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https://www.readbyqxmd.com/read/28230814/m1a%C3%A2-post-transcriptional%C3%A2-modification%C3%A2-in%C3%A2-trnas
#1
REVIEW
Stephanie Oerum, Clément Dégut, Pierre Barraud, Carine Tisné
To date, about 90 post-transcriptional modifications have been reported in tRNA expanding their chemical and functional diversity. Methylation is the most frequent post-transcriptional tRNA modification that can occur on almost all nitrogen sites of the nucleobases, on the C5 atom of pyrimidines, on the C2 and C8 atoms of adenosine and, additionally, on the oxygen of the ribose 2'-OH. The methylation on the N1 atom of adenosine to form 1-methyladenosine (m1A) has been identified at nucleotide position 9, 14, 22, 57, and 58 in different tRNAs...
February 21, 2017: Biomolecules
https://www.readbyqxmd.com/read/28229992/increased-5-hydroxymethylcytosine-and-ten-eleven-translocation-protein-expression-in-ultraviolet-b-irradiated-hacat-cells
#2
Dan Wang, Jin-Hua Huang, Qing-Hai Zeng, Can Gu, Shu Ding, Jian-Yun Lu, Jing Chen, Sheng-Bo Yang
BACKGROUND: DNA hydroxymethylation refers to a chemical modification process in which 5-methylcytosine (5mC) is catalyzed to 5- hydroxymethylcytosine (5hmC) by ten-eleven translocation (TET) family proteins. Recent studies have revealed that aberrant TETs expression or 5hmC level may play important roles in the occurrence and development of various pathological and physiological processes including cancer and aging. This study aimed to explore the relation between aberrant DNA hydroxymethylation with skin photoaging and to investigate the levels of TETs, 5mC, and 5hmC expression 24 h after 40 mJ/cm2 and 80 mJ/cm2 doses of ultraviolet B (UVB) irradiation to HaCaT cells...
2017: Chinese Medical Journal
https://www.readbyqxmd.com/read/28228863/medulloblastoma-and-ependymoma-cells-display-increased-levels-of-5-carboxylcytosine-and-elevated-tet1-expression
#3
Ashley Ramsawhook, Lara Lewis, Beth Coyle, Alexey Ruzov
BACKGROUND: Alteration of DNA methylation (5-methylcytosine, 5mC) patterns represents one of the causes of tumorigenesis and cancer progression. Tet proteins can oxidise 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine and 5-carboxylcytosine (5caC). Although the roles of these oxidised forms of 5mC (oxi-mCs) in cancer pathogenesis are still largely unknown, there are indications that they may be involved in the mechanisms of malignant transformation. Thus, reduction of 5hmC content represents an epigenetic hallmark of human tumours, and according to our recent report, 5caC is enriched in a proportion of breast cancers and gliomas...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28228264/lsd1-controls-timely-myod-expression-via-myod-core-enhancer-transcription
#4
Isabella Scionti, Shinichiro Hayashi, Sandrine Mouradian, Emmanuelle Girard, Joana Esteves de Lima, Véronique Morel, Thomas Simonet, Maud Wurmser, Pascal Maire, Katia Ancelin, Eric Metzger, Roland Schüle, Evelyne Goillot, Frederic Relaix, Laurent Schaeffer
MyoD is a master regulator of myogenesis. Chromatin modifications required to trigger MyoD expression are still poorly described. Here, we demonstrate that the histone demethylase LSD1/KDM1a is recruited on the MyoD core enhancer upon muscle differentiation. Depletion of Lsd1 in myoblasts precludes the removal of H3K9 methylation and the recruitment of RNA polymerase II on the core enhancer, thereby preventing transcription of the non-coding enhancer RNA required for MyoD expression (CEeRNA). Consistently, Lsd1 conditional inactivation in muscle progenitor cells during embryogenesis prevented transcription of the CEeRNA and delayed MyoD expression...
February 21, 2017: Cell Reports
https://www.readbyqxmd.com/read/28228067/epigenetic-characteristics-of-the-mitotic-chromosome-in-1d-and-3d
#5
Marlies E Oomen, Job Dekker
While chromatin characteristics in interphase are widely studied, characteristics of mitotic chromatin and their inheritance through mitosis are still poorly understood. During mitosis, chromatin undergoes dramatic changes: transcription stalls, chromatin-binding factors leave the chromatin, histone modifications change and chromatin becomes highly condensed. Many key insights into mitotic chromosome state and conformation have come from extensive microscopy studies over the last century. Over the last decade, the development of 3C-based techniques has enabled the study of higher order chromosome organization during mitosis in a genome-wide manner...
April 2017: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28226269/the-causes-and-consequences-of-dna-methylome-variation-in-plants
#6
REVIEW
Danelle K Seymour, Claude Becker
Epigenetic variation - polymorphisms at the level of DNA methylation or histone modifications - modulates chromatin accessibility, which can perturb transcriptional activity and spur phenotypic variation. Determining the origin, frequency spectrum, and consequences of epigenetic variants is key to understanding the role of this variation in generating stable phenotypic variation in plants. Here we review recent literature on DNA methylation variation in both model and crop plant species with a focus on the link between genotype, epigenotype, and transcription...
February 19, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28224919/characteristics-and-regulatory-pathway-of-the-prupesep1-sepallata-gene-during-ripening-and-softening-in-peach-fruits
#7
Jinjin Li, Fang Li, Ming Qian, Mingyu Han, Hangkong Liu, Dong Zhang, Juanjuan Ma, Caiping Zhao
SEPALLATA genes are members of a subfamily of MADS-box transcription factors, and have essential roles in floral organ development and fruit ripening. In this study, the PrupeSEP1 gene was cloned from peach flesh. Its deduced amino acid sequence was very similar to that of MdMADS8 and MdMADS9 in apple and MADS-RIN-like in strawberry. During storage of melting flesh (MF) peach, the pattern of SEP1 expression was similar to that of ethylene biosynthesis and ethylene signal transduction-related gene expression (EIN2 and ETR2)...
April 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28224725/quisinostat-treatment-improves-histone-acetylation-and-developmental-competence-of-porcine-somatic-cell-nuclear-transfer-embryos
#8
Long Jin, Qing Guo, Hai-Ying Zhu, Xiao-Xu Xing, Guang-Lei Zhang, Mei-Fu Xuan, Qi-Rong Luo, Zhao-Bo Luo, Jun-Xia Wang, Xi-Jun Yin, Jin-Dan Kang
Abnormal epigenetic modifications are considered a main contributing factor to low cloning efficiency. In the present study, we explored the effects of quisinostat, a novel histone deacetylase inhibitor, on blastocyst formation rate in porcine somatic-cell nuclear transfer (SCNT) embryos, on acetylation of histone H3 lysine 9 (AcH3K9), and on expression of POU5F1 protein and apoptosis-related genes BAX and BCL2. Our results showed that treatment with 10 nM quisinostat for 24 h significantly improved the development of reconstructed embryos compared to the untreated group (19...
February 22, 2017: Molecular Reproduction and Development
https://www.readbyqxmd.com/read/28223921/epigenetic-modulation-of-stem-cells-in-neurodevelopment-the-role-of-methylation-and-acetylation
#9
REVIEW
Martyna Podobinska, Ilona Szablowska-Gadomska, Justyna Augustyniak, Ioanna Sandvig, Axel Sandvig, Leonora Buzanska
The coordinated development of the nervous system requires fidelity in the expression of specific genes determining the different neural cell phenotypes. Stem cell fate decisions during neurodevelopment are strictly correlated with their epigenetic status. The epigenetic regulatory processes, such as DNA methylation and histone modifications discussed in this review article, may impact both neural stem cell (NSC) self-renewal and differentiation and thus play an important role in neurodevelopment. At the same time, stem cell decisions regarding fate commitment and differentiation are highly dependent on the temporospatial expression of specific genes contingent on the developmental stage of the nervous system...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/28223506/intragenic-cpg-islands-play-important-roles-in-bivalent-chromatin-assembly-of-developmental-genes
#10
Sun-Min Lee, Jungwoo Lee, Kyung-Min Noh, Won-Young Choi, Sejin Jeon, Goo Taeg Oh, Jeongsil Kim-Ha, Yoonhee Jin, Seung-Woo Cho, Young-Joon Kim
CpG, 5'-C-phosphate-G-3', islands (CGIs) have long been known for their association with enhancers, silencers, and promoters, and for their epigenetic signatures. They are maintained in embryonic stem cells (ESCs) in a poised but inactive state via the formation of bivalent chromatin containing both active and repressive marks. CGIs also occur within coding sequences, where their functional role has remained obscure. Intragenic CGIs (iCGIs) are largely absent from housekeeping genes, but they are found in all genes associated with organ development and cell lineage control...
February 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28223461/identification-of-a-pseudomonas-aeruginosa-pao1-dna-methyltransferase-its-targets-and-physiological-roles
#11
Sebastian Doberenz, Denitsa Eckweiler, Olga Reichert, Vanessa Jensen, Boyke Bunk, Cathrin Spröer, Adrian Kordes, Emanuela Frangipani, Khai Luong, Jonas Korlach, Stephan Heeb, Jörg Overmann, Volkhard Kaever, Susanne Häussler
DNA methylation is widespread among prokaryotes, and most DNA methylation reactions are catalyzed by adenine DNA methyltransferases, which are part of restriction-modification (R-M) systems. R-M systems are known for their role in the defense against foreign DNA; however, DNA methyltransferases also play functional roles in gene regulation. In this study, we used single-molecule real-time (SMRT) sequencing to uncover the genome-wide DNA methylation pattern in the opportunistic pathogen Pseudomonas aeruginosa PAO1...
February 21, 2017: MBio
https://www.readbyqxmd.com/read/28222153/dissecting-nutrient-related-co-expression-networks-in-phosphate-starved-poplars
#12
Mareike Kavka, Andrea Polle
Phosphorus (P) is an essential plant nutrient, but its availability is often limited in soil. Here, we studied changes in the transcriptome and in nutrient element concentrations in leaves and roots of poplars (Populus × canescens) in response to P deficiency. P starvation resulted in decreased concentrations of S and major cations (K, Mg, Ca), in increased concentrations of N, Zn and Al, while C, Fe and Mn were only little affected. In roots and leaves >4,000 and >9,000 genes were differently expressed upon P starvation...
2017: PloS One
https://www.readbyqxmd.com/read/28220154/dna-display-of-folded-rna-libraries-enabling-rna-selex-without-reverse-transcription
#13
I S MacPherson, J S Temme, I J Krauss
A method for the physical attachment of folded RNA libraries to their encoding DNA is presented as a way to circumvent the reverse transcription step during systematic evolution of RNA ligands by exponential enrichment (RNA-SELEX). A DNA library is modified with one isodC base to stall T7 polymerase and a 5' "capture strand" which anneals to the nascent RNA transcript. This method is validated in a selection of RNA aptamers against human α-thrombin with dissociation constants in the low nanomolar range. This method will be useful in the discovery of RNA aptamers and ribozymes containing base modifications that make them resistant to accurate reverse transcription...
February 21, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28220045/paternal-cocaine-taking-elicits-epigenetic-remodeling-and-memory-deficits-in-male-progeny
#14
M E Wimmer, L A Briand, B Fant, L A Guercio, A C Arreola, H D Schmidt, S Sidoli, Y Han, B A Garcia, R C Pierce
Paternal environmental perturbations including exposure to drugs of abuse can produce profound effects on the physiology and behavior of offspring via epigenetic modifications. Here we show that adult drug-naive male offspring of cocaine-exposed sires have memory formation deficits and associated reductions in NMDA receptor-mediated hippocampal synaptic plasticity. Reduced levels of the endogenous NMDA receptor co-agonist d-serine were accompanied by increased expression of the d-serine degrading enzyme d-amino acid oxidase (Dao1) in the hippocampus of cocaine-sired male progeny...
February 21, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28219769/epitranscriptomic-regulation-of-viral-replication
#15
REVIEW
Camila Pereira-Montecinos, Fernando Valiente-Echeverría, Ricardo Soto-Rifo
RNA plays central roles in biology and novel functions and regulation mechanisms are constantly emerging. To accomplish some of their functions within the cell, RNA molecules undergo hundreds of chemical modifications from which N6-methyladenosine (m(6)A), inosine (I), pseudouridine (ψ) and 5-methylcytosine (5mC) have been described in eukaryotic mRNA. Interestingly, the m(6)A modification was shown to be reversible, adding novel layers of regulation of gene expression through what is now recognized as epitranscriptomics...
February 17, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28219744/metabolic-labeling-and-recovery-of-nascent-rna-to-accurately-quantify-mrna-stability
#16
Joseph Russo, Adam M Heck, Jeffrey Wilusz, Carol J Wilusz
Changes in the rate of mRNA decay are closely coordinated with transcriptional changes and together these events have profound effects on gene expression during development and disease. Traditional approaches to assess mRNA decay have relied on inhibition of transcription, which can alter mRNA decay rates and confound interpretation. More recently, metabolic labeling combined with chemical modification and fractionation of labeled RNAs has allowed the isolation of nascent transcripts and the subsequent calculation of mRNA decay rates...
February 17, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28219680/the-regulation-of-transcriptional-repression-in-hypoxia
#17
Miguel A S Cavadas, Alex Cheong, Cormac T Taylor
A sufficient supply molecular oxygen is essential for the maintenance of physiologic metabolism and bioenergetic homeostasis for most metazoans. For this reason, mechanisms have evolved for eukaryotic cells to adapt to conditions where oxygen demand exceeds supply (hypoxia). These mechanisms rely on the modification of pre-existing proteins, translational arrest and transcriptional changes. The hypoxia inducible factor (HIF; a master regulator of gene induction in response to hypoxia) is responsible for the majority of induced gene expression in hypoxia...
February 17, 2017: Experimental Cell Research
https://www.readbyqxmd.com/read/28218427/two-vitellogenins-in-the-loliginid-squid-uroteuthis-edulis-identification-and-specific-expression-in-ovarian-follicles
#18
Hajime Kitano, Naoki Nagano, Keishi Sakaguchi, Michiya Matsuyama
Vitellogenenesis is a physiological process common in oviparous animals. The molecular profile, modifications, and utilization of vitellogenin (VTG), a precursor of yolk protein, have been characterized in various taxa to understand oogenesis within different modes of reproduction. Hormonal regulation of VTGs has been investigated in invertebrates, such as insects and crustaceans; conversely, little is known for cephalopods. In this study, we isolated two VTG genes (ue-VTG1 and ue-VTG2) from the loliginid swordtip squid, Uroteuthis edulis, via a comprehensive survey of a transcriptome database and subsequent cDNA cloning...
February 20, 2017: Molecular Reproduction and Development
https://www.readbyqxmd.com/read/28217257/regulation-of-hepatic-microrna-expression-by-hepatocyte-nuclear-factor-4-alpha
#19
Hong Lu, Xiaohong Lei, Jerry Liu, Curtis Klaassen
AIM: To uncover the role of hepatocyte nuclear factor 4 alpha (HNF4α) in regulating hepatic expression of microRNAs. METHODS: Microarray and real-time PCR were used to determine hepatic expression of microRNAs in young-adult mice lacking Hnf4α expression in liver (Hnf4α-LivKO). Integrative genomics viewer software was used to analyze the public chromatin immunoprecipitation-sequencing datasets for DNA-binding of HNF4α, RNA polymerase-II, and histone modifications to loci of microRNAs in mouse liver and human hepatoma cells...
February 8, 2017: World Journal of Hepatology
https://www.readbyqxmd.com/read/28217005/chromatin-based-epigenetic-regulation-of-plant-abiotic-stress-response
#20
Garima Pandey, Namisha Sharma, Pranav Pankaj Sahu, Manoj Prasad
Plants are continuously exposed to various abiotic and biotic factors limiting their growth and reproduction. In response, they need various sophisticated ways to adapt to adverse environmental conditions without compromising their proper development, reproductive success and eventually survival. This requires an intricate network to regulate gene expression at transcriptional and post-transcriptional levels, including epigenetic switches. Changes in chromatin modifications such as DNA and histone methylation have been observed in plants upon exposure to several abiotic stresses...
December 2016: Current Genomics
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