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RNA folding

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https://www.readbyqxmd.com/read/29782930/all-atom-four-body-knowledge-based-statistical-potential-to-distinguish-native-tertiary-rna-structures-from-nonnative-folds
#1
Majid Masso
Scientific breakthroughs in recent decades have uncovered the capability of RNA molecules to fulfill a wide array of structural, functional, and regulatory roles in living cells, leading to a concomitantly significant increase in both the number and diversity of experimentally determined RNA three-dimensional (3D) structures. Atomic coordinates from a representative training set of solved RNA structures, displaying low sequence and structure similarity, facilitate derivation of knowledge-based energy functions...
May 18, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29782832/nup159-weakens-gle1-binding-to-dbp5-but-does-not-accelerate-adp-release
#2
Emily V Wong, Shawn Gray, Wenxiang Cao, Rachel Montpetit, Ben Montpetit, Enrique M De La Cruz
Dbp5, DDX19 in humans, is an essential DEAD-box protein involved in mRNA export, which has also been linked to other cellular processes, including rRNA export and translation. Dbp5 ATPase activity is regulated by several factors, including RNA, the nucleoporin proteins Nup159 and Gle1, and the endogenous small molecule inositol hexakisphosphate (InsP6 ). To better understand how these factors modulate Dbp5 activity and how this modulation relates to in vivo RNA metabolism, a detailed characterization of the Dbp5 mechanochemical cycle in the presence of those regulators individually or together is necessary...
May 18, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29782652/adenosine-methylation-as-a-molecular-imprint-defining-the-fate-of-rna
#3
REVIEW
Philip Knuckles, Marc Bühler
Multiple lines of evidence suggest the RNA modification N6 -methyladonsine (m6 A), which is installed in the nucleus co-transcriptionally and, thereafter, serves as a reversible chemical imprint that influences several steps of mRNA metabolism. This includes but is not limited to RNA folding, splicing, stability, transport, and translation. In this Review we focus on the current view of the nuclear installation of m6 A as well the molecular players involved, the so called m6 A writers. We also explore the effector proteins, or m6 A readers, that decode the imprint in different cellular contexts and compartments, and ultimately, the way the modification influences the lifecycle of an RNA molecule...
May 21, 2018: FEBS Letters
https://www.readbyqxmd.com/read/29782519/increased-circulating-microrna-122-is-a-biomarker-for-discrimination-and-risk-stratification-in-patients-defined-by-sepsis-3-criteria
#4
Tim Rahmel, Simon T Schäfer, Ulrich H Frey, Michael Adamzik, Jürgen Peters
BACKGROUND: Sepsis is now operationally defined as life-threatening organ dysfunction caused by an infection, identified by an acute change in SOFA-Score of at least two points, including clinical chemistry such as creatinine or bilirubin concentrations. However, little knowledge exists about organ-specific microRNAs as potentially new biomarkers. Accordingly, we tested the hypotheses that micro-RNA-122, the foremost liver-related micro-RNA (miR), 1) discriminates between sepsis and infection, 2) is an early predictor for mortality, and 3) improves the prognostic value of the SOFA-score...
2018: PloS One
https://www.readbyqxmd.com/read/29781033/microarray-analysis-of-circular-rna-expression-profiles-associated-with-gemcitabine-resistance-in-pancreatic-cancer-cells
#5
Chao Xu, Yue Yu, Fei Ding
Pancreatic cancer (PC) is one of the most malignant tumors of the digestive system due to its rapid progression, metastasis and resistance to chemotherapy. Gemcitabine (GEM) chemotherapy is the first‑choice treatment for advanced PC. However, the effect of GEM‑based chemotherapy on PC is limited due to the development of chemoresistance, and the molecular mechanisms underlying this resistance have yet to be investigated. Circular RNAs (circRNAs), which can function as microRNA sponges, have been found to be involved in the development of several types of cancer...
May 17, 2018: Oncology Reports
https://www.readbyqxmd.com/read/29780546/modified-nucleoside-triphosphates-exist-in-mammals
#6
Han-Peng Jiang, Jun Xiong, Fei-Long Liu, Cheng-Jie Ma, Xing-Lin Tang, Bi-Feng Yuan, Yu-Qi Feng
DNA and RNA contain diverse chemical modifications that exert important influences in a variety of cellular processes. In addition to enzyme-mediated modifications of DNA and RNA, previous in vitro studies showed that pre-modified nucleoside triphosphates (NTPs) can be incorporated into DNA and RNA during replication and transcription. Herein, we established a chemical labeling method in combination with liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS) analysis for the determination of endogenous NTPs in the mammalian cells and tissues...
May 7, 2018: Chemical Science
https://www.readbyqxmd.com/read/29780465/identification-of-a-selective-dna-ligase-for-accurate-recognition-and-ultrasensitive-quantification-of-n-6-methyladenosine-in-rna-at-one-nucleotide-resolution
#7
Weiliang Liu, Jingli Yan, Zhenhao Zhang, Hongru Pian, Chenghui Liu, Zhengping Li
N 6 -Methyladenosine (m6 A) is the most frequent post-transcriptional modification in RNA, and it plays a critical role in biological processes. The functions of m6 A remain largely unexplored due to a lack of highly sensitive methods to quantitatively determine the m6 A modification fraction at a precise location. Here, we first reveal that T3 DNA ligase has significant selectivity towards the m6 A modification. On the basis of the new finding, we establish an ultrasensitive quantitation assay for accurately determining m6 A at one-nucleotide resolution in RNA...
April 7, 2018: Chemical Science
https://www.readbyqxmd.com/read/29779026/uromodulin-mrna-from-urinary-extracellular-vesicles-correlate-to-kidney-function-decline-in-type-2-diabetes-mellitus
#8
Cindy M Yamamoto, Taku Murakami, Melanie L Oakes, Masato Mitsuhashi, Colleen Kelly, Robert R Henry, Kumar Sharma
BACKGROUND: Extracellular vesicles (EVs) enclose mRNA derived from their cell of origin and are considered a source of potential biomarkers. We examined urinary EV mRNA from individuals with diabetic kidney disease (DKD), chronic kidney disease, type 2 diabetes (T2DM), and obese and healthy controls to determine if such biomarkers had the potential to classify kidney disease and predict patients at higher risk of renal function decline. METHODS: A total of 242 participants enrolled in this study...
May 18, 2018: American Journal of Nephrology
https://www.readbyqxmd.com/read/29778766/first-genetic-characterization-of-usutu-virus-from-culex-pipiens-mosquitoes-serbia-2014
#9
Gábor Kemenesi, Dóra Buzás, Brigitta Zana, Kornélia Kurucz, Bosiljka Krtinic, Anett Kepner, Fanni Földes, Ferenc Jakab
Since its first appearance in Europe, Usutu virus (USUV) diverged to several different genetic lineages. The virus was reported to date from multiple countries across Europe (Hungary, Italy, Switzerland, Spain, Germany, Czech Republic and Belgium). Considering the more frequently published impact of the virus on humans it is crucial to investigate locally circulating genetic variants and trace its evolution. We retrospectively analyzed mosquito samples from Serbia Vojvodina region, collected during 2014. In this study we report the results of the screening of 23,753 female mosquitoes (753 pools) for USUV-specific nucleic-acid...
May 17, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29778390/next-generation-sequencing-reveals-differentially-expressed-small-noncoding-rnas-in-uterine-leiomyoma
#10
Tsai-Der Chuang, Yeming Xie, Wei Yan, Omid Khorram
OBJECTIVE: To determine the expression profile of small noncoding RNAs (sncRNAs) in leiomyoma, which has not been investigated to date. DESIGN: Laboratory-based investigation. SETTING: Academic center. PATIENT(S): Women undergoing hysterectomy for benign indications. INTERVENTION(S): Next-generation sequencing and screening of an sncRNA database with confirmatory analysis by quantitative reverse-transcription polymerase chain reaction (qRT-PCR)...
May 2018: Fertility and Sterility
https://www.readbyqxmd.com/read/29777235/response-of-skeletal-muscle-ucp2-expression-during-metabolic-adaptation-to-caloric-restriction
#11
Sascha Heinitz, Paolo Piaggi, Shanshan Yang, Susan Bonfiglio, Jason Steel, Jonathan Krakoff, Susanne B Votruba
BACKGROUND/OBJECTIVES: Spendthrift vs. thrifty individuals expend more energy and experience greater weight loss during caloric restriction (CR). Adaptive mechanisms in skeletal muscle, adipose tissue, and on hormone level modulate energy expenditure (EE) during weight loss. Metabolic mechanisms underlying the variability in EE during CR are unclear. The present study explored whether during long-term CR (i) gene expression changes in skeletal muscle and adipose tissue relate with the individual EE response and weight loss, and (ii) altered catecholamine and FGF21-concentrations are associated with measures of metabolic adaptation...
May 17, 2018: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/29777089/human-plasma-and-serum-extracellular-small-rna-reference-profiles-and-their-clinical-utility
#12
Klaas E A Max, Karl Bertram, Kemal Marc Akat, Kimberly A Bogardus, Jenny Li, Pavel Morozov, Iddo Z Ben-Dov, Xin Li, Zachary R Weiss, Azadeh Azizian, Anuoluwapo Sopeyin, Thomas G Diacovo, Catherine Adamidi, Zev Williams, Thomas Tuschl
Circulating extracellular RNAs (exRNAs) have the potential to serve as biomarkers for a wide range of medical conditions. However, limitations in existing exRNA isolation methods and a lack of knowledge on parameters affecting exRNA variability in human samples may hinder their successful discovery and clinical implementation. Using combinations of denaturants, reducing agents, proteolysis, and revised organic extraction, we developed an automated, high-throughput approach for recovery of exRNAs and exDNA from the same biofluid sample...
May 18, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29777050/the-yeast-telomerase-recruitment-module-requires-a-specific-rna-architecture
#13
Nancy Laterreur, Bruno Lemieux, Hannah Neumann, Jean-Christophe Berger-Dancause, Daniel Lafontaine, Raymund J Wellinger
Telomerases are ribonucleoprotein (RNP) enzymes that are related to reverse transcriptases. While they maintain genome stability, their composition varies significantly between species. Yeast telomerase RNPs contain an RNA that is comparatively large and its overall folding shows long helical segments with distal functional parts. Here we investigated the essential stem IVc module of the budding yeast telomerase RNA, called Tlc1. The distal part of stem IVc includes a conserved sequence element CS2a and structurally conserved features to which bind the Pop1/Pop6/Pop7 proteins and which together function analogously to the P3 domains of the RNase P/MRP RNPs...
May 18, 2018: RNA
https://www.readbyqxmd.com/read/29776333/transcriptomic-analysis-of-genes-in-soybean-in-response-to-peronospora-manshurica-infection
#14
Hang Dong, Shuangfeng Shi, Chong Zhang, Sihui Zhu, Mei Li, Jie Tan, Yue Yu, Liping Lin, Shirong Jia, Xujing Wang, Yuanhua Wu, Yuhui Liu
BACKGROUND: Soybean downy mildew (SDM), caused by Peronospora manshurica (Pm), is a major fungal disease in soybean. To date, little is known regarding the defense mechanism at molecular level and how soybean plants response to Pm infection. In this study, differential gene expression in SDM-resistant (HR) and SDM-susceptible (HS) genotype was analyzed by RNA-seq to identify differentially expressed genes (DEGs) following Pm infection. RESULTS: Of a total of 55,017 genes mapped to the soybean reference genome sequences, 2581 DEGs were identified...
May 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29775108/high-trna-transferase-nsun2-gene-expression-is-associated-with-poor-prognosis-in-head-and-neck-squamous-carcinoma
#15
Lingeng Lu, Gongjian Zhu, Hongmei Zeng, Qian Xu, Klaus Holzmann
NSUN2 is a tRNA methyltransferase and plays an important role in cell development via modifying RNA methylation. We aimed to evaluate the expression of NSUN2 and its prognostic value in HNSCC. Random-effects model of meta-analysis shows 1.99-folds (95% CI: 1.89-2.09) upregulation of NSUN2 expression in HNSCC versus normal tissues. Patients with high NSUN2 levels had approximately 22 months shorter overall survival, and had a higher mortality risk than those with low one (p-trend = 0.020). In conclusion, NSUN2 is a potential independent prognostic marker and may be a potential therapeutic target in HNSCC...
April 21, 2018: Cancer Investigation
https://www.readbyqxmd.com/read/29771411/long-non-coding-rna-zeb1-as1-is-associated-with-poor-prognosis-in-gastric-cancer-and-promotes-cancer-cell-metastasis
#16
X-J Liu, S-L Li, J-S Li, H Lu, L-L Yin, W-F Zheng, W-C Wang
OBJECTIVE: To investigate the expression of long non-coding RNA zinc-finger E-box binding homeobox 1-AS1 (lncRNA ZEB1-AS1) in gastric cancer cells and tissues, to study its effect on the gastric cancer cell metastasis capacity, and analyze its clinical significance. PATIENTS AND METHODS: The relative expression level of lncRNA ZEB1-AS1 in gastric cancer cells was detected via quantitative reverse transcription polymerase chain reaction (qRT-PCR). Transwell assay was used to detect the effects of lncRNA ZEB1-AS1 on the invasion and metastasis capacities of gastric cancer cells...
May 2018: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/29769539/integrated-analysis-of-hepatic-mrna-and-mirna-profiles-identified-molecular-networks-and-potential-biomarkers-of-nafld
#17
Mingzhe Zhu, Qianlei Wang, Wenjun Zhou, Tao Liu, Lili Yang, Peiyong Zheng, Li Zhang, Guang Ji
To enhance our understanding of molecular mechanisms and mine novel biomarkers of non-alcoholic fatty liver disease (NAFLD), RNA sequencing was performed to gain hepatic expression profiles of mRNAs and miRNAs in NAFLD and normal rats. Using DESeq with thresholds of a two-fold change and a false discovery rate (FDR) less than 0.05, 336 mRNAs and 21 miRNAs were identified as differentially expressed. Among those, 17 miRNAs (e.g., miR-144-3p, miR-99a-3p, miR-200b-3p, miR-200b-5p, miR-200c-3p, etc.) might serve as novel biomarkers of NAFLD...
May 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29769207/mitigating-sox2-potentiated-immune-escape-of-head-and-neck-squamous-cell-carcinoma-with-a-sting-inducing-nanosatellite-vaccine
#18
Yee Sun Tan, Kanokwan Sansanaphongpricha, Yuying Xie, Christopher R Donnelly, Xiaobo Luo, Blake R Heath, Xinyi Zhao, Emily L Bellile, Hongxiang Hu, Hongwei Chen, Peter J Polverini, Qianming Chen, Simon Young, Thomas E Carey, Jacques E Nör, Robert L Ferris, Gregory Wolf, Duxin Sun, Yu L Lei
PURPOSE: The response rates of Head and Neck Squamous Cell Carcinoma (HNSCC) to checkpoint blockade are below 20%. We aim to develop a mechanism-based vaccine to prevent HNSCC immune escape. EXPERIMENTAL DESIGN: We performed RNA-Seq of sensitive and resistant HNSCC cells to discover central pathways promoting resistance to immune killing. Using biochemistry, animal models, HNSCC microarray and immune cell deconvolution, we assessed the role of SOX2 in inhibiting STING-type I interferon (IFN-I) signaling-mediated anti-tumor immunity...
May 16, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29768001/crystal-structures-of-the-mango-ii-rna-aptamer-reveal-heterogeneous-fluorophore-binding-and-guide-engineering-of-variants-with-improved-selectivity-and-brightness
#19
Robert Trachman, Amir Abdolahzadeh, Alessio Andreoni, Razvan Cojocaru, Jay R Knutson, Michaël Ryckelynck, Peter John Unrau, Adrian Ferré-D'Amaré
Several RNA aptamers that bind small molecules and enhance their fluorescence have been successfully used to tag and track RNAs in vivo, but these genetically encodable tags have not yet achieved single-fluorophore resolution. Recently, Mango-II, an RNA that binds TO1-Biotin with ~1 nM affinity and enhances its fluorescence by >1,500-fold was isolated by fluorescence selection from the pool that yielded the original RNA Mango. We determined the crystal structures of Mango-II in complex with two fluorophores, TO1-Biotin and TO3-Biotin, and found that despite their high affinity, the ligands adopt multiple distinct conformations, indicative of a binding pocket with modest stereoselectivity...
May 16, 2018: Biochemistry
https://www.readbyqxmd.com/read/29766841/case-control-study-on-risk-factors-for-acute-hepatitis-e-in-germany-2012-to-2014
#20
Mirko Faber, Mona Askar, Klaus Stark
BackgroundNotified cases of hepatitis E have increased 40-fold in the past 10 years in Germany. Food safety is a major concern as hepatitis E virus (HEV) RNA has been detected in ready-to-eat retail-level food products. The objective of this case-control study was to assess risk factors for autochthonous symptomatic hepatitis E and explore reasons for delays in diagnosis. Methods: Demographic, clinical and exposure data from notified hepatitis E cases and individually matched population controls were collected in semi-standardised telephone interviews...
May 2018: Euro Surveillance: Bulletin Européen sur les Maladies Transmissibles, European Communicable Disease Bulletin
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