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Cytosine methylation

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https://www.readbyqxmd.com/read/29343623/identifying-dna-methylation-biomarkers-for-non-endoscopic-detection-of-barrett-s-esophagus
#1
Helen R Moinova, Thomas LaFramboise, James D Lutterbaugh, Apoorva Krishna Chandar, John Dumot, Ashley Faulx, Wendy Brock, Omar De la Cruz Cabrera, Kishore Guda, Jill S Barnholtz-Sloan, Prasad G Iyer, Marcia I Canto, Jean S Wang, Nicholas J Shaheen, Prashanti N Thota, Joseph E Willis, Amitabh Chak, Sanford D Markowitz
We report a biomarker-based non-endoscopic method for detecting Barrett's esophagus (BE) based on detecting methylated DNAs retrieved via a swallowable balloon-based esophageal sampling device. BE is the precursor of, and a major recognized risk factor for, developing esophageal adenocarcinoma. Endoscopy, the current standard for BE detection, is not cost-effective for population screening. We performed genome-wide screening to ascertain regions targeted for recurrent aberrant cytosine methylation in BE, identifying high-frequency methylation within the CCNA1 locus...
January 17, 2018: Science Translational Medicine
https://www.readbyqxmd.com/read/29339652/smoking-and-promoter-specific-deoxyribonucleic-acid-methylation-of-the-atrial-natriuretic-peptide-gene-methylation-of-smokers-and-non-smokers-differs-significantly-during-withdrawal
#2
Alexander Glahn, Mathias Rhein, Helge Frieling, Rilana Schuster, Alain El Aissami, Stefan Bleich, Thomas Hillemacher, Marc Muschler
BACKGROUND: Atrial natriuretic peptide (ANP) is well known in psychiatric disorders to modulate hypothalamic-pituitary-adrenal axis activity. Disturbances of ANP have been described in early abstinent alcohol-dependent patients. This is the first longitudinal investigation on cytosine-phosphatidyl-guanine (CpG)-island promoter methylation of the ANP gene in the blood of tobacco-dependent patients. METHODS: In a longitudinal approach, we investigated whether changes in ANP serum levels correlated to CpG methylation of the respective gene promoters on days 1, 7, and 14 of tobacco withdrawal...
January 16, 2018: European Addiction Research
https://www.readbyqxmd.com/read/29335468/aicda-drives-epigenetic-heterogeneity-and-accelerates-germinal-center-derived-lymphomagenesis
#3
Matt Teater, Pilar M Dominguez, David Redmond, Zhengming Chen, Daisuke Ennishi, David W Scott, Luisa Cimmino, Paola Ghione, Jayanta Chaudhuri, Randy D Gascoyne, Iannis Aifantis, Giorgio Inghirami, Olivier Elemento, Ari Melnick, Rita Shaknovich
Epigenetic heterogeneity is emerging as a feature of tumors. In diffuse large B-cell lymphoma (DLBCL), increased cytosine methylation heterogeneity is associated with poor clinical outcome, yet the underlying mechanisms remain unclear. Activation-induced cytidine deaminase (AICDA), an enzyme that mediates affinity maturation and facilitates DNA demethylation in germinal center (GC) B cells, is required for DLBCL pathogenesis and linked to inferior outcome. Here we show that AICDA overexpression causes more aggressive disease in BCL2-driven murine lymphomas...
January 15, 2018: Nature Communications
https://www.readbyqxmd.com/read/29335298/crystal-structure-of-ispf-from-bacillus-subtilis-and-absence-of-protein-complex-assembly-among-ispd-ispe-ispf-enzymes-in-the-mep-pathway
#4
Zhongchuan Liu, Yun Jin, Weifeng Liu, Yong Tao, Ganggang Wang
2-C-methyl-d-erythritol 2, 4-cyclodiphosphate synthase (IspF) is a key enzyme in the 2-C-Methyl-d-erythritol-4-phosphate (MEP) pathway of isoprenoid biosynthesis. This enzyme catalyzes the 4-diphosphocytidyl-2-C-methyl-d-erythritol 2-phosphate (CDPME2P) to 2-C-methyl-d-erythritol 2, 4-cyclodiphosphate (MEcDP) with concomitant release of cytidine 5'-diphospate (cytosine monophosphate) (CMP). Bacillus subtilis is a potential host cell for the production of isoprenoids, but few studies are performed on the key enzymes of MEP pathway in B...
January 15, 2018: Bioscience Reports
https://www.readbyqxmd.com/read/29327208/analysis-of-dna-modifications-in-aging-research
#5
REVIEW
Dustin R Masser, Niran Hadad, Hunter Porter, Michael B Stout, Archana Unnikrishnan, David R Stanford, Willard M Freeman
As geroscience research extends into the role of epigenetics in aging and age-related disease, researchers are being confronted with unfamiliar molecular techniques and data analysis methods that can be difficult to integrate into their work. In this review, we focus on the analysis of DNA modifications, namely cytosine methylation and hydroxymethylation, through next-generation sequencing methods. While older techniques for modification analysis performed relative quantitation across regions of the genome or examined average genome levels, these analyses lack the desired specificity, rigor, and genomic coverage to firmly establish the nature of genomic methylation patterns and their response to aging...
January 11, 2018: GeroScience
https://www.readbyqxmd.com/read/29327010/dna-methylation-assay-using-droplet-based-dna-melting-curve-analysis
#6
F-W Liu, H-F Liao, S-P Lin, Y-W Lu
DNA methylation is an epigenetic regulation of gene expression, which has drawn great attention in biomedical research due to its association with various diseases. A robust, inexpensive platform to detect and quantify the methylation status in a specific genomic region is necessary. In this study, an on-chip analytical technique of cytosine methylation with droplets in a microchannel is proposed. Genomic DNA samples are encapsulated into a series of droplets and transported through a detection region, where a stable temperature gradient is created...
January 12, 2018: Lab on a Chip
https://www.readbyqxmd.com/read/29326313/dna-methylation-and-age-independent-cardiovascular-risk-an-epigenome-wide-approach-the-regicor-registre-giron%C3%A3-del-cor-study
#7
Alba Fernández-Sanlés, Sergi Sayols-Baixeras, Santiago Curcio, Isaac Subirana, Jaume Marrugat, Roberto Elosua
OBJECTIVE: The objectives of this study were to decipher whether age-independent cardiovascular risk is associated with DNA methylation at 5'-cytosine-phosphate-guanine-3' (CpG) level and to determine whether these differential methylation signatures are associated with the incidence of cardiovascular events. APPROACH AND RESULTS: We designed a 2-stage, cross-sectional, epigenome-wide association study. Age-independent cardiovascular risk calculation was based on vascular age and on the residuals of the relationship between age and cardiovascular risk...
January 11, 2018: Arteriosclerosis, Thrombosis, and Vascular Biology
https://www.readbyqxmd.com/read/29325454/down-expression-of-p2rx2-kcnq5-erbb3-and-socs3-through-dna-hypermethylation-in-elderly-women-with-presbycusis
#8
Amal Bouzid, Ibtihel Smeti, Leila Dhouib, Magali Roche, Imen Achour, Aida Khalfallah, Abdullah Ahmed Gibriel, Ilhem Charfeddine, Hammadi Ayadi, Joel Lachuer, Abdelmonem Ghorbel, Christine Petit, Saber Masmoudi
CONTEXT: Presbycusis, an age-related hearing impairment (ARHI), represents the most common sensory disability in adults. Today, the molecular mechanisms underlying presbycusis remain unclear. This is in particular due to the fact that ARHI is a multifactorial complex disorder resulting from several genomic factors interacting with lifelong cumulative effects of: disease, diet, and environment. OBJECTIVE: Identification of novel biomarkers for presbycusis. MATERIALS AND METHODS: We selectively ascertained eighteen elderly unrelated women lacking environmental and metabolic risk factors...
January 11, 2018: Biomarkers: Biochemical Indicators of Exposure, Response, and Susceptibility to Chemicals
https://www.readbyqxmd.com/read/29325019/deep-molecular-phenotypes-link-complex-disorders-and-physiological-insult-to-cpg-methylation
#9
Shaza B Zaghlool, Dennis O Mook-Kanamori, Sara Kader, Nisha Stephan, Anna Halama, Rudolf Engelke, Hina Sarwath, Eman K Al-Dous, Yasmin A Mohamoud, Werner Roemisch-Margl, Jerzy Adamski, Gabi Kastenmüller, Nele Friedrich, Alessia Visconti, Pei-Chien Tsai, Tim Spector, Jordana Bell, Mario Falchi, Annika Wahl, Melanie Waldenberger, Annette Peters, Christian Gieger, Maija Pezer, Gordan Lauc, Johannes Graumann, Joel A Malek, Karsten Suhre
Epigenetic regulation of cellular function provides a mechanism for rapid organismal adaptation to changes in health, lifestyle, and environment. Associations of cytosine-guanine di-nucleotide (CpG) methylation with clinical endpoints that overlap with metabolic phenotypes suggest a regulatory role for these CpG sites in the body's response to disease or environmental stress. We previously identified 20 CpG sites in an epigenome-wide association study (EWAS) with metabolomics that were also associated in recent EWASs with diabetes-, obesity-, and smoking-related endpoints...
January 8, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29324752/tet-protein-function-during-drosophila-development
#10
Fei Wang, Svetlana Minakhina, Hiep Tran, Neha Changela, Joseph Kramer, Ruth Steward
The TET (Ten-eleven translocation) 1, 2 and 3 proteins have been shown to function as DNA hydroxymethylases in vertebrates and their requirements have been documented extensively. Recently, the Tet proteins have been shown to also hydroxylate 5-methylcytosine in RNA. 5-hydroxymethylcytosine (5hmrC) is enriched in messenger RNA but the function of this modification has yet to be elucidated. Because Cytosine methylation in DNA is barely detectable in Drosophila, it serves as an ideal model to study the biological function of 5hmrC...
2018: PloS One
https://www.readbyqxmd.com/read/29323674/can-5-methylcytosine-analogues-with-extended-alkyl-side-chains-guide-dna-methylation
#11
D Kotandeniya, C L Seiler, J Fernandez, S S Pujari, L Curwick, K Murphy, S Wickramaratne, S Yan, D Murphy, Yuk Y Sham, N Y Tretyakova
5-Methylcytosine (MeC) is an endogenous modification of DNA that plays a crucial role in DNA-protein interactions, chromatin structure, epigenetic regulation, and DNA repair. MeC is produced via enzymatic methylation of the C-5 position of cytosine by DNA-methyltransferases (DNMT) which use S-adenosylmethionine (SAM) as a cofactor. Hemimethylated CG dinucleotides generated as a result of DNA replication are specifically recognized and methylated by maintenance DNA methyltransferase 1 (DNMT1). The accuracy of DNMT1-mediated methylation is essential for preserving tissue-specific DNA methylation and thus gene expression patterns...
January 11, 2018: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/29322419/analysis-of-dna-methylation-in-tissues-exposed-to-inflammation
#12
Naoko Hattori, Toshikazu Ushijima
Induction of aberrant DNA methylation is one of the most important mechanisms mediating the effect of inflammation on cancer development. Aberrant methylation of promoter CpG islands of tumor suppressor genes can silence their downstream genes, and that in cancer tissues is associated with prognosis or therapeutic effects. In addition, aberrant methylation can occur in tissues exposed to specific types of inflammation, producing a so-called "epigenetic field for cancerization," and its accumulation is correlated with cancer risk...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29321305/arabidopsis-rna-polymerase-v-mediates-enhanced-compaction-and-silencing-of-geminivirus-and-transposon-chromatin-during-host-recovery-from-infection
#13
Tami Coursey, Elizabeth Regedanz, David M Bisaro
Plants employ RNA-directed DNA methylation (RdDM) and dimethylation of histone 3 lysine 9 (H3K9me2) to silence geminiviruses and transposable elements (TEs). We previously showed that canonical RdDM (Pol IV-RdDM) involving RNA polymerases IV and V (Pol IV and Pol V) is required for Arabidopsis thaliana to recover from infection with Beet curly top virus lacking a suppressor protein that inhibits methylation (BCTV L2-). Recovery, which is characterized by reduced viral DNA levels and symptom remission, allows normal floral development...
January 10, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29277568/effect-of-dc-%C3%A2-d-m5c-substitutions-on-the-folding-of-intramolecular-triplexes-with-mixed-tat-and-c-gc-base-triplets
#14
Carolyn E Carr, Rajkumar Ganugula, Ronald Shikiya, Ana Maria Soto, Luis A Marky
Oligonucleotide-directed triple helix formation has been recognized as a potential tool for targeting genes with high specificity. Cystosine methylation in the 5' position is both ubiquitous and a stable regulatory modification, which could potentially stabilize triple helix formation. In this work, we have used a combination of calorimetric and spectroscopic techniques to study the intramolecular unfolding of four triplexes and two duplexes. We used the following triplex control sequence, named Control Tri, d(AGAGAC5TCTCTC5TCTCT), where C5 are loops of five cytosines...
December 22, 2017: Biochimie
https://www.readbyqxmd.com/read/29261844/crosstalk-between-histone-and-dna-methylation-in-regulation-of-retinal-matrix-metalloproteinase-9-in-diabetes
#15
Arul J Duraisamy, Manish Mishra, Renu A Kowluru
Purpose: Diabetes activates matrix metalloproteinase-9 (MMP-9), and MMP-9 via damaging retinal mitochondria, activates capillary cell apoptosis. MMP-9 promoter has binding sites for many transcription factors, and in diabetes its promoter undergoes epigenetic modifications, including histone modifications and DNA methylation. Enhancer of Zeste homolog 2 (Ezh2), which catalyzes dimethylation/trimethylation of histone 3 lysine 27 (H3K27me2 and me3), is also associated with DNA methylation...
December 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/29259859/mthfr-promoter-hypermethylation-may-lead-to-congenital-heart-defects-in-down-syndrome
#16
Ambreen Asim, Sarita Agarwal, Inusha Panigrahi, Nazia Saiyed, Sonal Bakshi
Altered global methylation levels revealed LINE-1 methylation in young mothers of Down syndrome (DS) compared to controls suggesting the possibility of impaired DNA methylation causing abnormal segregation of chromosome 21. Methylene Tetrahydrofolate Reductase (MTHFR) is one of the major enzymes of the folate metabolism pathway. MTHFR gene polymorphism has been associated with maternal risk for DS. Studies have revealed that increased MTHFR promoter methylation results in the reduction of MTHFR protein activity further leading to increased risk of various diseases...
November 2017: Intractable & Rare Diseases Research
https://www.readbyqxmd.com/read/29258436/an-optimized-rapid-bisulfite-conversion-method-with-high-recovery-of-cell-free-dna
#17
Shaohua Yi, Fei Long, Juanbo Cheng, Daixin Huang
BACKGROUND: Methylation analysis of cell-free DNA is a encouraging tool for tumor diagnosis, monitoring and prognosis. Sensitivity of methylation analysis is a very important matter due to the tiny amounts of cell-free DNA available in plasma. Most current methods of DNA methylation analysis are based on the difference of bisulfite-mediated deamination of cytosine between cytosine and 5-methylcytosine. However, the recovery of bisulfite-converted DNA based on current methods is very poor for the methylation analysis of cell-free DNA...
December 19, 2017: BMC Molecular Biology
https://www.readbyqxmd.com/read/29258399/perceived-racial-discrimination-and-dna-methylation-among-african-american-women-in-the-intergen-study
#18
Veronica Barcelona de Mendoza, Yunfeng Huang, Cindy A Crusto, Yan V Sun, Jacquelyn Y Taylor
INTRODUCTION: Experiences of racial discrimination have been associated with poor health outcomes. Little is known, however, about how perceived racial discrimination influences DNA methylation (DNAm) among African Americans (AAs). We examined the association of experiences of discrimination with DNAm among AA women in the Intergenerational Impact of Genetic and Psychological Factors on Blood Pressure (InterGEN) study. METHODS: The InterGEN study examines the effects of genetic and psychological factors on blood pressure among AA women and their children...
January 1, 2017: Biological Research for Nursing
https://www.readbyqxmd.com/read/29251421/recognition-of-oxidized-5-methylcytosine-derivatives-in-dna-by-natural-and-engineered-protein-scaffolds
#19
REVIEW
Álvaro Muñoz-López, Daniel Summerer
Methylation of genomic cytosine to 5-methylcytosine is a central regulatory element of mammalian gene expression with important roles in development and disease. 5-methylcytosine can be actively reversed to cytosine via oxidation to 5-hydroxymethyl-, 5-formyl-, and 5-carboxylcytosine by ten-eleven-translocation dioxygenases and subsequent base excision repair or replication-dependent dilution. Moreover, the oxidized 5-methylcytosine derivatives are potential epigenetic marks with unique biological roles. Key to a better understanding of these roles are insights into the interactions of the nucleobases with DNA-binding protein scaffolds: Natural scaffolds involved in transcription, 5-methylcytosine-reading and -editing as well as general chromatin organization can be selectively recruited or repulsed by oxidized 5-methylcytosines, forming the basis of their biological functions...
December 18, 2017: Chemical Record: An Official Publication of the Chemical Society of Japan ... [et Al.]
https://www.readbyqxmd.com/read/29247759/repeated-methamphetamine-and-modafinil-induce-differential-cognitive-effects-and-specific-histone-acetylation-and-dna-methylation-profiles-in-the-mouse-medial-prefrontal-cortex
#20
Betina González, Subramaniam Jayanthi, Natalia Gomez, Oscar V Torres, Máximo H Sosa, Alejandra Bernardi, Francisco J Urbano, Edgar García-Rill, Jean-Lud Cadet, Verónica Bisagno
Methamphetamine (METH) and modafinil are psychostimulants with different long-term cognitive profiles: METH is addictive and leads to cognitive decline, whereas modafinil has little abuse liability and is a cognitive enhancer. Increasing evidence implicates epigenetic mechanisms of gene regulation behind the lasting changes that drugs of abuse and other psychotropic compounds induce in the brain, like the control of gene expression by histones 3 and 4 tails acetylation (H3ac and H4ac) and DNA cytosine methylation (5-mC)...
December 13, 2017: Progress in Neuro-psychopharmacology & Biological Psychiatry
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