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Cytosine methylation

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https://www.readbyqxmd.com/read/28421879/dna-methylation-mechanism-of-intracellular-zinc-deficiency-induced-injury-in-primary-hippocampal-neurons-in-the-rat-brain
#1
Cong-Cong He, Zi-Yu Wang, Kun Tian, Wei Liu, Yi-Bo Li, Yan Hong, Li-Xia Yu, Wei Pang, Yu-Gang Jiang, Yan-Qiang Liu
OBJECTIVE: To explore Zn(2+) deficiency-induced neuronal injury in relation to DNA methylation, providing valuable data and basic information for clarifying the mechanism of Zn(2+) deficiency-induced neuronal injury. METHODS: Cultured hippocampal neurons were exposed to the cell membrane-permeant Zn(2+) chelator N,N,N',N'-Tetrakis (2-pyridylmethyl) ethylenediamine (TPEN) (2 μM), and to TPEN (2 μM) plus ZnSO4 (5 μM) for 24 hours. We analyzed intracellular Zn(2+) levels, neuronal viability, and protein/mRNA levels for DNA (cytosine-5) methyltransferase 1 (DNMT1), DNA (cytosine-5-) methyltransferase 3 alpha (DNMT3a), methyl CpG binding protein 2 (MeCP2), Brain-derived neurotrophic factor (BDNF), and growth arrest and DNA-damage-inducible, beta (GADD45b) in the treated neurons...
April 19, 2017: Nutritional Neuroscience
https://www.readbyqxmd.com/read/28408400/epigenetic-identity-in-aml-depends-on-disruption-of-non-promoter-regulatory-elements-and-is-affected-by-antagonistic-effects-of-mutations-in-epigenetic-modifiers
#2
Jacob Glass, Duane C Hassane, Bas Wouters, Hiroyoshi Kunimoto, Roberto Avellino, Francine E Garrett-Bakelman, Olga A Guryanova, Robert Bowman, Shira Redlich, Andrew Intlekofer, Cem Meydan, Tingting Qin, Mame P Fall, Alicia Alonso, Monica L Guzman, Peter Jm Valk, Craig B Thompson, Ross L Levine, Olivier Elemento, Ruud Delwel, Ari Melnick, Maria E Figueroa
Aberrant DNA methylation of gene promoters is a hallmark of AML. To define more precisely how cytosine methylation is redistributed in AML, we performed base-pair resolution methylome sequencing in 119 patients. We find that leukemic DNA methylation patterning is tightly linked to somatic mutations and primarily driven by regulatory elements outside of promoters and by CpG shores as opposed to CpG islands. Active enhancers displayed much stronger focal differential methylation than promoters and were generally aberrantly hypomethylated except in IDH2 mutant and CEBPA silenced AMLs...
April 13, 2017: Cancer Discovery
https://www.readbyqxmd.com/read/28403806/two-color-fluorescent-cytosine-extension-assay-for-the-determination-of-global-dna-methylation
#3
Gu Zhou, Craig Parfett, Cathy Cummings-Lorbetskie, Gong-Hua Xiao, Daniel Desaulniers
Here, we present a DNA restriction enzyme-based, fluorescent cytosine extension assay (CEA) to improve normalization and technical variation among sample-to-sample measurements. The assay includes end-labeling of parallel methylation-sensitive and methylation-insensitive DNA restriction enzyme digests along with co-purification and subsequent co-measurement of incorporated fluorescence. This non-radioactive, two-color fluorescent CEA (TCF-CEA) was shown to be a relatively rapid and accurate, with 3-fold greater precision than the one-color CEA...
April 1, 2017: BioTechniques
https://www.readbyqxmd.com/read/28401839/caregiver-maltreatment-causes-altered-neuronal-dna-methylation-in-female-rodents
#4
Jennifer Blaze, Tania L Roth
Negative experiences with a caregiver during infancy can result in long-term changes in brain function and behavior, but underlying mechanisms are not well understood. It is our central hypothesis that brain and behavior changes are conferred by early childhood adversity through epigenetic changes involving DNA methylation. Using a rodent model of early-life caregiver maltreatment (involving exposure to an adverse caregiving environment for postnatal days 1-7), we have previously demonstrated abnormal methylation of DNA associated with the brain-derived neurotrophic factor (Bdnf) gene in the medial prefrontal cortex (mPFC) of adult rats...
May 2017: Development and Psychopathology
https://www.readbyqxmd.com/read/28400750/methylation-on-rna-a-potential-mechanism-related-to-immune-priming-within-but-not-across-generations
#5
Cynthia Castro-Vargas, César Linares-López, Adolfo López-Torres, Katarzyna Wrobel, Juan C Torres-Guzmán, Gloria A G Hernández, Kazimierz Wrobel, Humberto Lanz-Mendoza, Jorge Contreras-Garduño
Invertebrate immune priming is a growing field in immunology. This phenomenon refers to the ability of invertebrates to generate a more vigorous immune response to a second encounter with a specific pathogen and can occur within and across generations. Although the precise mechanism has not been elucidated, it has been suggested that methylation of DNA is a cornerstone for this phenomenon. Here, using a novel method of analytical chemistry (a reversed-phase liquid chromatography procedure) and the beetle Tenebrio molitor as a model system, we did not find evidence to support this hypothesis taking into account the percentage of methylated cytosine entities in DNA (5mdC) within or across generations...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28396520/cytosine-modifications-modulate-the-chromatin-architecture-of-transcriptional-enhancers
#6
Elise A Mahé, Thierry Madigou, Aurélien A Sérandour, Maud Bizot, Stéphane Avner, Frédéric Chalmel, Gaëlle Palierne, Raphaël Métivier, Gilles Salbert
Epigenetic mechanisms are believed to play key roles in the establishment of cell-specific transcription programs. Accordingly, the modified bases 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) have been observed in DNA of genomic regulatory regions such as enhancers, and oxidation of 5mC into 5hmC by Ten Eleven Translocation (TET) proteins correlates with enhancer activation. However, the functional relationship between cytosine modifications and the chromatin architecture of enhancers remains elusive...
April 10, 2017: Genome Research
https://www.readbyqxmd.com/read/28394087/epigenome-wide-association-of-dna-methylation-in-whole-blood-with-bone-mineral-density
#7
John A Morris, Pei-Chien Tsai, Roby Joehanes, Jie Zheng, Katerina Trajanoska, Mette Soerensen, Vincenzo Forgetta, Juan Edgar Castillo-Fernandez, Morten Frost, Tim D Spector, Kaare Christensen, Lene Christiansen, Fernando Rivadeneira, Jonathan H Tobias, David M Evans, Douglas P Kiel, Yi-Hsiang Hsu, J Brent Richards, Jordana T Bell
Genetic and environmental determinants of skeletal phenotypes such as bone mineral density (BMD) may converge through the epigenome, providing a tool to better understand osteoporosis pathophysiology. As the epigenetics of BMD have been largely unexplored in humans, we performed an epigenome wide association study (EWAS) of BMD. We undertook a large-scale BMD EWAS using the Infinium HumanMethylation450 array to measure site-specific DNA methylation in up to 5,515 European descent individuals (NDiscovery  = 4,614, NValidation  = 901)...
April 10, 2017: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
https://www.readbyqxmd.com/read/28392841/assessing-alternative-base-substitutions-at-primer-cpg-sites-to-optimise-unbiased-pcr-amplification-of-methylated-sequences
#8
Ida L M Candiloro, Thomas Mikeska, Alexander Dobrovic
BACKGROUND: Determining the role of DNA methylation in various biological processes is dependent on the accurate representation of often highly complex patterns. Accurate representation is dependent on unbiased PCR amplification post bisulfite modification, regardless of methylation status of any given epiallele. This is highly dependent on primer design. Particular difficulties are raised by the analysis of CpG-rich regions, which are the usual regions of interest. Here, it is often difficult or impossible to avoid placing primers in CpG-free regions, particularly if one wants to target a specific part of a CpG-rich region...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28392157/context-and-complexity-analyzing-methylation-in-trinucleotide-sequences
#9
Xianwei Song, Xiaofeng Cao
Cytosine methylation in plants occurs in the mCG, mCHG, and mCHH (where H = A, T, or C) sequence contexts and specific pathways maintain methylation in each one. A recent publication revealed that substantial heterogeneity of methylated cytosine levels exists in the CHG/CHH trinucleotide contexts, which is associated with chromomethyltranferase functions in the maintenance of methylation.
April 6, 2017: Trends in Plant Science
https://www.readbyqxmd.com/read/28390507/a-cytosine-methyltransferase-ortholog-dmta-is-involved-in-the-sensitivity-of-aspergillus-flavus-to-environmental-stresses
#10
Qing-Qing Zhi, Jie-Ying Li, Qiu-Yun Liu, Zhu-Mei He
DNA methylation is an important epigenetic modification that depends on DNA methyltransferases (DMT). However, the filamentous fungus Aspergillus flavus has no detectable methylation, and role of a DMT homologue, DmtA, is undefined. Here we describe the role of the dmtA gene responding to changes in the environment by comparing knockout, point mutation, over-expression and wild type strains. Deletion of dmtA differentially affected conidia development in a media-dependent fashion, which suggests that dmtA plays an important role in conidiation...
May 2017: Fungal Biology
https://www.readbyqxmd.com/read/28389235/dna-methylated-alleles-of-the-phenylalanine-hydroxylase-promoter-remodeled-at-elevated-phenylalanine-levels-in-newborns-with-hyperphenylalaninemia
#11
Chike Bellarmine Item, Somayeh Farhadi, Andrea Schanzer, Susanne Greber-Platzer
OBJECTIVES: Although high phenylalanine (phe) exposure has been shown to influence the DNA methylation status of leukocytes in hyperphenylalaninemia (HPA), the potential of DNA methylation changes as a biomarker of pretreatment high phe exposure in diet free newborns with HPA has not been explored. We therefore investigated the DNA methylation pattern of the phenylalanine hydroxylase (PAH) gene promoter at different phe levels, and the possibility of DNA methylation pattern changes being a biomarker of high phe exposure in diet free newborns with HPA...
April 4, 2017: Clinical Biochemistry
https://www.readbyqxmd.com/read/28384069/salt-induced-tissue-specific-cytosine-methylation-downregulates-expression-of-hkt-genes-in-contrasting-wheat-triticum-aestivum-l-genotypes
#12
Suresh Kumar, Ananda Sankara Beena, Monika Awana, Archana Singh
Plants have evolved several strategies, including regulation of genes through epigenetic modifications, to cope with environmental stresses. DNA methylation is dynamically regulated through the methylation and demethylation of cytosine in response to environmental perturbations. High-affinity potassium transporters (HKTs) have accounted for the homeostasis of sodium and potassium ions in plants under salt stress. Wheat (Triticum aestivum L.) is sensitive to soil salinity, which impedes its growth and development, resulting in decreased productivity...
April 2017: DNA and Cell Biology
https://www.readbyqxmd.com/read/28379136/la-related-protein-1-larp1-binds-the-mrna-cap-blocking-eif4f-assembly-on-top-mrnas
#13
Roni M Lahr, Bruno D Fonseca, Gabrielle E Ciotti, Hiba A Al-Ashtal, Jian-Jun Jia, Marius R Niklaus, Sarah P Blagden, Tommy Alain, Andrea J Berman
The 5'terminal oligopyrimidine (5'TOP) motif is a cis-regulatory RNA element located immediately downstream of the 7-methyl-guanosine [m7G] cap of TOP mRNAs, which encode ribosomal proteins and translation factors. In eukaryotes, this motif coordinates the synchronous and stoichiometric expression of the protein components of the translation machinery. La-related protein 1 (LARP1) binds TOP mRNAs, regulating their stability and translation. We present crystal structures of the human LARP1 DM15 region in complex with a 5'TOP motif, a cap analog (m7GTP), and a capped cytosine (m(7)GpppC) resolved to 2...
April 5, 2017: ELife
https://www.readbyqxmd.com/read/28375986/the-new-frontier-of-epigenetic-heterogeneity-in-b-cell-neoplasms
#14
Pilar M Dominguez, Matt Teater, Rita Shaknovich
PURPOSE OF REVIEW: There is mounting evidence that heterogeneity of the epigenome is a feature of many cancers, including B-cell lymphomas, and presents important clinical implications. The purpose of this review is to explain the biological and clinical relevance of this epigenetic phenomenon in B-cell neoplasms. RECENT FINDINGS: Here, we summarize new findings demonstrating that B-cell lymphomas display increased DNA methylation heterogeneity compared to their normal counterparts...
April 1, 2017: Current Opinion in Hematology
https://www.readbyqxmd.com/read/28374217/methylation-targeted-specificity-of-the-dna-binding-proteins-r-dpni-and-mecp2-studied-by-molecular-dynamics-simulations
#15
Siba Shanak, Ozlem Ulucan, Volkhard Helms
DNA methylation plays a major role in organismal development and the regulation of gene expression. Methylation of cytosine bases and the cellular roles of methylated cytosine in eukaryotes are well established, as well as methylation of adenine bases in bacterial genomes. Still lacking, however, is a general mechanistic understanding, in structural and thermodynamic terms, of how proteins recognize methylated DNA. Toward this aim, we present the results of molecular dynamics simulations, alchemical free energy perturbation, and MM-PBSA calculations to explain the specificity of the R...
May 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28364795/the-significance-of-dna-methylation-profile-in-metastasis-related-genes-for-the-progression-of-colorectal-cancer
#16
P Tokarz, E Pawlowska, J Bialkowska-Warzecha, J Blasiak
DNA methylation, an epigenetic modification plays a role in the pathogenesis of colorectal cancer (CRC). CRC cases, both sporadic and familial, are often characterized by abnormal pattern of the cytosine methylation in CpG dinucleotides in regulatory regions of genes important for cancer transformation. Also genes mutated in CRC can have their epigenetic pattern altered and we suggest that changes in DNA methylation array can be important for CRC metastatic potential ‒ the main reason of CRC-associated mortality...
February 28, 2017: Cellular and Molecular Biology
https://www.readbyqxmd.com/read/28361696/p-hint-hunt-a-deep-parallelized-whole-genome-dna-methylation-detection-tool
#17
Shaoliang Peng, Shunyun Yang, Ming Gao, Xiangke Liao, Jie Liu, Canqun Yang, Chengkun Wu, Wenqiang Yu
BACKGROUND: The increasing studies have been conducted using whole genome DNA methylation detection as one of the most important part of epigenetics research to find the significant relationships among DNA methylation and several typical diseases, such as cancers and diabetes. In many of those studies, mapping the bisulfite treated sequence to the whole genome has been the main method to study DNA cytosine methylation. However, today's relative tools almost suffer from inaccuracies and time-consuming problems...
March 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28361273/widespread-5-methylcytosine-in-the-genomes-of-avian-coccidia-and-other-apicomplexan-parasites-detected-by-an-elisa-based-method
#18
Zhenxing Gong, Hao Yin, Xueting Ma, Baohong Liu, Zhenglan Han, Lingqiao Gou, Jianping Cai
To date, little is known about cytosine methylation in the genomic DNA of apicomplexan parasites, although it has been confirmed that this important epigenetic modification exists in many lower eukaryotes, plants, and animals. In the present study, ELISA-based detection demonstrated that low levels of 5-methylcytosine (5-mC) are present in Eimeria spp., Toxoplasma gondii, Cryptosporidium spp., and Neospora caninum. The proportions of 5-mC in genomic DNA were 0.18 ± 0.02% in E tenella sporulated oocysts, 0...
March 30, 2017: Parasitology Research
https://www.readbyqxmd.com/read/28350166/ippp-cloppa-analysis-of-the-influence-of-the-methylation-on-the-potential-energy-and-the-molecular-polarizability-of-the-hydrogen-bonds-in-the-cytosine-guanine-base-pair
#19
Claudia G Giribet, Martín C Ruiz de Azúa
The IPPP-CLOPPA method is applied to investigate the influence of a methyl group on the energy of the hydrogen bonds and the potential energy curve of the bridge protons in model compounds, which mimic the methylated and unmethylated cytosine-guanine base pairs. On the same grounds, this influence on the polarizability of the intermolecular hydrogen bonds of these compounds is also addressed, in order to determine whether this linear response property provides a significant proof of the electronic mechanisms that affect the stabilization of the hydrogen bonds...
April 20, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28349459/analysis-of-high-throughput-rna-bisulfite-sequencing-data
#20
Dietmar Rieder, Francesca Finotello
Methylation of the 5-cytosine (m(5)C) is a common but not well-understood RNA modification, which can be detected by sequencing of bisulfite-treated transcripts (RNA-BSseq). In this Chapter, we discuss computational RNA-BSseq data analysis methods for transcriptome-wide identification and quantification of m(5)C.
2017: Methods in Molecular Biology
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