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https://www.readbyqxmd.com/read/29241043/posttranscriptional-m6a-editing-of-hiv-1-mrnas-enhances-viral-gene-expression
#1
Edward M Kennedy, Hal P Bogerd, Anand V R Kornepati, Dong Kang, Delta Ghoshal, Joy B Marshall, Brigid C Poling, Kevin Tsai, Nandan S Gokhale, Stacy M Horner, Bryan R Cullen
No abstract text is available yet for this article.
December 13, 2017: Cell Host & Microbe
https://www.readbyqxmd.com/read/29240875/the-expanding-roles-of-argonautes-rna-interference-splicing-and-beyond
#2
Xiaoxia Ma, Ziwei Zuo, Weishan Shao, Yongfeng Jin, Yijun Meng
Argonaute (AGO) protein family is highly conserved in eukaryotes and prokaryotes, reflecting its evolutionarily indispensible role in maintaining normal life cycle of the organisms. Small RNA-guided, AGO-dependent RNA interference (RNAi) is a well-studied pathway for gene expression regulation, which can be performed at transcriptional, posttranscriptional or translational level. In addition to RNAi, growing pieces of evidence point to a novel role of AGOs in pre-mRNA (messenger RNA precursor) splicing in animals...
December 11, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29239917/natural-compounds-as-epigenetic-regulators-of-human-dendritic-cell-mediated-immune-function
#3
Sheefa Mirza, Kanisha Shah, Shanaya Patel, Nayan Jain, Rakesh Rawal
Dendritic cells (DCs) are the most potent professional antigen-presenting cells (APCs) and are poised to capture antigen, migrate to draining lymphoid organs, and postmaturation process. Recent evidences have suggested that tumor microenvironment has an effect on DCs by inactivating various components of the immune system responsible for tumor clearance, eventually leading to tumorigenesis. This inactivation is owed to the epigenetic modifications [ie, microRNA (miRNA)] at the posttranscriptional level, thus regulating the differentiation patterns and functional behavior of DCs...
December 12, 2017: Journal of Immunotherapy
https://www.readbyqxmd.com/read/29236255/identifying-mirna-targets-using-ago-ripseq
#4
Rebecca Petri, Johan Jakobsson
microRNAs (miRNA) are small, noncoding RNAs that bind to messenger RNAs (mRNAs) and regulate their activity. They are, therefore, important posttranscriptional regulators. In recent years it has become clear that miRNAs regulate large genetic networks, rather than single genes, and that one gene can be targeted by several miRNAs. To understand the role of miRNAs in cells or tissues, it is therefore important to analyze the targetome of miRNAs. Here, we present a technique called Argonaute-RNA Immunoprecipitation (AGO-RIP) which takes advantages of the fact that miRNAs and their targets are directly bound by the Argonaute protein family...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29236251/par-clip-for-discovering-target-sites-of-rna-binding-proteins
#5
Aitor Garzia, Pavel Morozov, Marcin Sajek, Cindy Meyer, Thomas Tuschl
RNA-binding proteins (RBPs) establish posttranscriptional gene regulation (PTGR) by coordinating the maturation, editing, transport, stability, and translation of cellular RNAs. A variety of experimental approaches have been developed to characterize the RNAs associated with RBPs in vitro as well as in vivo. Our laboratory developed Photoactivatable-Ribonucleoside-Enhanced Cross-Linking and Immunoprecipitation (PAR-CLIP), which in combination with next-generation sequencing enables the identification of RNA targets of RBPs at a nucleotide-level resolution...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29230533/regulation-of-type-i-collagen-expression-by-microrna-29-following-ionizing-radiation
#6
Hiroyuki Yano, Ryoji Hamanaka, Miki Nakamura-Ota, Juan Juan Zhang, Noritaka Matsuo, Hidekatsu Yoshioka
Radiation-induced fibrosis (RIF) is thought to involve the excessive accumulation of collagen and other extracellular matrix components; previously, we reported that ionizing radiation increased the type I collagen expression and that transforming growth factor (TGF)-β was involved in this increase through activating its downstream mediator, Smad3. A recent study found that microRNAs (miRNAs)-small, noncoding sequences approximately 20 nucleotides long-negatively regulate the gene expression posttranscriptionally, and it has been suggested that miRNAs play essential roles in cellular processes, including fibrosis...
December 11, 2017: Radiation and Environmental Biophysics
https://www.readbyqxmd.com/read/29229679/epigenetic-and-posttranscriptional-regulation-of-cd16-expression-during-human-nk-cell-development
#7
Aaron R Victor, Christoph Weigel, Steven D Scoville, Wing Keung Chan, Kelsey Chatman, Mary M Nemer, Charlene Mao, Karen A Young, Jianying Zhang, Jianhua Yu, Aharon G Freud, Christopher C Oakes, Michael A Caligiuri
The surface receptor FcγRIIIA (CD16a) is encoded by the FCGR3A gene and is acquired by human NK cells during maturation. NK cells bind the Fc portion of IgG via CD16a and execute Ab-dependent cell-mediated cytotoxicity, which is critical for the effectiveness of several antitumor mAb therapies. The role of epigenetic regulatory mechanisms controlling transcriptional and posttranscriptional CD16 expression in NK cells is unknown. In this study, we compared specific patterns of DNA methylation and expression of FCGR3A with FCGR3B, which differ in cell type-specific expression despite displaying nearly identical genomic sequences...
December 11, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/29228327/most-m6a-rna-modifications-in-protein-coding-regions-are-evolutionarily-unconserved-and-likely-nonfunctional
#8
Zhen Liu, Jianzhi Zhang
Methylation of the adenosine base at the nitrogen-6 position (m6A) is the most prevalent internal posttranscriptional modification of mRNAs in many eukaryotes. Despite the rapid progress in the transcriptome-wide mapping of m6As, identification of proteins responsible for writing, reading, and erasing m6As, and elucidation of m6A functions in splicing, RNA stability, translation, and other processes, it is unknown whether most observed m6A modifications are functional. To address this question, we respectively analyze the evolutionary conservation of yeast and human m6As in protein-coding regions...
December 8, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29214079/mir-19a-and-mir-20a-and-tissue-factor-expression-in-activated-human-peripheral-blood-mononuclear-cells
#9
Cristina Balia, Mirella Giordano, Valentina Scalise, Tommaso Neri, Gabriella Fontanini, Fulvio Basolo, Alessandro Celi, Roberto Pedrinelli
Background and Aims: To investigate the behaviour of miR-19a and miR-20a, two microRNAs involved in posttranscriptional modulation of TF expression in peripheral blood mononuclear cells (PBMCs) exposed to high glucose (HG) and lipopolysaccharide (LPS), and to evaluate the involvement of angiotensin II in that process. Methods: TF Procoagulant Activity (PCA, one-stage clotting assay), antigen (Ag, ELISA), and miR-19a and miR-20a levels (specific TaqMan® MicroRNA Assays) were evaluated in PBMCs exposed to high glucose (HG, 50 mM), LPS (100 ng/mL), and Olmesartan (OLM, 10-6 M), an angiotensin II type 1 receptor antagonist...
2017: Thrombosis
https://www.readbyqxmd.com/read/29212285/bancr-a-novel-oncogenic-long-non-coding-rna-in-human-cancers
#10
REVIEW
Yifan Zou, Jianfa Li, Yincong Chen, Huizhong Xiao, Fuyou Zhang, Dan Yu, Kewang Luo
Long non-coding RNAs account for large proportion of non-coding transcripts in human genomes. Though they lack of open reading framework and cannot encode protein, they can control endogenous gene expression though regulating cell life activities. They serve as transcriptional modulator, posttranscriptional processor, chromatin remodeler and splicing regulator during the process of gene modification. Moreover, long non-coding RNAs were regarded as potential tumor markers for cancer diagnosis and prognosis. BANCR was identified as a cancer-promoting long non-coding RNA in melanoma tissues...
November 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/29209619/circulating-micrornas-as-potential-biomarkers-for-veterinary-infectious-diseases
#11
REVIEW
Hao Dong, Qiang Gao, Xiaowei Peng, Yu Sun, Tao Han, Bolin Zhao, Yufu Liu, Chuanbin Wang, Xiaohui Song, Jiajun Wu, Lin Yang
MicroRNAs (miRNAs) are a kind of small non-coding RNA molecules that could regulate multiple biological pathways at posttranscriptional level. Over 2,000 miRNAs have so far been discovered in humans, and many of them are found to be linked to various kinds of diseases. Thus, miRNAs are being considered as clinical diagnostic and therapeutic targets. With the discovery of high stability of circulating miRNAs in various kinds of mammalian body fluids, the potential of circulating miRNAs as diagnostic/prognostic biomarkers of infectious diseases aroused great interest among researchers...
2017: Frontiers in Veterinary Science
https://www.readbyqxmd.com/read/29208745/the-complex-quorum-sensing-circuitry-of-burkholderia-thailandensis-is-both-hierarchically-and-homeostatically-organized
#12
Servane Le Guillouzer, Marie-Christine Groleau, Eric Déziel
The genome of the bacterium Burkholderia thailandensis encodes three complete LuxI/LuxR-type quorum sensing (QS) systems: BtaI1/BtaR1 (QS-1), BtaI2/BtaR2 (QS-2), and BtaI3/BtaR3 (QS-3). The LuxR-type transcriptional regulators BtaR1, BtaR2, and BtaR3 modulate the expression of target genes in association with various N-acyl-l-homoserine lactones (AHLs) as signaling molecules produced by the LuxI-type synthases BtaI1, BtaI2, and BtaI3. We have systematically dissected the complex QS circuitry of B. thailandensis strain E264...
December 5, 2017: MBio
https://www.readbyqxmd.com/read/29203677/dynamics-of-translation-can-determine-the-spatial-organization-of-membrane-bound-proteins-and-their-mrna
#13
Elgin Korkmazhan, Hamid Teimouri, Neil Peterman, Erel Levine
Unlike most macromolecules that are homogeneously distributed in the bacterial cell, mRNAs that encode inner-membrane proteins can be concentrated near the inner membrane. Cotranslational insertion of the nascent peptide into the membrane brings the translating ribosome and the mRNA close to the membrane. This suggests that kinetic properties of translation can determine the spatial organization of these mRNAs and proteins, which can be modulated through posttranscriptional regulation. Here we use a simple stochastic model of translation to characterize the effect of mRNA properties on the dynamics and statistics of its spatial distribution...
December 4, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29198340/emerging-roles-for-long-noncoding-rnas-in-b-cell-development-and-malignancy
#14
REVIEW
M Winkle, J L Kluiver, A Diepstra, A van den Berg
Long noncoding (lnc)RNAs have emerged as essential mediators of cellular biology, differentiation and malignant transformation. LncRNAs have a broad range of possible functions at the transcriptional, posttranscriptional and protein level and their aberrant expression significantly contributes to the hallmarks of cancer cell biology. In addition, their high tissue- and cell-type specificity makes lncRNAs especially interesting as biomarkers, prognostic factors or specific therapeutic targets. Here, we review current knowledge on lncRNA expression changes during normal B-cell development, indicating essential functions in the differentiation process...
December 2017: Critical Reviews in Oncology/hematology
https://www.readbyqxmd.com/read/29197992/identification-of-reference-genes-for-analysis-of-microrna-expression-patterns-in-equine-chorioallantoic-membrane-and-serum
#15
Pouya Dini, Shavahn C Loux, Kirsten E Scoggin, Alejandro Esteller-Vico, Edward L Squires, Mats H T Troedsson, Peter Daels, Barry A Ball
MicroRNAs (miRNAs) have important posttranscriptional regulatory abilities, and there is considerable interest in evaluating their expression patterns in different pathophysiological states. The most common method of quantifying miRNA expression is quantitative reverse transcription PCR; however, the identification of tissue-specific and species-specific reference miRNA is a prerequisite for miRNA expression analysis. Currently, no reference genes have been described for evaluating miRNA expression in equine serum and chorioallantoic membrane (CAM) during pregnancy...
December 2, 2017: Molecular Biotechnology
https://www.readbyqxmd.com/read/29196461/mirna-suppression-of-a-notch-repressor-directs-non-neuronal-fate-in-drosophila-mechanosensory-organs
#16
Joshua Kavaler, Hong Duan, Rajaguru Aradhya, Luis F de Navas, Brian Joseph, Boris Shklyar, Eric C Lai
Although there is abundant evidence that individual microRNA (miRNA) loci repress large cohorts of targets, large-scale knockout studies suggest that most miRNAs are phenotypically dispensable. Here, we identify a rare case of developmental cell specification that is highly dependent on miRNA control of an individual target. We observe that binary cell fate choice in the Drosophila melanogaster peripheral sensory organ lineage is controlled by the non-neuronally expressed mir-279/996 cluster, with a majority of notum sensory organs exhibiting transformation of sheath cells into ectopic neurons...
December 1, 2017: Journal of Cell Biology
https://www.readbyqxmd.com/read/29190554/a-potential-microrna-regulation-of-immune-related-genes-in-invertebrate-haemocytes
#17
REVIEW
Mario Alberto Burgos-Aceves, Amit Cohen, Yoav Smith, Caterina Faggio
Bivalve mollusks have been employed as sentinel organisms in environmental health programs due to their sedentary lifestyle, filter-feeding behavior and their ability to accumulate pathogens or toxin molecules inside tissues. Endocrine disrupting chemicals (EDCs) can be up taken and bioaccumulated, and due to sensibility of mollusks to these EDCs, being able to cause immune alterations. Recently, microRNAs (miRNAs) were shown to be involved in modulation and buffering developmental processes against the effects of environmental alterations and pathogenic microorganisms...
November 27, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29185492/interaction-profiling-of-rna-binding-ubiquitin-ligases-reveals-a-link-between-posttranscriptional-regulation-and-the-ubiquitin-system
#18
Andrea Hildebrandt, Gregorio Alanis-Lobato, Andrea Voigt, Kathi Zarnack, Miguel A Andrade-Navarro, Petra Beli, Julian König
RNA-binding ubiquitin ligases (RBULs) have the potential to link RNA-mediated mechanisms to protein ubiquitylation. Despite this, the cellular functions, substrates and interaction partners of most RBULs remain poorly characterized. Affinity purification (AP) combined with quantitative mass spectrometry (MS)-based proteomics is a powerful approach for analyzing protein functions. Mapping the physiological interaction partners of RNA-binding proteins has been hampered by their intrinsic properties, in particular the existence of low-complexity regions, which are prone to engage in non-physiological interactions...
November 29, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29183708/posttranscriptional-regulation-of-lipid-metabolism-by-non-coding-rnas-and-rna-binding-proteins
#19
REVIEW
Abhishek K Singh, Binod Aryal, Xinbo Zhang, Yuhua Fan, Nathan Price, Yajaira Suárez, Carlos Fernández-Hernando
Alterations in lipoprotein metabolism enhance the risk of cardiometabolic disorders including type-2 diabetes and atherosclerosis, the leading cause of death in Western societies. While the transcriptional regulation of lipid metabolism has been well characterized, recent studies have uncovered the importance of microRNAs (miRNAs), long-non-coding RNAs (lncRNAs) and RNA binding proteins (RBP) in regulating the expression of lipid-related genes at the posttranscriptional level. Work from several groups has identified a number of miRNAs, including miR-33, miR-122 and miR-148a, that play a prominent role in controlling cholesterol homeostasis and lipoprotein metabolism...
November 25, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/29182547/gene-silencing-of-argonaute5-negatively-affects-the-establishment-of-the-legume-rhizobia-symbiosis
#20
María Del Rocio Reyero-Saavedra, Zhenzhen Qiao, María Del Socorro Sánchez-Correa, M Enrique Díaz-Pineda, Jose L Reyes, Alejandra A Covarrubias, Marc Libault, Oswaldo Valdés-López
The establishment of the symbiosis between legumes and nitrogen-fixing rhizobia is finely regulated at the transcriptional, posttranscriptional and posttranslational levels. Argonaute5 (AGO5), a protein involved in RNA silencing, can bind both viral RNAs and microRNAs to control plant-microbe interactions and plant physiology. For instance, AGO5 regulates the systemic resistance of Arabidopsis against Potato Virus X as well as the pigmentation of soybean (Glycine max) seeds. Here, we show that AGO5 is also playing a central role in legume nodulation based on its preferential expression in common bean (Phaseolus vulgaris) and soybean roots and nodules...
November 28, 2017: Genes
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