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RNA methylation

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https://www.readbyqxmd.com/read/28335720/widespread-promoter-methylation-of-synaptic-plasticity-genes-in-long-term-potentiation-in-the-adult-brain-in-vivo
#1
Jesper L V Maag, Dominik C Kaczorowski, Debabrata Panja, Timothy J Peters, Clive R Bramham, Karin Wibrand, Marcel E Dinger
BACKGROUND: DNA methylation is a key modulator of gene expression in mammalian development and cellular differentiation, including neurons. To date, the role of DNA modifications in long-term potentiation (LTP) has not been explored. RESULTS: To investigate the occurrence of DNA methylation changes in LTP, we undertook the first detailed study to describe the methylation status of all known LTP-associated genes during LTP induction in the dentate gyrus of live rats...
March 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28335556/trm5-and-trmd-two-enzymes-from-distinct-origins-catalyze-the-identical-trna-modification-m%C3%A2-g37
#2
REVIEW
Sakurako Goto-Ito, Takuhiro Ito, Shigeyuki Yokoyama
The N¹-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. The resultant modified nucleotide m¹G37 positively regulates the aminoacylation of the tRNA, and simultaneously functions to prevent the +1 frameshift on the ribosome. Interestingly, Trm5 and TrmD have completely distinct origins, and therefore bear different tertiary folds. In this review, we describe the different strategies utilized by Trm5 and TrmD to recognize their substrate tRNAs, mainly based on their crystal structures complexed with substrate tRNAs...
March 21, 2017: Biomolecules
https://www.readbyqxmd.com/read/28334903/n6-methyladenosine-alters-rna-structure-to-regulate-binding-of-a-low-complexity-protein
#3
Nian Liu, Katherine I Zhou, Marc Parisien, Qing Dai, Luda Diatchenko, Tao Pan
N6-methyladenosine (m6A) is the most abundant internal modification in eukaryotic messenger RNA (mRNA), and affects almost every stage of the mRNA life cycle. The YTH-domain proteins can specifically recognize m6A modification to control mRNA maturation, translation and decay. m6A can also alter RNA structures to affect RNA-protein interactions in cells. Here, we show that m6A increases the accessibility of its surrounding RNA sequence to bind heterogeneous nuclear ribonucleoprotein G (HNRNPG). Furthermore, HNRNPG binds m6A-methylated RNAs through its C-terminal low-complexity region, which self-assembles into large particles in vitro...
February 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334849/icf-specific-dnmt3b-dysfunction-interferes-with-intragenic-regulation-of-mrna-transcription-and-alternative-splicing
#4
Sole Gatto, Miriam Gagliardi, Monica Franzese, Sylwia Leppert, Mariarosaria Papa, Marco Cammisa, Giacomo Grillo, Guillame Velasco, Claire Francastel, Shir Toubiana, Maurizio D'Esposito, Claudia Angelini, Maria R Matarazzo
Hypomorphic mutations in DNA-methyltransferase DNMT3B cause majority of the rare disorder Immunodeficiency, Centromere instability and Facial anomalies syndrome cases (ICF1). By unspecified mechanisms, mutant-DNMT3B interferes with lymphoid-specific pathways resulting in immune response defects. Interestingly, recent findings report that DNMT3B shapes intragenic CpG-methylation of highly-transcribed genes. However, how the DNMT3B-dependent epigenetic network modulates transcription and whether ICF1-specific mutations impair this process remains unknown...
March 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28333151/fto-is-required-for-myogenesis-by-positively-regulating-mtor-pgc-1%C3%AE-pathway-mediated-mitochondria-biogenesis
#5
Xiaobo Wang, Ning Huang, Min Yang, Dandan Wei, Haoran Tai, Xiaojuan Han, Hui Gong, Jiao Zhou, Jianqiong Qin, Xiawei Wei, Honghan Chen, Tingting Fang, Hengyi Xiao
Global germ line loss of fat mass- and obesity-associated (FTO) gene results in both the reduction of fat mass and lean mass in mice. The role of FTO in adipogenesis has been proposed, however, that in myogenesis has not. Skeletal muscle is the main component of body lean mass, so its connection with FTO physiologic significance need to be clarified. Here, we assessed the impact of FTO on murine skeletal muscle differentiation by in vitro and in vivo experiments. We found that FTO expression increased during myoblasts differentiation, while the silence of FTO inhibited the differentiation; in addition, skeletal muscle development was impaired in skeletal muscle FTO-deficient mice...
March 23, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28332701/the-epigenetic-landscape-related-to-reactive-oxygen-species-formation-in-the-cardiovascular-system
#6
REVIEW
Thomas Kietzmann, Andreas Petry, Antonina Shvetsova, Joachim M Gerhold, Agnes Görlach
Cardiovascular diseases are the leading cause of death worldwide. Reactive oxygen species (ROS) can act as damaging molecules but also represent central hubs in cellular signalling networks. Increasing evidence indicates that ROS play an important role in the pathogenesis of cardiovascular diseases, although the underlying mechanisms and consequences of pathophysiological elevated ROS in the cardiovascular system are still not completely resolved. More recently, alterations of the epigenetic landscape which can affect DNA methylation, post-translational histone modifications, ATP-dependent alterations to chromatin and non-coding RNA transcripts, have been considered to be of increasing importance in the pathogenesis of cardiovascular diseases...
March 23, 2017: British Journal of Pharmacology
https://www.readbyqxmd.com/read/28331435/methylated-dna-rna-in-body-fluids-as-biomarkers-for-lung-cancer
#7
REVIEW
Yan Lu, Shulin/Sl Li, Shiguo/Sg Zhu, Yabin/Yb Gong, Jun/J Shi, Ling/L Xu
DNA/RNA methylation plays an important role in lung cancer initiation and progression. Liquid biopsy makes use of cells, nucleotides and proteins released from tumor cells into body fluids to help with cancer diagnosis and prognosis. Methylation of circulating tumor DNA (ctDNA) has gained increasing attention as biomarkers for lung cancer. Here we briefly introduce the biological basis and detection method of ctDNA methylation, and review various applications of methylated DNA in body fluids in lung cancer screening, diagnosis, prognosis, monitoring and treatment prediction...
2017: Biological Procedures Online
https://www.readbyqxmd.com/read/28331197/efficient-generation-of-dirnas-requires-components-in-the-posttranscriptional-gene-silencing-pathway
#8
Daisuke Miki, Peiying Zhu, Wencan Zhang, Yanfei Mao, Zhengyan Feng, Huan Huang, Hui Zhang, Yanqiang Li, Renyi Liu, Huiming Zhang, Yijun Qi, Jian-Kang Zhu
It has been reported that double-stranded break (DSB)-induced small RNAs (diRNAs) are generated via the RNA-directed DNA methylation pathway and function in DSB repair in Arabidposis. However, important questions remain regarding the biogenesis and function of diRNAs. Here, we used CRISPR/Cas9- or TALEN-triggered DSBs to characterize diRNAs in Arabidopsis and rice. We found that 21-nt diRNAs were generated from a 35S promoter::GU-US reporter transgene targeted by CRISPR/Cas9. Unexpectedly, Pol II transcription of the transgene was required for efficient diRNA production and the level of diRNA accumulation correlated with the expression level of the transgene...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28322784/flaviviridae-viruses-use-a-common-molecular-mechanism-to-escape-nucleoside-analogue-inhibitors
#9
James J Valdés, Philip T Butterill, Daniel Růžek
The RNA-dependent RNA polymerases of Flaviviridae viruses are crucial for replication. The Flaviviridae polymerase is organized into structural motifs (A-G), with motifs F, A, C and E containing interrogating, priming and catalytic substrate-interacting sites. Modified nucleoside analogues act as antiviral drugs by targeting Flaviviridae polymerases and integrating into the synthesized product causing premature termination. A threonine mutation of a conserved serine residue in motif B of Flaviviridae polymerases renders resistance to 2'-C-methylated nucleoside analogues...
March 17, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28320778/the-epitranscriptome-of-noncoding-rnas-in-cancer
#10
REVIEW
Manel Esteller, Pier Paolo Pandolfi
The activity of RNA is controlled by different types of post-transcriptional modifications, such as the addition of methyl groups and other chemical and structural changes, that have been recently described in human cells by high-throughput sequencing. Herein, we will discuss how the so-called epitranscriptome is disrupted in cancer and what the contribution of its writers, readers, and erasers to the process of cellular transformation is, particularly focusing on the epigenetic modifications of ncRNAs.Significance: Chemical modifications of RNA play a central role in the control of messenger and ncRNA activity and, thus, are tightly regulated in cells...
March 20, 2017: Cancer Discovery
https://www.readbyqxmd.com/read/28320505/fine-tuning-of-gene-expression-dynamics-by-the-set2-rpd3s-pathway
#11
Bo Bae Lee, Ji Hyun Kim, TaeSoo Kim
RNA polymerase II-interacting the Set2 methyltransferase co-transcriptionally methylates histone H3 at lysine 36 within the body of genes. This modification facilitates histone deacetylation by Rpd3S HDAC in 3' transcribed regions to suppress cryptic initiation and slow elongation. Although this pathway is important for global deacetylation, no strong effects on genome-wide transcription have been seen under optimized laboratory conditions. In contrast, this pathway slows the kinetics of mRNA induction when target genes are induced upon environmental changes...
March 21, 2017: BMB Reports
https://www.readbyqxmd.com/read/28320442/analysis-of-monocyte-infiltration-in-mptp-mice-reveals-that-microglial-cx3cr1-protects-against-neurotoxic-over-induction-of-monocyte-attracting-ccl2-by-astrocytes
#12
Vincent R Parillaud, Guillaume Lornet, Yann Monnet, Anne-Laure Privat, Andrei T Haddad, Vanessa Brochard, Amaury Bekaert, Camille Baudesson de Chanville, Etienne C Hirsch, Christophe Combadière, Stéphane Hunot, Christian S Lobsiger
BACKGROUND: Evidence from mice suggests that brain infiltrating immune cells contribute to neurodegeneration, and we previously identified a deleterious lymphocyte infiltration in Parkinson's disease mice. However, this remains controversial for monocytes, due to artifact-prone techniques used to distinguish them from microglia. Our aim was to reassess this open question, by taking advantage of the recent recognition that chemokine receptors CCR2 and CX3CR1 can differentiate between inflammatory monocytes and microglia, enabling to test whether CCR2(+) monocytes infiltrate the brain during dopaminergic (DA) neurodegeneration and whether they contribute to neuronal death...
March 21, 2017: Journal of Neuroinflammation
https://www.readbyqxmd.com/read/28318165/-effects-of-rhoa-silencing-on-proliferation-of-tongue-squamous-cancer-cells
#13
Yan Guoxin, Fan Bing, Zou Ronghai, Zhang Jian, Sun Xiaofeng, Tong Lei, Wang Qimin, Han Jinhong, Lu Xufei, Wang Ying, Zhou Yuan, He Zongxuan, Liao Yixiang, Li Ning, Cao Lei, Chen Zhenggang
OBJECTIVE: This study investigated the effect of RhoA silencing through RNA interference on proliferation and growth of tongue cancer cells, as well as explored the possible mechanisms of this effect. METHODS: SSC-4 tongue cancer cells were cultured in vitro and then transfected with small interfering RNA to knock down RhoA expression. The tested cells were divided into three groups: experimental group (experimental group 1: transfected with RhoA-siRNA-1; experi-mental group 2: transfected with RhoA-siRNA-2), negative control group (transfected by random sequence NC-siRNA), and blank control group (transfected with Lipofectamine)...
December 1, 2016: Hua Xi Kou Qiang Yi Xue za Zhi, Huaxi Kouqiang Yixue Zazhi, West China Journal of Stomatology
https://www.readbyqxmd.com/read/28317076/an-experimental-tool-to-estimate-the-probability-of-a-nucleotide-presence-in-the-crystal-structures-of-the-nucleotide-protein-complexes
#14
Maria Nemchinova, Vitaly Balobanov, Ekaterina Nikonova, Natalia Lekontseva, Alisa Mikhaylina, Svetlana Tishchenko, Alexey Nikulin
A correlation between the ligand-protein affinity and the identification of the ligand in the experimental electron density maps obtained by X-ray crystallography has been tested for a number of RNA-binding proteins. Bacterial translation regulators ProQ, TRAP, Rop, and Hfq together with their archaeal homologues SmAP have been used. The equilibrium dissociation constants for the N-methyl-anthraniloyl-labelled adenosine and guanosine monophosphates titrated by the proteins have been determined by the fluorescent anisotropy measurements...
March 20, 2017: Protein Journal
https://www.readbyqxmd.com/read/28314689/dna-methylation-based-classification-and-grading-system-for-meningioma-a-multicentre-retrospective-analysis
#15
Felix Sahm, Daniel Schrimpf, Damian Stichel, David T W Jones, Thomas Hielscher, Sebastian Schefzyk, Konstantin Okonechnikov, Christian Koelsche, David E Reuss, David Capper, Dominik Sturm, Hans-Georg Wirsching, Anna Sophie Berghoff, Peter Baumgarten, Annekathrin Kratz, Kristin Huang, Annika K Wefers, Volker Hovestadt, Martin Sill, Hayley P Ellis, Kathreena M Kurian, Ali Fuat Okuducu, Christine Jungk, Katharina Drueschler, Matthias Schick, Melanie Bewerunge-Hudler, Christian Mawrin, Marcel Seiz-Rosenhagen, Ralf Ketter, Matthias Simon, Manfred Westphal, Katrin Lamszus, Albert Becker, Arend Koch, Jens Schittenhelm, Elisabeth J Rushing, V Peter Collins, Stefanie Brehmer, Lukas Chavez, Michael Platten, Daniel Hänggi, Andreas Unterberg, Werner Paulus, Wolfgang Wick, Stefan M Pfister, Michel Mittelbronn, Matthias Preusser, Christel Herold-Mende, Michael Weller, Andreas von Deimling
BACKGROUND: The WHO classification of brain tumours describes 15 subtypes of meningioma. Nine of these subtypes are allotted to WHO grade I, and three each to grade II and grade III. Grading is based solely on histology, with an absence of molecular markers. Although the existing classification and grading approach is of prognostic value, it harbours shortcomings such as ill-defined parameters for subtypes and grading criteria prone to arbitrary judgment. In this study, we aimed for a comprehensive characterisation of the entire molecular genetic landscape of meningioma to identify biologically and clinically relevant subgroups...
March 14, 2017: Lancet Oncology
https://www.readbyqxmd.com/read/28303387/caveolar-remodeling-is-a-critical-mechanotransduction-mechanism-of-the-stretch-induced-l-type-ca-2-channel-activation-in-vascular-myocytes
#16
Sang Woong Park, Kyung Chul Shin, Hyun Ji Park, Soon-Kyu Yoou, Jin-Yeon Park, Young-Sun Kang, Dong Jun Sung, Jae Gon Kim, Seung Hwa Park, BoKyung Kim, Hana Cho, Young Min Bae
Activation of L-type voltage-dependent Ca(2+) channels (VDCCL) by membrane stretch contributes to many biological responses such as myogenic contraction of arteries. However, mechanism for the stretch-induced VDCCL activation is unclear. In this study, we examined the hypothesis that caveolar remodeling and its related signaling cascade contribute to the stretch-induced activation of VDCCL in rat mesenteric arterial smooth muscle cells. The VDCCL currents were recorded with nystatin-perforated or with conventional whole-cell patch-clamp technique...
March 16, 2017: Pflügers Archiv: European Journal of Physiology
https://www.readbyqxmd.com/read/28301736/epigenetic-regulation-a-new-frontier-for-biomedical-engineers
#17
Zhen Chen, Shuai Li, Shankar Subramaniam, John Y-J Shyy, Shu Chien
Gene expression in mammalian cells depends on the epigenetic status of the chromatin, including DNA methylation, histone modifications, promoter-enhancer interactions, and noncoding RNA-mediated regulation. The coordinated actions of these multifaceted regulations determine cell development, cell cycle regulation, cell state and fate, and the ultimate responses in health and disease. Therefore, studies of epigenetic modulations are critical for our understanding of gene regulation mechanisms at the molecular, cellular, tissue, and organ levels...
March 6, 2017: Annual Review of Biomedical Engineering
https://www.readbyqxmd.com/read/28301256/sperm-epigenetics-in-the-study-of-male-fertility-offspring-health-and-potential-clinical-applications
#18
Timothy G Jenkins, Kenneth I Aston, Emma R James, Douglas T Carrell
The mammalian sperm contains a highly unique and specialized epigenetic landscape that offers a great degree of interesting research opportunities. One key discriminating feature of the mature sperm epigenome is that it, in theory, represents both remnant marks used throughout spermatogenesis to generate sperm cells competent to perform their function, but also marks that appear to be useful beyond fertilization. Key questions must be asked about the utility of these marks and the multiple purposes that may be served...
April 2017: Systems Biology in Reproductive Medicine
https://www.readbyqxmd.com/read/28300839/bidirectional-transcription-of-linc00441-and-rb1-via-h3k27-modification-dependent-way-promotes-hepatocellular-carcinoma
#19
Junwei Tang, Yu Xie, Xiaoliang Xu, Yin Yin, Runqiu Jiang, Lei Deng, Zhongming Tan, Venkatanarayana Gangarapu, Jinhai Tang, Beicheng Sun
The retinoblastoma gene (RB1), a known tumor-suppressor gene (TSG), was decreased in multiple cancers including hepatocellular carcinoma (HCC). Here we focused on the bidirectional transcripted long noncoding RNA (Linc00441) with neighbor gene RB1 to investigate whether Linc00441 is involved in the suppression of RB1 in HCC. We found that aberrant upregulated intranuclear Linc00441 was reversely correlated with RB1 expression in human HCC samples. The gain- and loss-of-function investigation revealed that Linc00441 could promote the proliferation of HCC cells in vitro and in vivo with an apoptosis suppression and cell cycle rearrangement...
March 16, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28297716/rna-m-6-a-methylation-regulates-the-ultraviolet-induced-dna-damage-response
#20
Yang Xiang, Benoit Laurent, Chih-Hung Hsu, Sigrid Nachtergaele, Zhike Lu, Wanqiang Sheng, Chuanyun Xu, Hao Chen, Jian Ouyang, Siqing Wang, Dominic Ling, Pang-Hung Hsu, Lee Zou, Ashwini Jambhekar, Chuan He, Yang Shi
Cell proliferation and survival require the faithful maintenance and propagation of genetic information, which are threatened by the ubiquitous sources of DNA damage present intracellularly and in the external environment. A system of DNA repair, called the DNA damage response, detects and repairs damaged DNA and prevents cell division until the repair is complete. Here we report that methylation at the 6 position of adenosine (m(6)A) in RNA is rapidly (within 2 min) and transiently induced at DNA damage sites in response to ultraviolet irradiation...
March 15, 2017: Nature
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