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Cytosine methylation

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https://www.readbyqxmd.com/read/28812361/ultrasensitive-and-accurate-assay-of-human-methyltransferase-activity-at-the-single-cell-level-based-on-a-single-integrated-magnetic-microprobe
#1
Haiyan Zhao, Lei Wang, Weiqi Li, Shumei Zhai, Wei Jiang
Human DNA methyltransferase (MTase) activity expression patterns and inhibition response are linked to related cancer initiation, progression and therapeutic responses. Sensitive and accurate human MTase activity assay in cancer cells, especially at the single-cell level, is essential for biological study, clinical diagnosis and therapy. Here, we developed an ultrasensitive and accurate DNA (cytosine-5)-methyltransferase 1 (Dnmt1) activity assay at the single-cell level based on a single integrated magnetic microprobe of functionalized double-stranded DNA (dsDNA) anchored to a single magnetic microbead surface...
August 16, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28811741/consistency-and-variability-of-dna-methylation-in-women-during-puberty-young-adulthood-and-pregnancy
#2
Su Chen, Nandini Mukherjee, Vimala Devi Janjanam, S Hasan Arshad, Ramesh J Kurukulaaratchy, John W Holloway, Hongmei Zhang, Wilfried Karmaus
Prior DNA methylation (DNA-m) analyses have identified cytosine-phosphate-guanine (CpG) sites, which show either a significant change or consistency during lifetime. However, the proportion of CpGs that are neither significantly different nor consistent over time (indifferent CpGs) is unknown. We investigated the methylation dynamics, both longitudinal changes and consistency, in women from preadolescence to late pregnancy using DNA-m of peripheral blood cells. Consistency of cell type-adjusted DNA-m between paired individuals was assessed by regressing CpGs of subsequent age on the prior, stability by intraclass correlation coefficients (>0...
2017: Genetics & Epigenetics
https://www.readbyqxmd.com/read/28802254/tdp1-is-critical-for-the-repair-of-dna-breaks-induced-by-sapacitabine-a-nucleoside-also-targeting-atm-and-brca-deficient-tumors
#3
Muthana Al Abo, Hiroyuki Sasanuma, Xiaojun Liu, Vinodh N Rajapakse, Shar-Yin N Huang, Evgeny Kiselev, Shunichi Takeda, William Plunkett, Yves Pommier
2'-C-cyano-2'-deoxy-1-β-D-arabino-pentofuranosylcytosine (CNDAC) is the active metabolite of the anticancer drug, sapacitabine. CNDAC is incorporated into the genome during DNA replication and subsequently undergoes beta-elimination that generates single-strand breaks with abnormal 3'-ends. Because tyrosyl-DNA phosphodiesterase 1 (TDP1) selectively hydrolyzes non-phosphorylated 3'-blocking ends, we tested its role in the repair of CNDAC-induced DNA damage. We show that cells lacking TDP1 (avian TDP1-/- DT40 cells and human TDP1 KO TSCER2 and HCT116 cells) exhibit marked hypersensitivity to CNDAC...
August 11, 2017: Molecular Cancer Therapeutics
https://www.readbyqxmd.com/read/28801067/dna-methylation-in-cho-cells
#4
Anna Wippermann, Thomas Noll
Chinese hamster ovary (CHO) cells account for the production of the majority of biopharmaceutical molecules - however, the molecular basis for their versatile properties is not entirely understood yet and the underlying cellular processes need to be characterized in detail. One such process that is supposed to contribute significantly to CHO cell phenotype is methylation of DNA at cytosine residues. DNA methylation was shown to be involved in several central biological processes in humans and to contribute to diseases like cancer...
August 8, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28797086/epigenetic-differences-between-monozygotic-twins-discordant-for-amyotrophic-lateral-sclerosis-als-provide-clues-to-disease-pathogenesis
#5
Paul E Young, Stephen Kum Jew, Michael E Buckland, Roger Pamphlett, Catherine M Suter
Amyotrophic lateral sclerosis (ALS) is a devastating late-onset neurodegenerative disorder in which only a small proportion of patients carry an identifiable causative genetic lesion. Despite high heritability estimates, a genetic etiology for most sporadic ALS remains elusive. Here we report the epigenetic profiling of five monozygotic twin pairs discordant for ALS, four with classic ALS and one with the progressive muscular atrophy ALS variant, in whom previous whole genome sequencing failed to uncover a genetic basis for their disease discordance...
2017: PloS One
https://www.readbyqxmd.com/read/28796917/single-base-methylome-analysis-reveals-dynamic-epigenomic-differences-associated-with-water-deficit-in-apple
#6
Jidi Xu, Shasha Zhou, Xiaoqing Gong, Yi Song, Steve van Nocker, Fengwang Ma, Qingmei Guan
Cytosine methylation is an essential feature of epigenetic regulation and is involved in various biological processes. Although cytosine methylation has been analyzed at the genomic scale for several plant species, there is a general lack of understanding of the dynamics of global and genic DNA methylation in plants growing in environments challenged with biotic and abiotic stresses. In this study, we mapped cytosine methylation at single-base resolution in the genome of commercial apple (Malus x domestica), and analyzed changes in methylation patterns associated with water deficit in representative drought-sensitive and drought-tolerant cultivars...
August 10, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28796162/the-variation-analysis-of-dna-methylation-in-wheat-carrying-gametocidal-chromosome-3c-from-aegilops-triuncialis
#7
Dan Wang, Jieyu Zhao, Yan Bai, You Ao, Changhong Guo
Gametocidal (Gc) chromosomes can ensure their preferential transmission by killing the gametes without themselves through causing chromosome breakage and therefore have been exploited as an effective tool for genetic breeding. However, to date very little is known about the molecular mechanism of Gc action. In this study, we used methylation-sensitive amplified polymorphism (MSAP) technique to assess the extent and pattern of cytosine methylation alterations at the whole genome level between two lines of wheat Gc addition line and their common wheat parent...
August 10, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28795735/detection-of-methylation-on-dsdna-using-nanopores-in-a-mos2-membrane
#8
Jiwook Shim, Shouvik Banerjee, Hu Qiu, Kirby K H Smithe, David Estrada, Julian Bello, Eric Pop, Klaus Schulten, Rashid Bashir
Methylation at the 5-carbon position of the cytosine nucleotide base in DNA has been shown to be a reliable diagnostic biomarker for carcinogenesis. Early detection of methylation and intervention could drastically increase the effectiveness of therapy and reduce the cancer mortality rate. Current methods for detecting methylation involve bisulfite genomic sequencing, which are cumbersome and demand a large sample size of bodily fluids to yield accurate results. Hence, more efficient and cost effective methods are desired...
August 10, 2017: Nanoscale
https://www.readbyqxmd.com/read/28794029/coordinate-regulation-of-tet2-and-ebna2-control-dna-methylation-state-of-latent-epstein-barr-virus
#9
Fang Lu, Andreas Wiedmer, Kayla A Martin, Priyankara J M S Wickramasinghe, Andrew V Kossenkov, Paul M Lieberman
Epstein-Barr Virus (EBV) latency and its associated carcinogenesis are regulated by dynamic changes in DNA methylation of both virus and host genomes. We show here that the Ten-Eleven Translocation 2 (TET2) gene, implicated in hydroxymethylation and active DNA demethylation, is a key regulator of EBV latency type DNA methylation patterning. EBV latency types are defined by DNA methylation patterns that restrict expression of viral latency genes. We show that TET2 mRNA and protein expression correlate with the highly demethylated EBV type III latency program permissive for expression of EBNA2, EBNA3s, and LMP transcripts...
August 9, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28780716/epigenetics-a-potential-key-mechanism-involved-in-the-pathogenesis-of-cardiorenal-syndromes
#10
REVIEW
Grazia Maria Virzì, Anna Clementi, Alessandra Brocca, Massimo de Cal, Claudio Ronco
Epigenetics is defined as the heritable changes in gene expression patterns which are not directly encoded by modifications in the nucleotide DNA sequence of the genome, including higher order chromatin organization, DNA methylation, cytosine modifications, covalent histone tail modifications, and short non-coding RNA molecules. Recently, much attention has been paid to the role and the function of epigenetics and epimutations in the cellular and subcellular pathways and in the regulation of genes in the setting of both kidney and cardiovascular disease...
August 5, 2017: Journal of Nephrology
https://www.readbyqxmd.com/read/28780481/ht-2-toxin-affects-development-of-porcine-parthenotes-by-altering-dna-and-histone-methylation-in-oocytes-matured-in%C3%A2-vitro
#11
Yue Zhang, Ru-Xia Jia, Meng-Hao Pan, Yujie Lu, Xiang-Shun Cui, Nam-Hyung Kim, Shao-Chen Sun
T-2 toxin is a type A mycotoxin produced by various Fusarium species, while HT-2 toxin is a major metabolite of T-2 toxin. Both T-2 toxin and HT-2 toxin are known to have deleterious effects on animals. Our previous work showed that HT-2 treatment caused the failure of porcine oocyte maturation. In this study, we reported that HT-2 also affected porcine embryo development. In HT-2 toxin treated group, all the percentages of embryos in 2-cell, 4-cell and blastocyst stage were significantly lower compared with those in control groups...
July 31, 2017: Theriogenology
https://www.readbyqxmd.com/read/28771164/crosstalk-between-microrna-and-dna-methylation-offers-potential-biomarkers-and-targeted-therapies-in-alk-positive-lymphomas
#12
REVIEW
Coralie Hoareau-Aveilla, Fabienne Meggetto
The discovery of microRNA (miRNA) has provided new and powerful tools for studying the mechanism, diagnosis and treatment of human cancers. The down-regulation of tumor suppressive miRNA by hypermethylation of CpG island (CpG is shorthand for 5'-C-phosphate-G-3', that is, cytosine and guanine separated by only one phosphate) is emerging as a common hallmark of cancer and appears to be involved in drug resistance. This review discusses the role of miRNA and DNA methylation in drug resistance mechanisms and highlights their potential as anti-cancer therapies in Anaplastic Lymphoma Kinase (ALK)-positive lymphomas...
August 3, 2017: Cancers
https://www.readbyqxmd.com/read/28769976/new-insights-into-5hmc-dna-modification-generation-distribution-and-function
#13
REVIEW
Dong-Qiao Shi, Iftikhar Ali, Jun Tang, Wei-Cai Yang
Dynamic DNA modifications, such as methylation/demethylation on cytosine, are major epigenetic mechanisms to modulate gene expression in both eukaryotes and prokaryotes. In addition to the common methylation on the 5th position of the pyrimidine ring of cytosine (5mC), other types of modifications at the same position, such as 5-hydroxymethyl (5hmC), 5-formyl (5fC), and 5-carboxyl (5caC), are also important. Recently, 5hmC, a product of 5mC demethylation by the Ten-Eleven Translocation family proteins, was shown to regulate many cellular and developmental processes, including the pluripotency of embryonic stem cells, neuron development, and tumorigenesis in mammals...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28763057/becon-a-tool-for-interpreting-dna-methylation-findings-from-blood-in-the-context-of-brain
#14
R D Edgar, M J Jones, M J Meaney, G Turecki, M S Kobor
Tissue differences are one of the largest contributors to variability in the human DNA methylome. Despite the tissue-specific nature of DNA methylation, the inaccessibility of human brain samples necessitates the frequent use of surrogate tissues such as blood, in studies of associations between DNA methylation and brain function and health. Results from studies of surrogate tissues in humans are difficult to interpret in this context, as the connection between blood-brain DNA methylation is tenuous and not well-documented...
August 1, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28761142/methylation-profile-of-a-satellite-dna-constituting-the-intercalary-g-c-rich-heterochromatin-of-the-cut-trough-shell-spisula-subtruncata-bivalvia-mactridae
#15
Daniel García-Souto, Brankica Mravinac, Eva Šatović, Miroslav Plohl, Paloma Morán, Juan J Pasantes
Tandemly repeated DNAs usually constitute significant portions of eukaryotic genomes. In bivalves, however, repetitive DNAs are habitually not widespread. In our search for abundant repetitive DNAs in trough shells, we discovered a novel satellite DNA, SSUsat, which constitutes at least 1.3% of the genome of Spisula subtruncata. As foreseen by the satellite DNA library hypothesis, we confirmed that this satellite DNA is also present in two other Mactridae species, showing a highly conserved nucleotide sequence together with a dramatic diminution in the number of repeats...
July 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28758879/genome-wide-analysis-of-cytosine-dna-methylation-revealed-salicylic-acid-promotes-defense-pathways-over-seedling-development-in-pearl-millet
#16
Baba Ngom, Ibrahima Sarr, Josphert Kimatu, Edward Mamati, Ndjido Ardo Kane
Cytosine DNA methylation is an epigenetic regulatory system used by plants to control gene expression. Methylation pattern always changes after abiotic stresses, pathogens and pest infections or after a treatment with salicylic acid (SA). The latter is a key player in plant development and defense against insect herbivores, pathogens, and abiotic stresses. The roles of SA on the methylation patterns and the plant development were carried out in four pearl millet (Pennisetum glaucum) varieties. Seedlings of four early-flowering photosensitive genotypes (PMS3, PMI8, PMG, and PMT2) were grown on MS medium supplemented with null or different doses of SA...
July 31, 2017: Plant Signaling & Behavior
https://www.readbyqxmd.com/read/28758831/tet1-deficiency-attenuates-the-dna-damage-response-and-promotes-resistance-to-dna-damaging-agents
#17
Jonathan B Coulter, Hernando Lopez-Bertoni, Katherine J Kuhns, Richard S Lee, John Laterra, Joseph P Bressler
Recent studies have shown that loss of TET1 may play a significant role in the formation of tumors. Because genomic instability is a hallmark of cancer, we examined the potential involvement of ten-eleven translocation 1 (TET1) in the DNA damage response (DDR). Here we demonstrate that, in response to clinically relevant doses of ionizing radiation (IR), human glial cells made TET1-deficient with lentiviral vectors displayed greater numbers of colony forming units and lower levels of apoptotic markers compared to glial cells transduced with control vectors; yet, they harbored greater DNA strand breaks...
July 31, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28756210/the-role-of-epigenomic-alterations-in-furan-induced-hepatobiliary-pathologies
#18
Aline de Conti, Frederick A Beland, Igor P Pogribny
Furan, a volatile heterocyclic organic chemical found in a wide spectrum of common human foods, is a liver toxicant and carcinogen in mice and rats. The carcinogenic effects of furan have been attributed to genotoxic and non-genotoxic mechanisms. Among the broad range of non-genotoxic alterations induced by furan, epigenetic alterations are of special interest because of their connection to all other non-genotoxic events. This review summarizes current evidence of alterations for epigenetic mechanisms, including cytosine DNA methylation, histone modifications, and microRNA expression, caused by furan exposure and highlights the role of these aberrations in furan-associated hepatobiliary pathologies...
July 26, 2017: Food and Chemical Toxicology
https://www.readbyqxmd.com/read/28755272/polymorphism-and-methylation-of-the-mc4r-gene-in-obese-and-non-obese-dogs
#19
Monika Mankowska, Joanna Nowacka-Woszuk, Aneta Graczyk, Paulina Ciazynska, Monika Stachowiak, Marek Switonski
The dog is considered to be a useful biomedical model for human diseases and disorders, including obesity. One of the numerous genes associated with human polygenic obesity is MC4R, encoding the melanocortin 4 receptor. The aim of our study was to analyze polymorphisms and methylation of the canine MC4R in relation to adiposity. Altogether 270 dogs representing four breeds predisposed to obesity: Labrador Retriever (n = 187), Golden Retriever (n = 38), Beagle (n = 28) and Cocker Spaniel (n = 17), were studied...
July 28, 2017: Molecular Biology Reports
https://www.readbyqxmd.com/read/28746368/the-genome-wide-identification-and-transcriptional-levels-of-dna-methyltransferases-and-demethylases-in-globe-artichoke
#20
Silvia Gianoglio, Andrea Moglia, Alberto Acquadro, Cinzia Comino, Ezio Portis
Changes to the cytosine methylation status of DNA, driven by the activity of C5 methyltransferases (C5-MTases) and demethylases, exert an important influence over development, transposon movement, gene expression and imprinting. Three groups of C5-MTase enzymes have been identified in plants, namely MET (methyltransferase 1), CMT (chromomethyltransferases) and DRM (domains rearranged methyltransferases). Here the repertoire of genes encoding C5-MTase and demethylase by the globe artichoke (Cynara cardunculus var...
2017: PloS One
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