin
It is urgent to explore effective diagnostic and prognostic biomarkers for hepatocellular carcinoma (HCC). Now, both lncRNAs and lipid metabolism are involved in tumor pathogenesis. Long noncoding RNA, RP11-466I1.1, could likely be linked to lipid metabolism according to our bioinformatics analysis, yet studies about RP11-466I1.1 expression in tumors and its potential functions are still lacking. We aimed to explore the expression and correlations with clinical features of a long noncoding RNA, RP11-466I1.1, and further analyze its diagnostic and prognostic values in hepatocellular carcinoma...
May 23, 2018: Cancer Medicine
https://www.readbyqxmd.com/read/29789783/mir-142-5p-in-bone-marrow-derived-mesenchymal-stem-cells-promotes-osteoporosis-involving-targeting-adhesion-molecule-vcam-1-and-inhibiting-cell-migration
#5
Zhaowei Teng, Xueguan Xie, Yun Zhu, Jianping Liu, Xingbo Hu, Qiang Na, Xiongwen Zhang, Guojun Wei, Shen Xu, Yugang Liu, Xiguang Zhang, Cory J Xian
Osteoporosis is a systemic bone metabolic disease that is highly prevalent in the elderly population, particularly in postmenopausal women, which results in enhanced bone fragility and an increased susceptibility to fractures. However, the underlying molecular pathogenesis mechanisms still remain to be further elucidated. In this study, in a rat ovariectomy- (OVX-) induced postmenopausal osteoporosis model, aberrant expression of a microRNA miR-142-5p and vascular cell adhesion molecule 1 (VCAM-1) was found by RNA sequencing analysis and qRT-PCR...
2018: BioMed Research International
https://www.readbyqxmd.com/read/29789616/rbfox1-mbnl1-competition-for-ccug-rna-repeats-binding-contributes-to-myotonic-dystrophy-type-1-type-2-differences
#6
Chantal Sellier, Estefanía Cerro-Herreros, Markus Blatter, Fernande Freyermuth, Angeline Gaucherot, Frank Ruffenach, Partha Sarkar, Jack Puymirat, Bjarne Udd, John W Day, Giovanni Meola, Guillaume Bassez, Harutoshi Fujimura, Masanori P Takahashi, Benedikt Schoser, Denis Furling, Ruben Artero, Frédéric H T Allain, Beatriz Llamusi, Nicolas Charlet-Berguerand
Myotonic dystrophy type 1 and type 2 (DM1, DM2) are caused by expansions of CTG and CCTG repeats, respectively. RNAs containing expanded CUG or CCUG repeats interfere with the metabolism of other RNAs through titration of the Muscleblind-like (MBNL) RNA binding proteins. DM2 follows a more favorable clinical course than DM1, suggesting that specific modifiers may modulate DM severity. Here, we report that the rbFOX1 RNA binding protein binds to expanded CCUG RNA repeats, but not to expanded CUG RNA repeats...
May 22, 2018: Nature Communications
https://www.readbyqxmd.com/read/29789545/dynamic-transcriptomic-m-6-a-decoration-writers-erasers-readers-and-functions-in-rna-metabolism
#7
Ying Yang, Phillip J Hsu, Yu-Sheng Chen, Yun-Gui Yang
N6 -methyladenosine (m6 A) is a chemical modification present in multiple RNA species, being most abundant in mRNAs. Studies on enzymes or factors that catalyze, recognize, and remove m6 A have revealed its comprehensive roles in almost every aspect of mRNA metabolism, as well as in a variety of physiological processes. This review describes the current understanding of the m6 A modification, particularly the functions of its writers, erasers, readers in RNA metabolism, with an emphasis on its role in regulating the isoform dosage of mRNAs...
May 22, 2018: Cell Research
https://www.readbyqxmd.com/read/29789369/-wolbachia-w-stri-blocks-zika-virus-growth-at-two-independent-stages-of-viral-replication
#8
M J Schultz, A L Tan, C N Gray, S Isern, S F Michael, H M Frydman, J H Connor
Mosquito-transmitted viruses are spread globally and present a great risk to human health. Among the many approaches investigated to limit the diseases caused by these viruses are attempts to make mosquitos resistant to virus infection. Coinfection of mosquitos with the bacterium Wolbachia pipientis from supergroup A is a recent strategy employed to reduce the capacity for major vectors in the Aedes mosquito genus to transmit viruses, including dengue virus (DENV), Chikungunya virus (CHIKV), and Zika virus (ZIKV)...
May 22, 2018: MBio
https://www.readbyqxmd.com/read/29789027/ethanolamine-enhances-intestinal-functions-by-altering-gut-microbiome-and-mucosal-anti-stress-capacity-in-weaned-rats
#9
Jian Zhou, Xia Xiong, Ke-Xing Wang, Li-Jun Zou, Peng Ji, Yu-Long Yin
Ethanolamine (Etn) contained in milk is the base constituent of phosphatidylethanolamine and is required for the proliferation of intestinal epithelial cells and bacteria, which is important for maintenance of the gut microbiome and intestinal development. The present study investigated the effect of Etn on intestinal function and microbiome using 21-d-old Sprague-Dawley rats treated with 0, 250, 500 and 1000 μm Etn in drinking water for 2 weeks immediately after weaning. Growth performance, intestinal morphology, antioxidant capacity and mucosal immunity, as well as gut microbiota community composition, were evaluated...
May 23, 2018: British Journal of Nutrition
https://www.readbyqxmd.com/read/29788408/effects-of-4-hydroxy-2-3-3-4-5-pentachlorobiphenyl-4-oh-cb107-on-liver-transcriptome-in-rats-implication-in-the-disruption-of-circadian-rhythm-and-fatty-acid-metabolism
#10
Mari Ochiai, Midori Iida, Tetsuro Agusa, Kohki Takaguchi, Satoshi Fujiic, Kei Nomiyama, Hisato Iwata
Polychlorinated biphenyls (PCBs) and their hydroxylated metabolites (OH-PCBs) have been detected in tissues of both wild animals and humans. Several previous studies have suggested adverse effects of OH-PCBs on the endocrine and nervous systems in mammals. However, there have been no studies on transcriptome analysis of the effects of OH-PCBs, and thus, the whole picture and mechanisms underlying the adverse effects induced by OH-PCBs are still poorly understood. We therefore investigated the mRNA expression profile in the liver of adult male Wistar rats treated with 4-hydroxy-2,3,3',4',5-pentachlorobiphenyl (4-OH-CB107) to explore the genes responsive to OH-PCBs and to understand the potential effects of the chemical...
May 21, 2018: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/29788229/subtiwiki-in-2018-from-genes-and-proteins-to-functional-network-annotation-of-the-model-organism-bacillus-subtilis
#11
Bingyao Zhu, Jörg Stülke
Living cells are made up of individual parts, i.e. the genome, the proteins, the RNA and lipid molecules as well as the metabolites and ions. However, life depends on the functional interaction among these components which is often organized in networks. Here, we present the recent development of SubtiWiki, the integrated database for the model bacterium Bacillus subtilis (http://subtiwiki.uni-goettingen.de/). SubtiWiki is based on a relational database and provides access to published information about the genes and proteins of B...
January 4, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29786868/cis-acting-allele-specific-expression-ase-differences-induced-by-alcohol-and-impacted-by-sex-as-well-as-parental-genotype-of-origin
#12
Chiao-Ling Lo, Lawrence Lumeng, Richard L Bell, Tiebing Liang, Amy C Lossie, Williams M Muir, Feng C Zhou
BACKGROUND: Alcohol use disorders (AUDs) are influenced by complex interactions between the genetics of the individual and their environment. We have previously identified hundreds of polygenic genetic variants between the selectively bred high and low alcohol drinking (HAD and LAD) rat lines. Here we report allele specific expression (ASE) differences, between the HAD2 and LAD2 rat lines. METHODS: The HAD2 and LAD2 rats which have been sequenced were reciprocally crossed to generate 10 litters of F1 progeny...
May 22, 2018: Alcoholism, Clinical and Experimental Research
https://www.readbyqxmd.com/read/29786750/microrna%C3%A2-20b%C3%A2-5p-promotes-ventricular-remodeling-by-targeting-the-tgf%C3%A2-%C3%AE-smad-signaling-pathway-in-a-rat-model-of-ischemia%C3%A2-reperfusion-injury
#13
Zhao-Guang Liang, Hong Yao, Rong-Sheng Xie, Chun-Lin Gong, Ye Tian
Myocardial ischemic injury results from severe impairment of the coronary blood supply and may lead to metabolic and ultrastructural changes, thereby causing irreversible damage. MicroRNA (miR)‑20b‑5p has been demonstrated to be involved in malignancies of the breast, colorectum, stomach, blood and oropharynx. The present study aimed to investigate the effects of miR‑20b‑5p on ventricular remodeling following myocardial ischemia‑reperfusion (IR) injury in rats by targeting small mothers against decapentaplegic homolog 7 (Smad7) via the transforming growth factor‑β (TGF‑β)/Smad signaling pathway...
May 18, 2018: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29786670/deubiquitinylase-usp47-promotes-rela-phosphorylation-and-survival-in-gastric-cancer-cells
#14
Lara Naghavi, Martin Schwalbe, Ahmed Ghanem, Michael Naumann
Every year, gastric cancer causes around 819,000 deaths worldwide. The incidence of gastric cancer in the western world is slowly declining, but the prognosis is unpromising. In Germany, the 5-year-survival rate is around 32%, and the average life span after diagnosis is 6 to 9 months. Therapy of gastric cancer patients comprises a gastrectomy and perioperative or adjuvant chemotherapy. However, resistance of gastric cancer cells to these agents is widespread; thus, improved chemotherapeutic approaches are required...
May 22, 2018: Biomedicines
https://www.readbyqxmd.com/read/29786565/modelling-non-alcoholic-fatty-liver-disease-in-human-hepatocyte-like-cells
#15
Marcus J Lyall, Jessy Cartier, John P Thomson, Kate Cameron, Jose Meseguer-Ripolles, Eoghan O'Duibhir, Dagmara Szkolnicka, Baltasar Lucendo Villarin, Yu Wang, Giovanny Rodriguez Blanco, Warwick B Dunn, Richard R Meehan, David C Hay, Amanda J Drake
Non-alcoholic fatty liver disease (NAFLD) is the most common cause of liver disease in developed countries. An in vitro NAFLD model would permit mechanistic studies and enable high-throughput therapeutic screening. While hepatic cancer-derived cell lines are a convenient, renewable resource, their genomic, epigenomic and functional alterations mean their utility in NAFLD modelling is unclear. Additionally, the epigenetic mark 5-hydroxymethylcytosine (5hmC), a cell lineage identifier, is rapidly lost during cell culture, alongside expression of the Ten-eleven-translocation ( TET ) methylcytosine dioxygenase enzymes, restricting meaningful epigenetic analysis...
July 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29784957/metabolic-reprogramming-in-leaf-lettuce-grown-under-different-light-quality-and-intensity-conditions-using-narrow-band-leds
#16
Kazuyoshi Kitazaki, Atsushi Fukushima, Ryo Nakabayashi, Yozo Okazaki, Makoto Kobayashi, Tetsuya Mori, Tomoko Nishizawa, Sebastian Reyes-Chin-Wo, Richard W Michelmore, Kazuki Saito, Kazuhiro Shoji, Miyako Kusano
Light-emitting diodes (LEDs) are an artificial light source used in closed-type plant factories and provide a promising solution for a year-round supply of green leafy vegetables, such as lettuce (Lactuca sativa L.). Obtaining high-quality seedlings using controlled irradiation from LEDs is critical, as the seedling health affects the growth and yield of leaf lettuce after transplantation. Because key molecular pathways underlying plant responses to a specific light quality and intensity remain poorly characterised, we used a multi-omics-based approach to evaluate the metabolic and transcriptional reprogramming of leaf lettuce seedlings grown under narrow-band LED lighting...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29784949/neuronal-activity-regulates-drosha-via-autophagy-in-spinal-muscular-atrophy
#17
Inês do Carmo G Gonçalves, Johanna Brecht, Maximilian P Thelen, Wiebke A Rehorst, Miriam Peters, Hyun Ju Lee, Susanne Motameny, Laura Torres-Benito, Darius Ebrahimi-Fakhari, Natalia L Kononenko, Janine Altmüller, David Vilchez, Mustafa Sahin, Brunhilde Wirth, Min Jeong Kye
Dysregulated miRNA expression and mutation of genes involved in miRNA biogenesis have been reported in motor neuron diseases including spinal muscular atrophy (SMA) and amyotrophic lateral sclerosis (ALS). Therefore, identifying molecular mechanisms governing miRNA expression is important to understand these diseases. Here, we report that expression of DROSHA, which is a critical enzyme in the microprocessor complex and essential for miRNA biogenesis, is reduced in motor neurons from an SMA mouse model. We show that DROSHA is degraded by neuronal activity induced autophagy machinery, which is also dysregulated in SMA...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29784767/vacuolar-iron-stores-gated-by-nramp3-and-nramp4-are-the-primary-source-of-iron-in-germinating-seeds
#18
Emma L Bastow, Vanesa S Garcia de la Torre, Andrew E Maclean, Robert T Green, Sylvain Merlot, Sebastien Thomine, Janneke Balk
During seed germination, iron (Fe) stored in vacuoles is exported by the redundant NRAMP3 and NRAMP4 transporter proteins. A double nramp3 nramp4 mutant is unable to mobilize Fe stores and does not develop in the absence of external Fe. We used RNA sequencing to compare gene expression in nramp3 nramp4 and wild type during germination and early seedling development. Even though sufficient Fe was supplied, the Fe-responsive transcription factors bHLH38, 39, 100 and 101 and their downstream targets FRO2 and IRT1 mediating Fe uptake were strongly upregulated in the nramp3 nramp4 mutant...
May 21, 2018: Plant Physiology
https://www.readbyqxmd.com/read/29783948/expansion-of-the-sos-regulon-of-vibrio-cholerae-through-extensive-transcriptome-analysis-and-experimental-validation
#19
Evelyne Krin, Sebastian Aguilar Pierlé, Odile Sismeiro, Bernd Jagla, Marie-Agnès Dillies, Hugo Varet, Oihane Irazoki, Susana Campoy, Zoé Rouy, Stéphane Cruveiller, Claudine Médigue, Jean-Yves Coppée, Didier Mazel
BACKGROUND: The SOS response is an almost ubiquitous response of cells to genotoxic stresses. The full complement of genes in the SOS regulon for Vibrio species has only been addressed through bioinformatic analyses predicting LexA binding box consensus and in vitro validation. Here, we perform whole transcriptome sequencing from Vibrio cholerae treated with mitomycin C as an SOS inducer to characterize the SOS regulon and other pathways affected by this treatment. RESULTS: Comprehensive transcriptional profiling allowed us to define the full landscape of promoters and transcripts active in V...
May 21, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29782846/abnormal-small-intestinal-epithelial-microvilli-in-patients-with-crohn-s-disease
#20
Kelli L VanDussen, Aleksandar Stojmirović, Katherine Li, Ta-Chiang Liu, Patrick K Kimes, Brian D Muegge, Katherine F Simpson, Matthew A Ciorba, Jacqueline G Perrigoue, Joshua R Friedman, Jennifer E Towne, Richard D Head, Thaddeus S Stappenbeck
BACKGROUND & AIMS: Crohn's disease (CD) presents as chronic and often progressive intestinal inflammation, but the contributing pathogenic mechanisms are unclear. We aimed to identify alterations in intestinal cells that could contribute to the chronic and progressive course of CD. METHODS: We took an unbiased, system-wide approach, performing sequence analysis of RNA extracted from formalin-fixed, paraffin-embedded ileal tissue sections from patients with CD (n=36) and without CD (controls, n=32)...
May 18, 2018: Gastroenterology
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