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Cytosine methylation

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https://www.readbyqxmd.com/read/28928877/mechanisms-of-breast-cancer-in-shift-workers-dna-methylation-in-five-core-circadian-genes-in-nurses-working-night-shifts
#1
Johanna Samulin Erdem, Øivind Skare, Marte Petersen-Øverleir, Heidi Ødegaard Notø, Jenny-Anne S Lie, Edyta Reszka, Beata Pepłońska, Shanbeh Zienolddiny
Shift work has been suggested to be associated with breast cancer risk, and circadian disruption in shift workers is hypothesized as one of the mechanisms of increased cancer risk. There is, however, insufficient molecular evidence supporting this hypothesis. Using the quantitative methodology of pyrosequencing, epigenetic changes in 5-methyl cytosine (5mC) in five circadian genes CLOCK, BMAL1, CRY1, PER1 and PER2 in female nurses working night shift work (278 breast cancer cases, 280 controls) were analyzed...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28925547/biogeographic-conservation-of-the-cytosine-epigenome-in-the-globally-important-marine-nitrogen-fixing-cyanobacterium-trichodesmium
#2
Nathan G Walworth, David A Hutchins, Egor Dolzhenko, Michael D Lee, Feixue Fu, Andrew D Smith, Eric A Webb
Cytosine methylation has been shown to regulate essential cellular processes and impact biological adaptation. Despite its evolutionary importance, only a handful of bacterial, genome-wide cytosine studies have been conducted, with none for marine bacteria. Here, we examine the genome-wide, C(5) -Methyl-cytosine (m5C) methylome and its correlation to global transcription in the marine nitrogen-fixing cyanobacterium Trichodesmium. We characterize genome-wide methylation and highlight conserved motifs across 3 Trichodesmium isolates and 2 Trichodesmium metagenomes, thereby identifying highly conserved, novel genomic signatures of potential gene regulation in Trichodesmium...
September 19, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28923005/methods-for-discovering-genomic-loci-exhibiting-complex-patterns-of-differential-methylation
#3
Thomas J Hardcastle
BACKGROUND: Cytosine methylation is widespread in most eukaryotic genomes and is known to play a substantial role in various regulatory pathways. Unmethylated cytosines may be converted to uracil through the addition of sodium bisulphite, allowing genome-wide quantification of cytosine methylation via high-throughput sequencing. The data thus acquired allows the discovery of methylation 'loci'; contiguous regions of methylation consistently methylated across biological replicates. The mapping of these loci allows for associations with other genomic factors to be identified, and for analyses of differential methylation to take place...
September 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28919411/homocysteine-upregulates-interleukin-17a-expression-via-nsun2-mediated-rna-methylation-in-t-lymphocytes
#4
Nan Wang, Hao Tang, Xian Wang, Wengong Wang, Juan Feng
Interleukin-17A (IL-17A) has been proven to participate in the process of various autoimmune diseases. The elevation of plasma homocysteine (Hcy), known as hyperhomocysteinemia (HHcy), is related to various chronic inflammatory diseases. Though HHcy-induced upregulation of IL-17A expression in T lymphocytes has been examined, the way in which IL-17A is regulated remains unclear. In this study, western blotting assays showed that Hcy (100 μM) upregulated NOP2/Sun domain family, member 2 (NSun2) expression in rat T lymphocytes...
September 15, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28901692/synthesis-and-multiple-incorporations-of-2-o-methyl-5-hydroxymethyl-5-hydroxymethyl-and-5-formylcytidine-monomers-into-rna-oligonucleotides
#5
Shankar Balasubramanian, Arun Ankush Tanpure
The synthesis of 2'-O-methyl-5-hydroxymethylcytidine (hm5Cm), 5-hydroxymethylcytidine (hm5C) and 5-formylcytidine (f5C) phosphoramidite monomers has been developed. Optimization of mild post-synthetic deprotection conditions enabled the synthesis of RNA containing all four naturally occurring cytosine-modifications (hm5Cm, hm5C, f5C plus 5-methylcytosine). Given the considerable interest in RNA modifications and epitranscriptomics, the availability of synthetic monomers and RNAs containing these modifications will be valuable to elucidate their biological function(s)...
September 13, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28894047/the-role-of-vitamin-c-in-epigenetic-regulation
#6
Jolanta Guz, Ryszard Oliński
Vitamin C (L-ascorbic acid) is a micronutrient best known for its anti-scurvy activity in humans. Vitamin C is involved in many biological processes involving enzymatic reactions that are catalyzed by members of dioxygenases which use Fe(II) and 2-oxoglutarate as a co-substrate.The article reviews recent data that suggest the involvement of ascorbate in dioxygenases catalyzed chromatin and DNA modifications which thereby contribute to epigenetic regulation. Concerning chromatin modification, the dioxygenases are involved in distinct demethylation reactions with varying specificity for the position of the lysine on the target histone...
August 24, 2017: Postȩpy Higieny i Medycyny Doświadczalnej
https://www.readbyqxmd.com/read/28889481/a-review-of-the-biologic-and-clinical-significance-of-genetic-mutations-in-angioimmunoblastic-t-cell-lymphoma
#7
REVIEW
Kota Fukumoto, Tran B Nguyen, Shigeru Chiba, Mamiko Sakata-Yanagimoto
Angioimmunoblastic T-cell lymphoma (AITL) is an age-related malignant lymphoma, characterized by immune system-dysregulated symptoms. Recent sequencing studies have clarified the recurrent mutations in ras homology family member A (RHOA) and in genes encoding epigenetic regulators, tet methyl cytosine dioxygenase 2 (TET2), DNA methyl transferase 3 alpha (DNMT3A), and isocitrate dehydrogenase 2, mitochondrial (IDH2), as well as those related to the T-cell receptor signaling pathway in AITL. In this review, we will focus on how this genetic information has changed the understanding of the developmental process of AITL and will in future lead to individualized therapies for AITL patients...
September 10, 2017: Cancer Science
https://www.readbyqxmd.com/read/28889390/dna-methylation-analysis-from-body-fluids
#8
Dimo Dietrich
Circulating cell-free DNA (ccfDNA) can be found in various body fluids, i.e., blood (serum and plasma), urine, pleural effusions, and ascites. While ccfDNA predominantly originates from physiological processes, a fraction might be related to pathological events, e.g., cancer. Aberrant DNA methylation, which is considered a hallmark of cancer, can be assessed accurately in ccfDNA. Consequently, DNA methylation testing in body fluids represents a powerful diagnostic tool in the clinical management of malignant diseases...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28889069/electrochemical-assay-for-continuous-monitoring-of-dynamic-dna-methylation-process
#9
Li Zhang, Xiaofen Xiao, Yuzhi Xu, Danping Chen, Jun Chen, Yingjun Ma, Zong Dai, Xiaoyong Zou
A simple electrochemical strategy is reported for continuous monitoring of dynamic DNA methylation process over time. An electrochemical sensor was prepared by co-assembling of DNA probe and 6-mercapto-1-hexanol onto a gold electrode. The top of the DNA probe was labeled with 6-ferrocenylhexanethiol modified gold nanoparticle. The charge density between the C•G base pair was verified to be slightly reduced by DNA methylation, and could be further decelerated by ~ 25% upon co-locating a Br group onto methylated cytosine (mC)...
September 4, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28887432/maternal-pregravid-obesity-remodels-the-dna-methylation-landscape-of-cord-blood-monocytes-disrupting-their-inflammatory-program
#10
Suhas Sureshchandra, Randall M Wilson, Maham Rais, Nicole E Marshall, Jonathan Q Purnell, Kent L Thornburg, Ilhem Messaoudi
Prepregnancy maternal obesity is associated with adverse outcomes for the offspring, including increased incidence of neonatal bacterial sepsis and necrotizing enterocolitis. We recently reported that umbilical cord blood (UCB) monocytes from babies born to obese mothers generate a reduced IL-6/TNF-α response to TLR 1/2 and 4 ligands compared to those collected from lean mothers. These observations suggest altered development of the offspring's immune system, which in turn results in dysregulated function...
September 8, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28881727/adult-t-cell-leukemia-aggressivenness-correlates-with-loss-of-both-5-hydroxymethylcytosine-and-tet2-expression
#11
Ambroise Marçais, Laetitia Waast, Julie Bruneau, Katia Hanssens, Vahid Asnafi, Philippe Gaulard, Felipe Suarez, Patrice Dubreuil, Antoine Gessain, Olivier Hermine, Claudine Pique
Mutations in TET2, encoding one of the TET members responsible for the conversion of DNA cytosine methylation to hydroxymethylation (5-hmc), have been recently described in Human T-lymphotropic virus type 1-associated adult T-cell leukemia/lymphoma (ATLL). However, neither the amount of genomic 5-hmc in ATLL tumor cells nor TET2 expression has been studied yet. In this study, we analyzed these two parameters as well as the mutational status of TET2 in ATLL patients. By employing a direct in situ approach, we documented that tumor T cells infiltrating lymph nodes exhibit low level of 5-hmc compared to residual normal T cells...
August 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28870318/assay-of-dna-methyltransferase-1-activity-based-on-uracil-specific-excision-reagent-digestion-induced-g-quadruplex-formation
#12
Jinlong Li, Guangwu He, Chaoli Mu, Keming Wang, Yang Xiang
DNA methylation catalyzed by DNA methyltransferase plays an important role in many biological processes including gene transcription, genomic imprinting and cellular differentiation. Herein, a novel and effective electrochemical method for the assay of DNA methyltransferase 1(DNMT1) activity has been successfully developed by using uracil-specific excision reagent (USER) induced G-quadruplex formation. Briefly, double stranded DNA containing the recognition sequence of DNMT1 is immobilized on the electrode...
September 15, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28869544/potential-roles-of-intrinsic-disorder-in-maternal-effect-proteins-involved-in-the-maintenance-of-dna-methylation
#13
Hongliang Liu, Qing Wei, Chenyang Huang, Yong Zhang, Zekun Guo
DNA methylation is an important epigenetic modification that needs to be carefully controlled as a prerequisite for normal early embryogenesis. Compelling evidence now suggests that four maternal-effect proteins, primordial germ cell 7 (PGC7), zinc finger protein 57 (ZFP57), tripartite motif-containing 28 (TRIM28) and DNA methyltransferase (cytosine-5) 1 (DNMT1) are involved in the maintenance of DNA methylation. However, it is still not fully understood how these maternal-effect proteins maintain the DNA methylation imprint...
September 4, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28866733/single-base-resolution-mapping-of-5-hydroxymethylcytosine-modifications-in-hippocampus-of-alzheimer-s-disease-subjects
#14
Elizabeth M Ellison, Melissa A Bradley-Whitman, Mark A Lovell
Epigenetic modifications to cytosine have been shown to regulate transcription in cancer, embryonic development, and recently neurodegeneration. While cytosine methylation studies are now common in neurodegenerative research, hydroxymethylation studies are rare, particularly genome-wide mapping studies. As an initial study to analyze 5-hydroxymethylcytosine (5-hmC) in the Alzheimer's disease (AD) genome, reduced representation hydroxymethylation profiling (RRHP) was used to analyze more than 2 million sites of possible modification in hippocampal DNA of sporadic AD and normal control subjects...
September 2, 2017: Journal of Molecular Neuroscience: MN
https://www.readbyqxmd.com/read/28866690/molecular-analysis-of-fragile-x-syndrome-fxs-among-malaysian-patients-with-developmental-disability
#15
E Z Ali, Y Yakob, N Md Desa, T Ishak, Z Zakaria, L K Ngu, W T Keng
Fragile X syndrome (FXS) is a neurodevelopmental disorder commonly found worldwide, caused by the silencing of fragile X mental retardation 1 (FMR1) gene on the X-chromosome. Most of the patients lost FMR1 function due to an expansion of cytosine-guanine-guanine (CGG) repeat at the 5' untranslated region (5'UTR) of the gene. The purpose of this study is to identify the prevalence of FXS and characterize the FMR1 gene CGG repeats distribution among children with developmental disability in Malaysia. Genomic DNA of 2201 samples from different ethnicities (Malays, Chinese, Indian and others) of both genders were PCR-amplified from peripheral blood leukocytes based on specific primers at 5'UTR of FMR1 gene...
August 2017: Malaysian Journal of Pathology
https://www.readbyqxmd.com/read/28865007/cryphonectria-hypovirus-1-induced-epigenetic-changes-in-infected-phytopathogenic-fungus-cryphonectria-parasitica
#16
Lucija Nuskern, Marin Ježić, Zlatko Liber, Jelena Mlinarec, Mirna Ćurković-Perica
Biotic stress caused by virus infections induces epigenetic changes in infected plants and animals, but this is the first report on methylation pattern changes in a fungus after mycovirus infection. As a model pathosystem for mycovirus-host interactions, we used Cryphonectria hypovirus 1 (CHV1) and its host fungus Cryphonectria parasitica, in which deregulation of methylation cycle enzymes upon virus infection was observed previously. Six CHV1 strains of different subtypes were transferred into three different C...
September 1, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28860502/bi-directional-and-shared-epigenomic-signatures-following-proton-and-56-fe-irradiation
#17
Soren Impey, Timothy Jopson, Carl Pelz, Amanuel Tafessu, Fatema Fareh, Damian Zuloaga, Tessa Marzulla, Lara-Kirstie Riparip, Blair Stewart, Susanna Rosi, Mitchell S Turker, Jacob Raber
The brain's response to radiation exposure is an important concern for patients undergoing cancer therapy and astronauts on long missions in deep space. We assessed whether this response is specific and prolonged and is linked to epigenetic mechanisms. We focused on the response of the hippocampus at early (2-weeks) and late (20-week) time points following whole body proton irradiation. We examined two forms of DNA methylation, cytosine methylation (5mC) and hydroxymethylation (5hmC). Impairments in object recognition, spatial memory retention, and network stability following proton irradiation were observed at the two-week time point and correlated with altered gene expression and 5hmC profiles that mapped to specific gene ontology pathways...
August 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28855337/an-epigenetic-switch-repressing-tet1-in-gonadotropes-activates-the-reproductive-axis
#18
Yahav Yosefzon, Cfir David, Anna Tsukerman, Lilach Pnueli, Sen Qiao, Ulrich Boehm, Philippa Melamed
The TET enzymes catalyze conversion of 5-methyl cytosine (5mC) to 5-hydroxymethyl cytosine (5hmC) and play important roles during development. TET1 has been particularly well-studied in pluripotent stem cells, but Tet1-KO mice are viable, and the most marked defect is abnormal ovarian follicle development, resulting in impaired fertility. We hypothesized that TET1 might play a role in the central control of reproduction by regulating expression of the gonadotropin hormones, which are responsible for follicle development and maturation and ovarian function...
August 30, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28855224/dha-rich-n-3-fatty-acid-supplementation-decreases-dna-methylation-in-blood-leukocytes-the-omegad-study
#19
Mohsen Karimi, Inger Vedin, Yvonne Freund Levi, Hans Basun, Gerd Faxén Irving, Maria Eriksdotter, Lars-Olof Wahlund, Marianne Schultzberg, Erik Hjorth, Tommy Cederholm, Jan Palmblad
Background: Dietary fish oils, rich in long-chain n-3 (ω-3) fatty acids (FAs) [e.g., docosahexaenoic acid (DHA, 22:6n-3) and eicosapentaenoic acid (EPA, 20:5n-3)], modulate inflammatory reactions through various mechanisms, including gene expression, which is measured as messenger RNA concentration. However, the effects of long-term treatment of humans with DHA and EPA on various epigenetic factors-such as DNA methylation, which controls messenger RNA generation-are poorly described.Objective: We wanted to determine the effects of 6 mo of dietary supplementation with an n-3 FA preparation rich in DHA on global DNA methylation of peripheral blood leukocytes (PBLs) and the relation to plasma EPA and DHA concentrations in Alzheimer disease (AD) patients...
August 30, 2017: American Journal of Clinical Nutrition
https://www.readbyqxmd.com/read/28854222/rahu-is-a-mutant-allele-of-dnmt3c-encoding-a-dna-methyltransferase-homolog-required-for-meiosis-and-transposon-repression-in-the-mouse-male-germline
#20
Devanshi Jain, Cem Meydan, Julian Lange, Corentin Claeys Bouuaert, Nathalie Lailler, Christopher E Mason, Kathryn V Anderson, Scott Keeney
Transcriptional silencing by heritable cytosine-5 methylation is an ancient strategy to repress transposable elements. It was previously thought that mammals possess four DNA methyltransferase paralogs-Dnmt1, Dnmt3a, Dnmt3b and Dnmt3l-that establish and maintain cytosine-5 methylation. Here we identify a fifth paralog, Dnmt3c, that is essential for retrotransposon methylation and repression in the mouse male germline. From a phenotype-based forward genetics screen, we isolated a mutant mouse called 'rahu', which displays severe defects in double-strand-break repair and homologous chromosome synapsis during male meiosis, resulting in sterility...
August 2017: PLoS Genetics
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