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Rna Interactions

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https://www.readbyqxmd.com/read/30322266/identification-of-mir-708-5p-in-peripheral-blood-monocytes-potential-marker-for-postmenopausal-osteoporosis-in-mexican-mestizo-population
#1
Aldo H De-La-Cruz-Montoya, Eric G Ramírez-Salazar, Mayeli M Martínez-Aguilar, Pablo M González-de-la-Rosa, Manuel Quiterio, Cei Abreu-Goodger, Jorge Salmerón, Rafael Velázquez-Cruz
Osteoporosis is the most frequent disorder of bone metabolism, owing to an alteration between osteoclast and osteoblast activity, which results from the interaction of genetic, environmental, and epigenetic factors. microRNAs, small non-coding RNAs of around 22 nucleotides with important regulatory roles in gene regulation, that target mRNAs for post-transcriptional destabilization have been suggested as biomarkers in several disorders. In this work, we used small RNA sequencing to identify microRNAs from peripheral blood monocytes that were differentially expressed between non-osteoporotic and osteoporotic Mexican postmenopausal women, to elucidate the potential role of microRNAs as non-invasive marker candidates in osteoporosis...
October 15, 2018: Experimental Biology and Medicine
https://www.readbyqxmd.com/read/30321635/evaluation-of-antileishmanial-potential-of-computationally-screened-compounds-targeting-dead-box-rna-helicase-of-leishmania-donovani
#2
Satish Chandra Pandey, Anubhuti Jha, Awanish Kumar, Mukesh Samant
Visceral leishmaniasis (VL) is one of the most devastating diseases of the tropical region caused by protozoan parasite Leishmania donovani. So far, there is no effective drug and vaccine available against this fatal disease. The DEAD-box RNA helicase is quite essential for the RNA processing, amastigote differentiation and infectivity in Leishmania. In this study, L. donovani DEAD-box RNA helicase (LdHel-67) was evaluated as a potential drug target against VL. Using in-silico approach we have identified ligands that can specifically bind to this protein by using various application of Schrodinger (Maestro, version 10...
October 12, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/30321561/identification-of-key-genes-in-ankylosing-spondylitis
#3
Zhong-Yang Xu, Chao Zhou, Ke-Feng Zhang, Yan-Ping Zheng
Ankylosing spondylitis (AS) is a common form of seronegative spondyloarthritis. We had identified differentially expressed genes (DEGs) in AS based on our previous RNA-sequencing results. Our study aimed to identify key genes in AS by integrated microarray analysis. In this present study, we identified 1328 DEGs between AS and normal control by using integrated analysis of two datasets derived from the Gene Expression Omnibus (GEO) database. Functional annotation of DEGs were performed. Pathways in cancer, Pancreatic cancer and Natural killer cell mediated cytotoxicity were significantly enriched pathways for DEGs...
October 12, 2018: Immunology Letters
https://www.readbyqxmd.com/read/30321559/mucosal-bromodomain-containing-protein-4-brd4-mediates-aeroallergen-induced-inflammation-and-remodeling
#4
Bing Tian, Koa Hosoki, Zhiqing Liu, Jun Yang, Yingxin Zhao, Hong Sun, Jia Zhou, Erik Rytting, Lata Kaphalia, William J Calhoun, Sanjiv Sur, Allan R Brasier
BACKGROUND: Frequent exacerbations of allergic asthma leads to airway remodeling and a decline in pulmonary function, producing morbidity. Cat dander is an aeroallergen associated with asthma risk. OBJECTIVE: We sought to elucidate the mechanism of cat dander-induced inflammation-remodeling. METHODS: We identified remodeling in mucosal samples from allergic asthma by Q-RT-PCR. We developed a model of aeroallergen-induced experimental asthma by repetitive cat dander extract exposure...
October 12, 2018: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/30321541/prediction-of-rna-protein-interactions-by-combining-deep-convolutional-neural-network-with-feature-selection-ensemble-method
#5
Lei Wang, Xin Yan, Meng-Lin Liu, Ke-Jian Song, Xiao-Fei Sun, Wen-Wen Pan
RNA-protein interaction (RPI) plays an important role in the basic cellular processes of organisms. Unfortunately, due to time and cost constraints, it is difficult for biological experiments to determine the relationship between RNA and protein to a large extent. So there is an urgent need for reliable computational methods to quickly and accurately predict RNA-protein interaction. In this study, we propose a novel computational method RPIFSE (predicting RPI with Feature Selection Ensemble method) based on RNA and protein sequence information to predict RPI...
October 12, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30321408/region-3-2-of-the-%C3%AF-factor-controls-the-stability-of-rrna-promoter-complexes-and-potentiates-their-repression-by-dksa
#6
Danil Pupov, Ivan Petushkov, Daria Esyunina, Katsuhiko S Murakami, Andrey Kulbachinskiy
The σ factor drives promoter recognition by bacterial RNA polymerase (RNAP) and is also essential for later steps of transcription initiation, including RNA priming and promoter escape. Conserved region 3.2 of the primary σ factor ('σ finger') directly contacts the template DNA strand in the open promoter complex and facilitates initiating NTP binding in the active center of RNAP. Ribosomal RNA promoters are responsible for most RNA synthesis during exponential growth but should be silenced during the stationary phase to save cell resources...
October 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/30321378/human-gtpbp10-is-required-for-mitoribosome-maturation
#7
Priyanka Maiti, Hyun-Jung Kim, Ya-Ting Tu, Antoni Barrientos
Most steps on the biogenesis of the mitochondrial ribosome (mitoribosome) occur near the mitochondrial DNA nucleoid, in RNA granules, which contain dedicated RNA metabolism and mitoribosome assembly factors. Here, analysis of the RNA granule proteome identified the presence of a set of small GTPases that belong to conserved families of ribosome assembly factors. We show that GTPBP10, a member of the conserved Obg family of P-loop small G proteins, is a mitochondrial protein and have used gene-editing technologies to create a HEK293T cell line KO for GTPBP10...
October 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/30321353/siabasic-a-comprehensive-database-for-potent-sirna-6%C3%A3-sequences-without-off-target-effects
#8
Jongyeun Park, Seung Hyun Ahn, Kwang Moon Cho, Dowoon Gu, Eun-Sook Jang, Sung Wook Chi
Small interfering RNA (siRNA) is widely used to specifically silence target gene expression, but its microRNA (miRNA)-like function inevitably suppresses hundreds of off-targets. Recently, complete elimination of the off-target repression has been achieved by introducing an abasic nucleotide to the pivot (position 6; siRNA-6Ø), of which impaired base pairing destabilizes transitional nucleation (positions 2-6). However, siRNA-6Ø varied in its conservation of on-target activity (∼80-100%), demanding bioinformatics to discover the principles underlying its on-target efficiency...
January 1, 2018: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/30321077/knockdown-of-lncrna-kcnq1ot1-suppresses-the-adipogenic-and-osteogenic-differentiation-of-tendon-stem-cell-via-downregulating-mir-138-target-genes-ppar%C3%AE-and-runx2
#9
Yang Yu, Ying Chen, Xiaolei Zhang, Xiaolang Lu, Jianjun Hong, Xiaoshan Guo, Dongsheng Zhou
ObjectiveThe study aimed to investigate the mechanism and biological roles of long noncoding RNAKCNQ1OT1 in adipogenic and osteogenic differentiation of tendon stem cell. MethodsTendon injury mice model was established to detect the expression of lncRNA KCNQ1OT1, miR-138, peroxisome proliferator-activated receptor gamma (PPARγ) and runt-related gene 2 (RUNX2) using quantitative real-time PCR (qRT-PCR) and western blot. Mechanical testing was carried out to assess tendon function. Adiponectin and Osterix were used to evaluate the adipogenic and osteogenic differentiation of tendon stem cells (TSCs)...
October 15, 2018: Cell Cycle
https://www.readbyqxmd.com/read/30320910/interactome-analysis-of-the-human-cap-specific-mrna-nucleoside-2-o-methyltransferase-1-hmtr1-protein
#10
Fernando Moreira Simabuco, Isadora Carolina Betim Pavan, Nathalie Fortes Pestana, Paulo Costa Carvalho, Fernanda Luisa Basei, Daniela Campos Granato, Adriana Franco Paes Leme, Nilson Ivo Tonin Zanchin
In a previous study, we have shown that the gene promoter of a protein termed KIAA0082 is regulated by interferon and that this protein interacts with the RNA polymerase II. It has been subsequently shown that KIAA0082 is the human cap-specific messenger RNA (mRNA) (nucleoside-2'-O-)-methyltransferase 1 (hMTr1), which catalyzes methylation of the 2'-O -ribose of the first nucleotide of capped mRNAs. Pre-mRNAs are cotranscriptionally processed, requiring coordinate interactions or dissociations of hundreds of proteins...
October 15, 2018: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/30320360/glis2-redundancy-causes-chemoresistance-and-poor-prognosis-of-gastric-cancer-based-on-co%C3%A2-expression-network-analysis
#11
Jingsheng Yuan, Lulu Tan, Zhijie Yin, Kaixiong Tao, Guobing Wang, Wenjia Shi, Jinbo Gao
Gastric cancer is currently the fourth most common cancer and the third leading cause of cancer‑associated mortality worldwide. Studies have identified that certain biomarkers contribute to the prognosis, diagnosis and treatment of gastric cancer. However, the biomarkers of gastric cancer are rarely used clinically. Therefore, it is imperative to define novel molecular networks and key genes to guide the further study and clinical treatment of gastric cancer. In the present study, raw RNA sequencing data and clinicopathological information on patients with gastric cancer were downloaded from The Cancer Genome Atlas, and a weighted gene co‑expression network analysis was conducted...
October 15, 2018: Oncology Reports
https://www.readbyqxmd.com/read/30320339/microarray-analysis-reveals-long-non%C3%A2-coding-rna-sox2ot-as-a-novel-candidate-regulator-in-diabetic-nephropathy
#12
Xiaoxue Zhang, Jin Shang, Xiaoyang Wang, Genyang Cheng, Yumin Jiang, Dong Liu, Jing Xiao, Zhanzheng Zhao
Diabetic nephropathy (DN) is a highly complex syndrome involving multiple dysregulated biological processes. Long non‑coding RNAs (lncRNAs) are now believed to have an important function in various diseases. However, their roles in DN remain largely unknown. Therefore, the present study was performed in order to investigate the lncRNAs that have a crucial role in DN. db/db mice were used as a DN model while db/m mice served as a control to search for lncRNAs which may have important roles in DN. Microarray and bioinformatics analysis gave an overview of the features of differentially expressed genes...
October 4, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/30319635/flavivirus-receptors-diversity-identity-and-cell-entry
#13
REVIEW
Mathilde Laureti, Divya Narayanan, Julio Rodriguez-Andres, John K Fazakerley, Lukasz Kedzierski
Flaviviruses are emerging and re-emerging arthropod-borne pathogens responsible for significant mortality and morbidity worldwide. The genus comprises more than seventy small, positive-sense, single-stranded RNA viruses, which are responsible for a spectrum of human and animal diseases ranging in symptoms from mild, influenza-like infection to fatal encephalitis and haemorrhagic fever. Despite genomic and structural similarities across the genus, infections by different flaviviruses result in disparate clinical presentations...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/30319614/hypervariable-region-1-in-envelope-protein-2-of-hepatitis-c-virus-a-linchpin-in-neutralizing-antibody-evasion-and-viral-entry
#14
REVIEW
Jannick Prentoe, Jens Bukh
Chronic hepatitis C virus (HCV) infection is the cause of about 400,000 annual liver disease-related deaths. The global spread of this important human pathogen can potentially be prevented through the development of a vaccine, but this challenge has proven difficult, and much remains unknown about the multitude of mechanisms by which this heterogeneous RNA virus evades inactivation by neutralizing antibodies (NAbs). The N-terminal motif of envelope protein 2 (E2), termed hypervariable region 1 (HVR1), changes rapidly in immunoglobulin-competent patients due to antibody-driven antigenic drift...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/30319604/herpesviruses-and-micrornas-new-pathogenesis-factors-in-oral-infection-and-disease
#15
REVIEW
Afsar R Naqvi, Jennifer Shango, Alexandra Seal, Deepak Shukla, Salvador Nares
The oral cavity incessantly encounters a plethora of microorganisms. Effective and efficient oral innate and adaptive immune responses are incumbent to maintain healthy mucosa. A higher prevalence of Human Herpesviruses (HHV), a family of large enveloped DNA viruses, has been reported in multiple oral inflammatory diseases suggesting their involvement in disease progression. However, the viral components contributing to oral disease remain obscure. MicroRNAs (miRNA) are non-protein coding, single stranded ribonucleic acid (RNA) molecules that post-transcriptionally regulate diverse messenger RNAs...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/30319351/new-insights-into-the-role-of-ca-v-2-protein-family-in-calcium-flux-deregulation-in-fmr1-ko-neurons
#16
Sara Castagnola, Sébastien Delhaye, Alessandra Folci, Agnès Paquet, Frédéric Brau, Fabrice Duprat, Marielle Jarjat, Mauro Grossi, Méline Béal, Stéphane Martin, Massimo Mantegazza, Barbara Bardoni, Thomas Maurin
Fragile X syndrome (FXS), the most common form of inherited intellectual disability (ID) and a leading cause of autism, results from the loss of expression of the Fmr1 gene which encodes the RNA-binding protein Fragile X Mental Retardation Protein (FMRP). Among the thousands mRNA targets of FMRP, numerous encode regulators of ion homeostasis. It has also been described that FMRP directly interacts with Ca2+ channels modulating their activity. Collectively these findings suggest that FMRP plays critical roles in Ca2+ homeostasis during nervous system development...
2018: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/30318850/integrated-analysis-of-long-noncoding-rna-interactions-reveals-the-potential-role-in-progression-of-human-papillary-thyroid-cancer
#17
Xin You, Yixin Zhao, Jing Sui, Xianbiao Shi, Yulu Sun, Jiahan Xu, Geyu Liang, Qingxiang Xu, Yongzhong Yao
Recent scientific evidence has suggested that long noncoding RNAs (lncRNAs) play an important part in tumorigenesis as an important member of competing endogenous RNAs (ceRNAs). Hundreds of RNA sequence data and relevant clinic information are freely accessible in The Cancer Genome Atlas (TCGA) datasets. However, the role of cancer-related lncRNAs in papillary thyroid cancer (PTC) is not fully understood yet. In this study, we identified 461 RNA sequencing data from TCGA. Subsequently, 45 lncRNAs, 21 miRNAs, and 78 mRNAs were chosen to construct a ceRNA network of PTC...
October 14, 2018: Cancer Medicine
https://www.readbyqxmd.com/read/30318468/structural-basis-for-trna-mimicry-by-a-bacterial-y-rna
#18
Wei Wang, Xinguo Chen, Sandra L Wolin, Yong Xiong
Noncoding Y RNAs are present in both animal cells and many bacteria. In all species examined, Y RNAs tether the Ro60 protein to an effector protein to perform various cellular functions. Recently, a new Y RNA subfamily was identified in bacteria. Bioinformatic analyses of these YrlA (Y RNA-like A) RNAs predict that the effector-binding domain resembles tRNA. We present the structure of this domain, the overall folding of which is strikingly similar to canonical tRNAs. The tertiary interactions that are responsible for stabilizing tRNA are present in YrlA, making it a close tRNA mimic...
September 27, 2018: Structure
https://www.readbyqxmd.com/read/30318443/a-short-tandem-repeat-enriched-rna-assembles-a-nuclear-compartment-to-control-alternative-splicing-and-promote-cell-survival
#19
Karen Yap, Svetlana Mukhina, Gen Zhang, Jason S C Tan, Hong Sheng Ong, Eugene V Makeyev
Functions of many long noncoding RNAs (lncRNAs) depend on their ability to interact with multiple copies of specific RNA-binding proteins (RBPs). Here, we devised a workflow combining bioinformatics and experimental validation steps to systematically identify RNAs capable of multivalent RBP recruitment. This uncovered a number of previously unknown transcripts encoding high-density RBP recognition arrays within genetically normal short tandem repeats. We show that a top-scoring hit in this screen, lncRNA PNCTR, contains hundreds of pyrimidine tract-binding protein (PTBP1)-specific motifs allowing it to sequester a substantial fraction of PTBP1 in a nuclear body called perinucleolar compartment...
October 6, 2018: Molecular Cell
https://www.readbyqxmd.com/read/30318149/lung-single-cell-signaling-interaction-map-reveals-basophil-role-in-macrophage-imprinting
#20
Merav Cohen, Amir Giladi, Anna-Dorothea Gorki, Dikla Gelbard Solodkin, Mor Zada, Anastasiya Hladik, Andras Miklosi, Tomer-Meir Salame, Keren Bahar Halpern, Eyal David, Shalev Itzkovitz, Tibor Harkany, Sylvia Knapp, Ido Amit
Lung development and function arises from the interactions between diverse cell types and lineages. Using single-cell RNA sequencing (RNA-seq), we characterize the cellular composition of the lung during development and identify vast dynamics in cell composition and their molecular characteristics. Analyzing 818 ligand-receptor interaction pairs within and between cell lineages, we identify broadly interacting cells, including AT2, innate lymphocytes (ILCs), and basophils. Using interleukin (IL)-33 receptor knockout mice and in vitro experiments, we show that basophils establish a lung-specific function imprinted by IL-33 and granulocyte-macrophage colony-stimulating factor (GM-CSF), characterized by unique signaling of cytokines and growth factors important for stromal, epithelial, and myeloid cell fates...
September 28, 2018: Cell
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