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Dna hydroxymethylation

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https://www.readbyqxmd.com/read/29327208/analysis-of-dna-modifications-in-aging-research
#1
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/29325627/epigenetic-mechanisms-underlying-nervous-system-diseases
#2
Irfan A Qureshi, Mark F Mehler
Epigenetic mechanisms act as control systems for modulating genomic structure and activity in response to evolving profiles of cell-extrinsic, cell-cell, and cell-intrinsic signals. These dynamic processes are responsible for mediating cell- and tissue-specific gene expression and function and gene-gene and gene-environmental interactions. The major epigenetic mechanisms include DNA methylation and hydroxymethylation; histone protein posttranslational modifications, nucleosome remodeling/repositioning, and higher-order chromatin reorganization; noncoding RNA regulation; and RNA editing...
2018: Handbook of Clinical Neurology
https://www.readbyqxmd.com/read/29316399/enrichment-and-quantitative-determination-of-5-hydroxymethyl-2-deoxycytidine-5-formyl-2-deoxycytidine-and-5-carboxyl-2-deoxycytidine-in-human-urine-of-breast-cancer-by-magnetic-high-cross-linked-microporous-polymers-based-on-poly-ionic-liquid
#3
Mengzhe Guo, Liyan Zhang, Yan Du, Wencheng Du, Dantong Liu, Cheng Guo, Yuanjiang Pan, Dao-Quan Tang
5-(hydroxymethyl)-2'-deoxycytidine (5-hmdC), 5-(formyl)-2'-deoxycytidine (5-fodC), and 5-(carboxyl)-2'-deoxycytidine (5-cadC) are crucial intermediate products of DNA demethylation pathway, which can also act as potential biomarker reflecting the diagnosis and prognosis in multiple tumors. Detecting 5-hmdC, 5-fodC, and 5-cadC in human urine has various advantages including readily available samples and non-invasive to patients. However, few works have reported the detection of 5-fodC and 5-cadC due to their trace amounts...
January 9, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29286410/an-engineered-split-tet2-enzyme-for-chemical-inducible-dna-hydroxymethylation-and-epigenetic-remodeling
#4
Minjung Lee, Yubin Zhou, Yun Huang
DNA methylation is a stable and heritable epigenetic modification in the mammalian genome and is involved in regulating gene expression to control cellular functions. The reversal of DNA methylation, or DNA demethylation, is mediated by the ten-eleven translocation (TET) protein family of dioxygenases. Although it has been widely reported that aberrant DNA methylation and demethylation are associated with developmental defects and cancer, how these epigenetic changes directly contribute to the subsequent alteration in gene expression or disease progression remains unclear, largely owing to the lack of reliable tools to accurately add or remove DNA modifications in the genome at defined temporal and spatial resolution...
December 18, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29277934/fam20c-could-be-targeted-by-tet1-to-promote-odontoblastic-differentiation-potential-of-human-dental-pulp-cells
#5
Qimeng Li, Baicheng Yi, Zhihui Feng, Runsha Meng, Cheng Tian, Qiong Xu
OBJECTIVES: Ten-eleven translocation 1 (TET1) is a DNA methylcytosine (mC) dioxygenase discovered recently that can convert 5-mC into 5-hydroxymethylcytosine (5hmC). We previously reported that TET1 promotes odontoblastic differentiation of human dental pulp cells (hDPCs). The gene encoding the family with sequence similarity 20, member C (FAM20C) protein, is a potential TET1 target and showed demethylation during odontoblastic differentiation of hDPCs in our previous study. This study aimed to explore whether TET1-mediated hydroxymethylation could activate the FAM20C gene, thereby regulating hDPC differentiation...
December 25, 2017: Cell Proliferation
https://www.readbyqxmd.com/read/29261844/crosstalk-between-histone-and-dna-methylation-in-regulation-of-retinal-matrix-metalloproteinase-9-in-diabetes
#6
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/29251421/recognition-of-oxidized-5-methylcytosine-derivatives-in-dna-by-natural-and-engineered-protein-scaffolds
#7
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/29239726/camp-signaling-regulates-dna-hydroxymethylation-by-augmenting-the-intracellular-labile-ferrous-iron-pool
#8
Vladimir Camarena, David W Sant, Tyler C Huff, Sushmita Mustafi, Ryan K Muir, Allegra T Aron, Christopher J Chang, Adam R Renslo, Paula V Monje, Gaofeng Wang
It is widely accepted that cAMP regulates gene transcription principally by activating the protein kinase A (PKA)-targeted transcription factors. Here, we show that cAMP enhances the generation of 5-hydroxymethylcytosine (5hmC) in multiple cell types. 5hmC is converted from 5-methylcytosine (5mC) by Tet methylcytosine dioxygenases, for which Fe(II) is an essential cofactor. The promotion of 5hmC was mediated by a prompt increase of the intracellular labile Fe(II) pool (LIP). cAMP enhanced the acidification of endosomes for Fe(II) release to the LIP likely through RapGEF2...
December 14, 2017: ELife
https://www.readbyqxmd.com/read/29224170/affinity-based-enrichment-techniques-for-the-genome-wide-analysis-of-5-hydroxymethylcytosine
#9
John P Thomson, Richard R Meehan
Since its initial characterization in 2009 there has been a great degree of interest in comparative profiling of 5-hydroxymethylcytosine (5hmC) nucleotides in vertebrate DNA. Through a host of genome-wide studies the distribution of 5hmC has been mapped in a range of cell lines, tissue types and organisms; the majority of which have been generated through affinity-based methods for 5hmC enrichment. Although recent advances in the field have resulted in the ability to investigate the levels of both methylated and hydroxymethylated cytosines at single base resolution, such studies are still relatively cost-prohibitive as well as technically challenging...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224167/dna-methylation-analysis-of-free-circulating-dna-in-body-fluids
#10
Maria Jung, Glen Kristiansen, Dimo Dietrich
Circulating cell-free DNA in body fluids is an analyte of great interest in basic and clinical research. The analyses of DNA methylation and hydroxymethylation patterns in body fluids might allow one to determine the certain state of a disease, in particular of cancer. DNA methylation biomarkers in liquid biopsies, i.e. blood plasma samples, may help optimizing personalized therapy for individual patients. DNA methylation analyses of specific loci usually require a bisulfite conversion of the DNA, which requires a sufficiently high amount of DNA at the appropriate concentration...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224146/the-help-based-dna-methylation-assays
#11
John M Greally
Restriction enzymes have been valuable tools for representing the genome for DNA methylation assays, whether by using methylation-dependent enzymes or by sampling a reduced representation of the genome using a methylation-insensitive enzyme. These survey assays have remained mainstays of genome-wide approaches even with the development of more comprehensive shotgun genome-wide bisulphite sequencing-based assays, as they are significantly more affordable. DNA methylation survey assays are numerous and include reduced representation bisulphite sequencing (RRBS), the Illumina HumanMethylation450K and EPIC microarray system, and our evolving series of HELP-based assays...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224138/quantification-of-global-dna-methylation-levels-by-mass-spectrometry
#12
Agustin F Fernandez, Luis Valledor, Fernando Vallejo, Maria Jesús Cañal, Mario F Fraga
Global DNA methylation was classically considered the relative percentage of 5-methylcysine (5mC) with respect to total cytosine (C). Early approaches were based on the use of high-performance separation technologies and UV detection. However, the recent development of protocols using mass spectrometry for the detection has increased sensibility and permitted the precise identification of peak compounds based on their molecular masses. This allows work to be conducted with much less genomic DNA starting material and also to quantify 5-hydroxymethyl-cytosine (5hmC), a recently identified form of methylated cytosine that could play an important role in active DNA demethylation...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29217223/temporal-variability-of-global-dna-methylation-and-hydroxymethylation-in-buccal-cells-of-healthy-adults-association-with-air-pollution
#13
Siemon De Nys, Radu-Corneliu Duca, Tim Nawrot, Peter Hoet, Bart Van Meerbeek, Kirsten L Van Landuyt, Lode Godderis
BACKGROUND: Epigenetic changes, such as DNA methylation, are observed in response to environmental exposure and in the development of several chronic diseases. Consequently, DNA methylation alterations might serve as indicators of early effects. In this context, the aim of this study was to assess the temporal variability of global DNA methylation and hydroxymethylation levels in buccal cells from healthy adult volunteers. METHODS: Global DNA methylation (%5mdC) and hydroxymethylation (%5hmdC) levels in human buccal cells, collected from 26 healthy adults at different time points, were quantified by UPLC-MS/MS...
December 4, 2017: Environment International
https://www.readbyqxmd.com/read/29211825/bicycle-a-bioinformatics-pipeline-to-analyze-bisulfite-sequencing-data
#14
Osvaldo Graña, Hugo López-Fernández, Florentino Fdez-Riverola, David González Pisano, Daniel Glez-Peña
Summary: High-throughput sequencing of bisulfite-converted DNA is a technique used to measure DNA methylation levels. Although a considerable number of computational pipelines have been developed to analyze such data, none of them tackles all the peculiarities of the analysis together, revealing limitations that can force the user to manually perform additional steps needed for a complete processing of the data. This article presents bicycle, an integrated, flexible analysis pipeline for bisulfite sequencing data...
December 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29194108/epigenetics-of-inflammatory-arthritis
#15
Deepa Hammaker, Gary S Firestein
PURPOSE OF REVIEW: Aberrant epigenetic changes in DNA methylation, histone marks, and noncoding RNA expression regulate the pathogenesis of many rheumatic diseases. The present article will review the recent advances in the epigenetic profile of inflammatory arthritis and discuss diagnostic biomarkers and potential therapeutic targets. RECENT FINDINGS: Methylation signatures of fibroblast-like synoviocytes not only distinguish rheumatoid arthritis (RA) and osteoarthritis (OA), but also early RAs from late RAs or juvenile idiopathic arthritis...
November 30, 2017: Current Opinion in Rheumatology
https://www.readbyqxmd.com/read/29191310/dietary-exposure-to-di-isobutyl-phthalate-increases-urinary-5-methyl-2-deoxycytidine-level-and-affects-reproductive-function-in-adult-male-mice
#16
Yitao Pan, Xiaoyang Wang, Leo W Y Yeung, Nan Sheng, Qianqian Cui, Ruina Cui, Hongxia Zhang, Jiayin Dai
Phthalates are a large family of ubiquitous environmental pollutants suspected of being endocrine disruptors. Epidemiological studies have associated phthalate metabolites with decreased reproductive parameters and linked phthalate exposure with the level of urinary 5-methyl-2'-deoxycytidine (5mdC, a product of methylated DNA). In this study, adult male mice were exposed to 450mg di-isobutyl phthalate (DiBP)/(kg·day) via dietary exposure for 28days. Mono-isobutyl phthalate (MiBP, the urinary metabolite) and reproductive function parameters were determined...
November 2017: Journal of Environmental Sciences (China)
https://www.readbyqxmd.com/read/29191063/changes-in-dna-methylation-induced-by-multi-walled-carbon-nanotube-exposure-in-the-workplace
#17
Manosij Ghosh, Deniz Öner, Katrien Poels, Ali M Tabish, Jelle Vlaanderen, Anjoeka Pronk, Eelco Kuijpers, Qing Lan, Roel Vermeulen, Bram Bekaert, Peter Hm Hoet, Lode Godderis
This study was designed to assess the epigenetic alterations in blood cells, induced by occupational exposure to multi-wall carbon nanotubes (MWCNT). The study population comprised of MWCNT-exposed workers (n=24) and unexposed controls (n=43) from the same workplace. We measured global DNA methylation/hydroxymethylation levels on the 5th cytosine residues using a validated liquid chromatography tandem-mass spectrometry (LC-MS/MS) method. Sequence-specific methylation of LINE1 retrotransposable element 1 (L1RE1) elements, and promoter regions of functionally important genes associated with epigenetic regulation [DNA methyltransferase-1 (DNMT1) and histone deacetylase 4 (HDAC4)], DNA damage/repair and cell cycle pathways [nuclear protein, coactivator of histone transcription/ATM serine/threonine kinase (NPAT/ATM)], and a potential transforming growth factor beta (TGF-β) repressor [SKI proto-oncogene (SKI)] were studied using bisulfite pyrosequencing...
November 30, 2017: Nanotoxicology
https://www.readbyqxmd.com/read/29190698/profiles-of-a-broad-spectrum-of-epigenetic-dna-modifications-in-normal-and-malignant-human-cell-lines-proliferation-rate-is-not-the-major-factor-responsible-for-the-5-hydroxymethyl-2-deoxycytidine-level-in-cultured-cancerous-cell-lines
#18
Marek Foksinski, Ewelina Zarakowska, Daniel Gackowski, Magdalena Skonieczna, Karolina Gajda, Dorota Hudy, Anna Szpila, Karol Bialkowski, Marta Starczak, Anna Labejszo, Jaroslaw Czyz, Joanna Rzeszowska-Wolny, Ryszard Olinski
Active demethylation of 5-methylcytosine moiety in DNA occurs by its sequential oxidation to 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxycytosine, catalysed by enzymes of the Ten-Eleven Translocation family proteins (TETs 1, 2 and 3). Here we analyzed for the first time all the intermediate products of DNA demethylation pathway in the form of deoxynucleosides (5-methyl-2'-deoxycytidine, 5-(hydroxymethyl)-2'-deoxycytidine, 5-formyl-2'-deoxycytidine and 5-carboxy-2'-deoxycytidine as well as 5-(hydroxymethyl)-2'-deoxyuridine) using automated isotope-dilution online two-dimensional ultra-performance liquid chromatography with tandem mass spectrometry...
2017: PloS One
https://www.readbyqxmd.com/read/29185898/both-enantiomers-of-6-isoneplanocin
#19
Chong Liu, Qi Chen, Stewart W Schneller
Both enantiomers of the isomer of neplanocin where the C-4' hydroxymethyl has been displaced to the 6'-position (that is, 6'-isoneplanocin) have been prepared in 5 steps from known, protected iodocyclopentenones. Both products were evaluated against a number of DNA and RNA viruses and found to be inactive. This observation is suggested to be due to the displacement of the C-4' hydroxymethyl of neplanocin (in the D-like form) away from the lysine425 of S-adenosylhomocysteine hydrolase, which is important for inhibition by neplanocin and, in turn, its antiviral activity...
November 29, 2017: Nucleosides, Nucleotides & Nucleic Acids
https://www.readbyqxmd.com/read/29184924/5-hydroxymethyl-uracil-and-cytosine-as-potential-epigenetic-marks-enhancing-or-inhibiting-transcription-with-bacterial-rna-polymerase
#20
Martina Janoušková, Zuzana Vaníková, Fabrizia Nici, Soňa Boháčová, Dragana Vítovská, Hana Šanderová, Michal Hocek, Libor Krásný
DNA templates containing 5-hydroxymethyluracil or 5-hydroxymethylcytosine were used in an in vitro transcription assay with RNA polymerase from Escherichia coli. A strong enhancement of transcription was observed from DNA containing the Pveg promoter whereas a decrease was observed from DNA containing the rrnB P1 promoter, suggesting that they may act as epigenetic marks.
November 29, 2017: Chemical Communications: Chem Comm
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