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Dna methylation

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https://www.readbyqxmd.com/read/28651214/dna-methylation-and-the-preservation-of-cell-identity
#1
REVIEW
Ozren Bogdanović, Ryan Lister
DNA methylation is a major epigenetic modification of vertebrate genomes that is mostly associated with transcriptional repression. During embryogenesis, DNA methylation together with other epigenetic factors plays an essential role in selecting and maintaining cell identity. Recent technological advances are now allowing for the exploration of this mark at unprecedented resolution. This has resulted in a wealth of studies describing the developmental roles of DNA methylation in various vertebrate model systems...
June 23, 2017: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/28651167/error-prone-bypass-of-o-6-methylguanine-by-dna-polymerase-of-pseudomonas-aeruginosa-phage-pap1
#2
Shiling Gu, Jingyuan Xiong, Ying Shi, Jia You, Zhenyu Zou, Xiaoying Liu, Huidong Zhang
O(6)-Methylguanine (O(6)-MeG) is highly mutagenic and is commonly found in DNA exposed to methylating agents, generally leads to G:C to A:T mutagenesis. To study DNA replication encountering O(6)-MeG by the DNA polymerase (gp90) of P. aeruginosa phage PaP1, we analyzed steady-state and pre-steady-state kinetics of nucleotide incorporation opposite O(6)-MeG by gp90 exo(-). O(6)-MeG partially inhibited full-length extension by gp90 exo(-). O(6)-MeG greatly reduces dNTP incorporation efficiency, resulting in 67-fold preferential error-prone incorporation of dTTP than dCTP...
June 10, 2017: DNA Repair
https://www.readbyqxmd.com/read/28651088/genetic-and-epigenetic-alterations-in-normal-and-sensitive-copd-diseased-human-bronchial-epithelial-cells-repeatedly-exposed-to-air-pollution-derived-pm2-5
#3
B Leclercq, A Platel, S Antherieu, L Y Alleman, E M Hardy, E Perdrix, N Grova, V Riffault, B M Appenzeller, M Happillon, F Nesslany, P Coddeville, J-M Lo-Guidice, G Garçon
Even though clinical, epidemiological and toxicological studies have progressively provided a better knowledge of the underlying mechanisms by which air pollution-derived particulate matter (PM) exerts its harmful health effects, further in vitro studies on relevant cell systems are still needed. Hence, aiming of getting closer to the human in vivo conditions, primary human bronchial epithelial cells derived from normal subjects (NHBE) or sensitive chronic obstructive pulmonary disease (COPD)-diseased patients (DHBE) were differentiated at the air-liquid interface...
June 23, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28651060/mechanism-underlying-methyl-eugenol-attenuation-of-intestinal-ischemia-reperfusion-injury
#4
Hanan Saleh, Haidan M El-Shorbagy
Intestinal Ischemia/Reperfusion injury (I/R) is associated with a high risk of mortality in the clinical situation. Many factors are involved in I/R including reactive oxygen species (ROS), cytokine release and apoptosis. We aimed to determine whether a pure methyl eugenol (ME) given before intestinal ischemia, protects against intestinal I/R and the possible mechanism involved in this protection. Rat received ME (100 mg/kg) for 30 days then underwent intestinal I/R with 30 min ischemia and 60 min reperfusion...
June 26, 2017: Applied Physiology, Nutrition, and Metabolism, Physiologie Appliquée, Nutrition et Métabolisme
https://www.readbyqxmd.com/read/28650965/epigenetic-adaptation-of-the-placental-serotonin-transporter-gene-slc6a4-to-gestational-diabetes-mellitus
#5
Sofia Blazevic, Marina Horvaticek, Maja Kesic, Peter Zill, Dubravka Hranilovic, Marina Ivanisevic, Gernot Desoye, Jasminka Stefulj
We tested the hypothesis that gestational diabetes mellitus (GDM) alters the DNA methylation pattern of the fetal serotonin transporter gene (SLC6A4), and examined the functional relevance of DNA methylation for regulation of the SLC6A4 expression in the human placenta. The study included 50 mother-infant pairs. Eighteen mothers were diagnosed with GDM and 32 had normal glucose tolerance (NGT). All neonates were of normal birth weight and born at term by planned Cesarean section. DNA and RNA were isolated from samples of tissue collected from the fetal side of the placenta immediately after delivery...
2017: PloS One
https://www.readbyqxmd.com/read/28650314/natrinema-soli-sp-nov-a-novel-halophilic-archaeon-isolated-from-a-hypersaline-wetland
#6
Mehrnoosh Rasooli, Ali Naghoni, Mohammad Ali Amoozegar, Leila Mirfeizi, Mahdi Moshtaghi Nikou, Seyed Abolhassan Shahzadeh Fazeli, Hiroaki Minegishi, Antonio Ventosa
An extremely halophilic archaeon, designated strain 5-3T, was isolated from a soil sample of Meighan wetland in Iran. Strain 5-3T was strictly aerobic, catalase-positive and oxidase-negative. Cells were Gram-stain-negative, non-motile and ovoid. Colonies of strain 5-3T were cream-coloured. The isolate showed optimum growth at 4.0 M NaCl, 40 °C and pH 7.0. The major polar lipids of the strain were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, two unknown phospholipids and three glycolipids (including one that was chromatographically identical to S2-DGD)...
June 26, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28650214/distinct-dna-methylation-profiles-in-bone-and-blood-of-osteoporotic-and-healthy-postmenopausal-women
#7
Sjur Reppe, Tonje G Lien, Yi-Hsiang Hsu, Vigdis T Gautvik, Ole K Olstad, Rona Yu, Hege G Bakke, Robert Lyle, Marianne K Kringen, Ingrid K Glad, Kaare M Gautvik
DNA methylation affects expression of associated genes and may contribute to the missing genetic effects from genome-wide association studies of osteoporosis. To improve insight into the mechanisms of postmenopausal osteoporosis, we combined transcript profiling with DNA methylation analyses in bone. RNA and DNA were isolated from 84 bone biopsies of postmenopausal donors varying markedly in bone mineral density (BMD). In all, 2529 CpGs in the top 100 genes most significantly associated with BMD were analyzed...
June 26, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28649287/regulating-role-of-fetal-thyroid-hormones-on-placental-mitochondrial-dna-methylation-epidemiological-evidence-from-the-environage-birth-cohort-study
#8
Bram G Janssen, Hyang-Min Byun, Harry A Roels, Wilfried Gyselaers, Joris Penders, Andrea A Baccarelli, Tim S Nawrot
BACKGROUND: Fetal development largely depends on thyroid hormone availability and proper placental function with an important role played by placental mitochondria. The biological mechanisms by which thyroid hormones exert their effects on mitochondrial function are not well understood. We investigated the role of fetal thyroid hormones on placental mitochondrial DNA (mtDNA) content and mtDNA methylation. We collected placental tissue and cord blood from 305 mother-child pairs that were enrolled between February 2010 and June 2014 in the ENVIRONAGE (ENVIRonmental influence ON early AGEing) birth cohort (province of Limburg, Belgium)...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28649282/asymmetric-dna-methylation-of-cpg-dyads-is-a-feature-of-secondary-dmrs-associated-with-the-dlk1-gtl2-imprinting-cluster-in-mouse
#9
Megan Guntrum, Ekaterina Vlasova, Tamara L Davis
BACKGROUND: Differential DNA methylation plays a critical role in the regulation of imprinted genes. The differentially methylated state of the imprinting control region is inherited via the gametes at fertilization, and is stably maintained in somatic cells throughout development, influencing the expression of genes across the imprinting cluster. In contrast, DNA methylation patterns are more labile at secondary differentially methylated regions which are established at imprinted loci during post-implantation development...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28648900/tet-catalyzed-5-hydroxymethylation-precedes-hnf4a-promoter-choice-during-differentiation-of-bipotent-liver-progenitors
#10
Pierre-Benoit Ancey, Szilvia Ecsedi, Marie-Pierre Lambert, Fazlur Rahman Talukdar, Marie-Pierre Cros, Denise Glaise, Diana Maria Narvaez, Veronique Chauvet, Zdenko Herceg, Anne Corlu, Hector Hernandez-Vargas
Understanding the processes that govern liver progenitor cell differentiation has important implications for the design of strategies targeting chronic liver diseases, whereby regeneration of liver tissue is critical. Although DNA methylation (5mC) and hydroxymethylation (5hmC) are highly dynamic during early embryonic development, less is known about their roles at later stages of differentiation. Using an in vitro model of hepatocyte differentiation, we show here that 5hmC precedes the expression of promoter 1 (P1)-dependent isoforms of HNF4A, a master transcription factor of hepatocyte identity...
June 19, 2017: Stem Cell Reports
https://www.readbyqxmd.com/read/28648898/genome-wide-single-cell-dna-methylomics-reveals-increased-non-cpg-methylation-during-human-oocyte-maturation
#11
Bo Yu, Xiao Dong, Silvia Gravina, Önder Kartal, Timothy Schimmel, Jacques Cohen, Drew Tortoriello, Raifa Zody, R David Hawkins, Jan Vijg
The establishment of DNA methylation patterns in oocytes is a highly dynamic process marking gene-regulatory events during fertilization, embryonic development, and adulthood. However, after epigenetic reprogramming in primordial germ cells, how and when DNA methylation is re-established in developing human oocytes remains to be characterized. Here, using single-cell whole-genome bisulfite sequencing, we describe DNA methylation patterns in three different maturation stages of human oocytes. We found that while broad-scale patterns of CpG methylation have been largely established by the immature germinal vesicle stage, localized changes continue into later development...
June 19, 2017: Stem Cell Reports
https://www.readbyqxmd.com/read/28648661/de-novo-epigenetic-programs-inhibit-pd-1-blockade-mediated-t-cell-rejuvenation
#12
Hazem E Ghoneim, Yiping Fan, Ardiana Moustaki, Hossam A Abdelsamed, Pradyot Dash, Pranay Dogra, Robert Carter, Walid Awad, Geoff Neale, Paul G Thomas, Ben Youngblood
Immune-checkpoint-blockade (ICB)-mediated rejuvenation of exhausted T cells has emerged as a promising approach for treating various cancers and chronic infections. However, T cells that become fully exhausted during prolonged antigen exposure remain refractory to ICB-mediated rejuvenation. We report that blocking de novo DNA methylation in activated CD8 T cells allows them to retain their effector functions despite chronic stimulation during a persistent viral infection. Whole-genome bisulfite sequencing of antigen-specific murine CD8 T cells at the effector and exhaustion stages of an immune response identified progressively acquired heritable de novo methylation programs that restrict T cell expansion and clonal diversity during PD-1 blockade treatment...
June 21, 2017: Cell
https://www.readbyqxmd.com/read/28648249/ranaviruses-and-other-members-of-the-family-iridoviridae-their-place-in-the-virosphere
#13
V Gregory Chinchar, Thomas B Waltzek, Kuttichantran Subramaniam
Members of the family Iridoviridae, collectively referred to as iridovirids, are large, double-stranded DNA-containing viruses that infect invertebrates and cold-blooded (ectothermic) vertebrates. Infections in the former often lead to massive levels of virus replication resulting in iridescence of the infected animal and ultimately death. Among the latter, infections target a variety of organs and are capable of causing high levels of morbidity and mortality among commercially and ecologically important fish and amphibian species...
June 22, 2017: Virology
https://www.readbyqxmd.com/read/28647531/a-rapid-mass-spectrometric-method-for-the-measurement-of-catalytic-activity-of-ten-eleven-translocation-enzymes
#14
Babu Sudhamalla, Debasis Dey, Megan Breski, Kabirul Islam
Enzymatic methylation at carbon five on cytosine (5mC) in DNA is a hallmark of mammalian epigenetic programming and is critical to gene regulation during early embryonic development. It has recently been shown that dynamic erasure of 5mC by three members of the ten-eleven translocation (TET) family plays a key role in cellular differentiation. TET enzymes belong to Fe (II)- and 2-ketoglutarate (2KG) dependent dioxygenases that successively oxidize 5mC to 5-hydroxymethyl cytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxycytosine (5CaC), thus providing a chemical basis for the removal of 5mC which once was thought to be a permanent mark in mammalian genome...
June 21, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28646162/associations-between-global-dna-methylation-and-telomere-length-in-healthy-adolescents
#15
Yutong Dong, Ying Huang, Bernard Gutin, Anas Raed, Yanbin Dong, Haidong Zhu
Emerging evidence suggests that epigenetics regulates telomere dynamics in adults. However, the relationship between these pathways in children and youth remains unknown. Thus, we examined this association in 542 healthy adolescents aged 14 to 18 years old (44.8% African Americans; 55.2% females). Global DNA methylation level (%5-mC) was quantified using ELISA method. Leukocyte telomere length (LTL) was defined as relative telomere to single copy gene (T/S) ratio. Multiple linear regression models, adjusted for age, gender, ethnicity, Tanner stage, BMI, PA, and batch effect, revealed that %5 mC was associated with LTL (adjusted β = 0...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28645871/aflatoxin-b1-induced-epigenetic-alterations-an-overview
#16
Yaqi Dai, Kunlun Huang, Boyang Zhang, Liye Zhu, Wentao Xu
Aflatoxin B1 (AFB1) is widely distributed in nature, especially in a variety of food commodities. It is confirmed to be the most toxic of all the aflatoxins. The toxicity of AFB1 has been well investigated, and it may result in severe health problems including carcinogenesis, mutagenesis, growth retardation, and immune suppression. Epigenetic modifications including DNA methylation, histone modifications and regulation of non-coding RNA play an important role in AFB1-induced disease and carcinogenesis. To better understand the evidence for AFB1-induced epigenetic alterations and the potential mechanisms of the toxicity of AFB1, we conducted a review of published studies of AFB1-induced epigenetic alterations...
June 20, 2017: Food and Chemical Toxicology
https://www.readbyqxmd.com/read/28645790/vitamin-e-deficiency-during-embryogenesis-in-zebrafish-causes-lasting-metabolic-and-cognitive-impairments-despite-refeeding-adequate-diets
#17
Melissa McDougall, Jaewoo Choi, Lisa Truong, Robert Tanguay, Maret G Traber
Vitamin E (α-tocopherol; VitE) is a lipophilic antioxidant required for normal embryonic development in vertebrates, but the long-term effects of embryonic VitE deficiency, and whether they are ameliorated by feeding VitE-adequate diets, remain unknown. We addressed these questions using a zebrafish (Danio rerio) model of developmental VitE deficiency followed by dietary remediation. Adult zebrafish maintained on VitE-deficient (E-) or sufficient (E+) diets were spawned to obtained E- and E+ embryos, respectively, which we evaluated up to 12 days post-fertilization (dpf)...
June 20, 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/28645747/a-review-of-dna-methylation-in-depression
#18
REVIEW
Dongmei Chen, Lin Meng, Fei Pei, Yang Zheng, Jiyan Leng
As one of the most common psychiatric disorders, depression has been a major public health problem. Growing evidence suggests that epigenetic modification is essential in biological processes of depression. Recently, DNA methylation has been regarded as a potential link between environment and depression. In this review, we reviewed current studies of the association between DNA methylation and depression. The association between DNA methylation of seven genes, including BDNF, SLC6A4, NR3C1, 5-HTR (1A, 2A, and 3A), FKBP5, MAO-A and OXTR, and depression were reviewed in this study...
June 20, 2017: Journal of Clinical Neuroscience: Official Journal of the Neurosurgical Society of Australasia
https://www.readbyqxmd.com/read/28645745/dna-methylation-of-dlg4-and-gja-1-of-human-hippocampus-and-prefrontal-cortex-in-major-depression-is-unchanged-in-comparison-to-healthy-individuals
#19
Oliver Kaut, Amit Sharma, Ina Schmitt, René Hurlemann, Ullrich Wüllner
Epigenetic alterations provide a potential mechanism to account for the numerous gene-environment interactions that have been reported in association with neuropsychiatric phenotypes. In context to major depression disorder (MDD), where postmortem and neuroimaging studies provide insights into dysfunctional brain regions, involvement of genetic heterogeneity also revealed the complexity of this disorder. Despite intensive research during the past several decades and information from genome wide studies, pathophysiology of depressive disorders remained elusive...
June 20, 2017: Journal of Clinical Neuroscience: Official Journal of the Neurosurgical Society of Australasia
https://www.readbyqxmd.com/read/28645654/epigenome-dysregulation-in-cholangiocarcinoma
#20
REVIEW
Colm J O'Rourke, Patricia Munoz-Garrido, Esmeralda L Aguayo, Jesper B Andersen
Epigenomics is a fast-evolving field of research that has lately attracted considerable interest, mainly due to the reversibility of epigenetic marks. Clinically, among solid tumors, the field is still limited. In cholangiocarcinoma (CCA) it is well known that the epigenetic landscape is deregulated both during carcinogenesis and disease progression as a consequence of aberrant mechanisms leading to genome instability. In this article, we will briefly review the molecular alterations that have been described in the transformation of normal cholangiocytes into malignant derivatives, focusing on the role of non-coding RNA (ncRNA) interactions, DNA methylation, post-translational modifications (PTMs) of histones and chromatin remodeling complexes...
June 20, 2017: Biochimica et Biophysica Acta
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