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Posttranscriptional modification

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https://www.readbyqxmd.com/read/28280365/downregulation-of-long-noncoding-rna-hotairm1-promotes-monocyte-dendritic-cell-differentiation-through-competitively-binding-to-endogenous-mir-3960
#1
Jiaxuan Xin, Jing Li, Yue Feng, Liyang Wang, Yuan Zhang, Rongcun Yang
Myeloid differentiation is controlled by a multilayered regulatory circuitry consisting of various elements, including histone modifications, transcription factors, and posttranscriptional regulators such as miRNAs, long noncoding RNAs, and circular RNAs. However, the molecular mechanism underlying this biological process remains unclear. In this study, through epigenetic profiling analysis using chromatin immunoprecipitation (ChIP) followed by sequencing (ChIP-seq), we identified an lncRNA, HOTAIRM1, with a critical role in myeloid development...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28278381/alternative-splicing-of-stat3-is-affected-by-rna-editing
#2
Lior Goldberg, Mor Abutbul-Amitai, Gideon Paret, Yael Nevo-Caspi
A-to-I RNA editing, carried out by adenosine deaminase acting on RNA (ADAR) enzymes, is an epigenetic phenomenon of posttranscriptional modifications on pre-mRNA. RNA editing in intronic sequences may influence alternative splicing of flanking exons. We have previously shown that conditions that induce editing result in elevated expression of signal transducer and activator of transcription 3 (STAT3), preferentially the alternatively-spliced STAT3β isoform. Mechanisms regulating alternative splicing of STAT3 have not been elucidated...
March 9, 2017: DNA and Cell Biology
https://www.readbyqxmd.com/read/28277930/wobble-uridine-modifications-a-reason-to-live-a-reason-to-die
#3
Raffael Schaffrath, Sebastian A Leidel
Wobble uridines (U34) are generally modified in all species. U34 modifications can be essential in metazoans but are not required for viability in fungi. In this review, we provide an overview on the types of modifications and how they affect the physico-chemical properties of wobble uridines. We describe the molecular machinery required to introduce these modifications into tRNA posttranscriptionally and discuss how posttranslational regulation may affect the activity of the modifying enzymes. We highlight the activity of anticodon specific RNases that target U34 containing tRNA...
February 23, 2017: RNA Biology
https://www.readbyqxmd.com/read/28263563/alkyne-functionalized-coumarin-compound-for-analytic-and-preparative-4-thiouridine-labeling
#4
Katharina Schmid, Maria Adobes-Vidal, Mark Helm
Bioconjugation of RNA is a dynamic field recently reinvigorated by a surge in research on posttranscriptional modification. This work focusses on the bioconjugation of 4-thiouridine, a nucleoside that occurs as a post-transcriptional modification in bacterial RNA, and is used as a metabolic label and for crosslinking purposes in eukaryotic RNA. A newly designed coumarin compound, named 7-propargyloxy-4-bromomethylcoumarin (PBC) is introduced, which exhibits remarkable selectivity for 4-thiouridine. Bearing a terminal alkyne group, it is conductive to secondary bioconjugation via "click chemistry", thereby offering a wide range of preparative and analytical options...
March 6, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28247053/cell-fate-maintenance-and-reprogramming-during-the-oocyte-to-embryo-transition
#5
Christina Fassnacht, Rafal Ciosk
This chapter reviews our current understanding of the mechanisms that regulate reprogramming during the oocyte-to-embryo transition (OET). There are two major events reshaping the transcriptome during OET. One is the clearance of maternal transcripts in the early embryo, extensively reviewed by others. The other event, which is the focus of this chapter, is the embryonic (or zygotic) genome activation (EGA). The mechanisms controlling EGA can be broadly divided into transcriptional and posttranscriptional. The former includes the regulation of the basal transcription machinery, the regulation by specific transcription factors and chromatin modifications...
2017: Results and Problems in Cell Differentiation
https://www.readbyqxmd.com/read/28202819/-melas-mitochondrial-encephalomyopathy-lactic-acidosis-and-stroke-like-episodes
#6
Hidetomo Murakami, Kenjiro Ono
Mitochondrial disease is caused by a deficiency in the energy supply to cells due to mitochondrial dysfunction. Mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes (MELAS) is a mitochondrial disease that presents with stroke-like episodes such as acute onset of neurological deficits and characteristic imaging findings. Stroke-like episodes in MELAS have the following features: 1) neurological deficits due to localization of lesions in the brain, 2) episodes often accompany epilepsy, 3) lesions do not follow the vascular supply area, 4) lesions are more often seen in the posterior brain than in the anterior brain, 5) lesions spread to an adjacent area in the brain, and 6) neurological symptoms often disappear together with imaging findings, but later relapse...
February 2017: Brain and Nerve, Shinkei Kenkyū No Shinpo
https://www.readbyqxmd.com/read/28149289/pore-forming-proteins-as-mediators-of-novel-epigenetic-mechanism-of-epilepsy
#7
Andrei Surguchov, Irina Surgucheva, Mukut Sharma, Ram Sharma, Vikas Singh
Epilepsy is a disorder of the brain characterized by an enduring predisposition to generate epileptic seizures. In the last two decades, numerous gene defects underlying different forms of epilepsy have been identified with most of these genes encoding ion channel proteins. Despite these developments, the etiology of majority of non-familial epilepsies has no known associated genetic mutations and cannot be explained by defects in identified ion channels alone. We hypothesize that de novo formation of ion channels by naturally unfolded proteins (NUPs) increases neuronal excitability...
2017: Frontiers in Neurology
https://www.readbyqxmd.com/read/28109165/melatonin-and-sirtuins-a-not-so-unexpected-relationship
#8
REVIEW
Juan C Mayo, Rosa M Sainz, Pedro González Menéndez, Vanesa Cepas, Dun-Xian Tan, Russel J Reiter
Epigenetic modifications, including methylation or acetylation as well as post-transcriptional modifications, are mechanisms used by eukaryotic cells to increase the genome diversity in terms of differential gene expression and protein diversity. Among these modifying enzymes, sirtuins, a class III histone deacetylase (HDAC) enzymes, are of particular importance. Sirtuins regulate the cell cycle, DNA repair, cell survival, and apoptosis, thus having important roles in normal and cancer cells. Sirtuins can also regulate metabolic pathways by changing preference for glycolysis under aerobic conditions as well as glutaminolysis...
January 21, 2017: Journal of Pineal Research
https://www.readbyqxmd.com/read/28077169/distinct-5-methylcytosine-profiles-in-poly-a-rna-from-mouse-embryonic-stem-cells-and-brain
#9
Thomas Amort, Dietmar Rieder, Alexandra Wille, Daria Khokhlova-Cubberley, Christian Riml, Lukas Trixl, Xi-Yu Jia, Ronald Micura, Alexandra Lusser
BACKGROUND: Recent work has identified and mapped a range of posttranscriptional modifications in mRNA, including methylation of the N6 and N1 positions in adenine, pseudouridylation, and methylation of carbon 5 in cytosine (m5C). However, knowledge about the prevalence and transcriptome-wide distribution of m5C is still extremely limited; thus, studies in different cell types, tissues, and organisms are needed to gain insight into possible functions of this modification and implications for other regulatory processes...
January 5, 2017: Genome Biology
https://www.readbyqxmd.com/read/28013306/inhibition-of-rac1-signaling-downregulates-inflammasome-activation-and-attenuates-lung-injury-in-neonatal-rats-exposed-to-hyperoxia
#10
Julia K Hummler, Fredrick Dapaah-Siakwan, Ruben Vaidya, Ronald Zambrano, Siwei Luo, Shaoyi Chen, Nadine Kerr, Juan Pablo de Rivero Vaccari, Robert W Keane, W Dalton Dietrich, Eduardo Bancalari, Karen C Young, Shu Wu
BACKGROUND: Inflammatory injury, particularly the production of active interleukin (IL)-1β plays a major role in the pathogenesis of bronchopulmonary dysplasia (BPD) in preterm infants. The release of active IL-1β is controlled by posttranscriptional modifications of its proform (pro-IL-1β) through the inflammasome. Rac1 is a member of the Rho family of GTPases that regulate the inflammatory process. OBJECTIVE: This study tested the hypothesis that Rac1 signaling increases inflammasome activation that results in damaging inflammation, and that the inhibition of Rac1 signaling prevents lung injury, by inhibiting inflammasome activation in a newborn rat model of BPD induced by hyperoxia...
2017: Neonatology
https://www.readbyqxmd.com/read/27998975/the-major-protein-arginine-methyltransferase-in-trypanosoma-brucei-functions-as-an-enzyme-prozyme-complex
#11
Lucie Kafková, Erik W Debler, John C Fisk, Kanishk Jain, Steven G Clarke, Laurie K Read
Prozymes are catalytically inactive enzyme paralogs that dramatically stimulate the function of weakly active enzymes through complex formation. The two prozymes described to date reside in the polyamine biosynthesis pathway of the human parasite Trypanosoma brucei, an early branching eukaryote that lacks transcriptional regulation and regulates its proteome through posttranscriptional and posttranslational means. Arginine methylation is a common posttranslational modification in eukaryotes catalyzed by protein arginine methyltransferases (PRMTs) that are typically thought to function as homodimers...
February 10, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27903241/abundant-rna-editing-sites-of-chloroplast-protein-coding-genes-in-ginkgo-biloba-and-an-evolutionary-pattern-analysis
#12
Peng He, Sheng Huang, Guanghui Xiao, Yuzhou Zhang, Jianing Yu
BACKGROUND: RNA editing is a posttranscriptional modification process that alters the RNA sequence so that it deviates from the genomic DNA sequence. RNA editing mainly occurs in chloroplasts and mitochondrial genomes, and the number of editing sites varies in terrestrial plants. Why and how RNA editing systems evolved remains a mystery. Ginkgo biloba is one of the oldest seed plants and has an important evolutionary position. Determining the patterns and distribution of RNA editing in the ancient plant provides insights into the evolutionary trend of RNA editing, and helping us to further understand their biological significance...
December 1, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/27878160/chemo-enzymatic-modification-of-eukaryotic-mrna
#13
Fabian Muttach, Nils Muthmann, Andrea Rentmeister
Messenger RNA may not be very abundant in the cell but its central role in gene expression is indisputable. In addition to being the template for translation it can be subject for a variety of regulatory mechanisms affecting gene expression, ranging from simple structural changes to modifications and active transport. To elucidate and potentially control the underlying changes in vitro and in cells, site-specific modification and labeling strategies are required. In this perspective, we introduce chemo-enzymatic concepts for posttranscriptional modification focusing on eukaryotic mRNAs...
November 23, 2016: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/27834201/identification-of-ybey-protein-interactions-involved-in-16s-rrna-maturation-and-stress-regulation-in-escherichia-coli
#14
Maarten Vercruysse, Caroline Köhrer, Yang Shen, Sandra Proulx, Anubrata Ghosal, Bryan W Davies, Uttam L RajBhandary, Graham C Walker
YbeY is part of a core set of RNases in Escherichia coli and other bacteria. This highly conserved endoribonuclease has been implicated in several important processes such as 16S rRNA 3' end maturation, 70S ribosome quality control, and regulation of mRNAs and small noncoding RNAs, thereby affecting cellular viability, stress tolerance, and pathogenic and symbiotic behavior of bacteria. Thus, YbeY likely interacts with numerous protein or RNA partners that are involved in various aspects of cellular physiology...
November 8, 2016: MBio
https://www.readbyqxmd.com/read/27826833/dna-and-rna-pyrimidine-nucleobase-alkylation-at-the-carbon-5-position
#15
Yuri Motorin, Salifu Seidu-Larry, Mark Helm
The carbon 5 of pyrimidine nucleobases is a privileged position in terms of nucleoside modification in both DNA and RNA. The simplest modification of uridine at this position is methylation leading to thymine. Thymine is an integral part of the standard nucleobase repertoire of DNA that is synthesized at the nucleotide level. However, it also occurs in RNA, where it is synthesized posttranscriptionally at the polynucleotide level. The cytidine analogue 5-methylcytidine also occurs in both DNA and RNA, but is introduced at the polynucleotide level in both cases...
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27811057/elp3-links-trna-modification-to-ires-dependent-translation-of-lef1-to-sustain-metastasis-in-breast-cancer
#16
Sylvain Delaunay, Francesca Rapino, Lars Tharun, Zhaoli Zhou, Lukas Heukamp, Martin Termathe, Kateryna Shostak, Iva Klevernic, Alexandra Florin, Hadrien Desmecht, Christophe J Desmet, Laurent Nguyen, Sebastian A Leidel, Anne E Willis, Reinhard Büttner, Alain Chariot, Pierre Close
Quantitative and qualitative changes in mRNA translation occur in tumor cells and support cancer progression and metastasis. Posttranscriptional modifications of transfer RNAs (tRNAs) at the wobble uridine 34 (U34) base are highly conserved and contribute to translation fidelity. Here, we show that ELP3 and CTU1/2, partner enzymes in U34 mcm(5)s(2)-tRNA modification, are up-regulated in human breast cancers and sustain metastasis. Elp3 genetic ablation strongly impaired invasion and metastasis formation in the PyMT model of invasive breast cancer...
October 17, 2016: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/27800139/the-effect-of-microrna-375-overexpression-an-inhibitor-of-helicobacter-pylori-induced-carcinogenesis-on-lncrna-sox2ot
#17
Mohammad Shafiee, Seyed Ahmad Aleyasin, Seyed Javad Mowla, Mohammad Vasei, Seyed Amir Yazdanparast
BACKGROUND: Helicobacter pylori is a major human pathogenic bacterium in gastric mucosa. Although the association between gastric cancer and H. pylori has been well-established, the molecular mechanisms underlying H. pylori-induced carcinogenesis are still under investigation. MicroRNAs (miRNAs) are small noncoding RNAs that modulate gene expression at the posttranscriptional level. Recently, studies have revealed that miRNAs are involved in immune response and host cell response to bacteria...
September 2016: Jundishapur Journal of Microbiology
https://www.readbyqxmd.com/read/27777593/genetic-and-epigenetic-studies-of-atopic-dermatitis
#18
REVIEW
Lianghua Bin, Donald Y M Leung
BACKGROUND: Atopic dermatitis (AD) is a chronic inflammatory disease caused by the complex interaction of genetic, immune and environmental factors. There have many recent discoveries involving the genetic and epigenetic studies of AD. METHODS: A retrospective PubMed search was carried out from June 2009 to June 2016 using the terms "atopic dermatitis", "association", "eczema", "gene", "polymorphism", "mutation", "variant", "genome wide association study", "microarray" "gene profiling", "RNA sequencing", "epigenetics" and "microRNA"...
2016: Allergy, Asthma, and Clinical Immunology
https://www.readbyqxmd.com/read/27770365/stem-loop-qrt-pcr-for-the-detection-of-plant-micrornas
#19
Erika Varkonyi-Gasic
Plant microRNAs (miRNAs) play important roles in the posttranscriptional regulation of protein-coding genes, and they are essential for a normal development and survival. Mature miRNAs are cleaved from larger precursor RNAs and are typically 21-22 nt long.The small size, the lack of a common feature like a poly(A) tail, 3' end-modifications, and presence of a precursor-all these factors affect the detection and hinder the quantification of miRNAs. The stem-loop qRT-PCR method described here is designed to detect and quantify mature miRNAs in a fast, specific, accurate, and reliable manner...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27734409/regulation-of-il-6-in-immunity-and-diseases
#20
Toshio Tanaka, Masashi Narazaki, Kazuya Masuda, Tadamitsu Kishimoto
Interleukin-6 (IL-6) is a prototypical cytokine with functional pleiotropy and plays an important role in host defense. When infections or tissue injuries occur, IL-6 is promptly produced by monocytes and macrophages and contributes to removal of infectious agents and restoration of damaged tissues through activation of immune, hematological, and acute-phase responses. Once stress is removed from the host, IL-6 synthesis ends, but uncontrolled excessive or persistent IL-6 production plays a pathological role in the development of various inflammatory diseases and cancers, indicating that IL-6 is a double-edged sword for the host...
2016: Advances in Experimental Medicine and Biology
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