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Cytosine methylation

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https://www.readbyqxmd.com/read/28092081/epigenetics-in-alzheimer-s-disease-perspective-of-dna-methylation
#1
REVIEW
Talal Jamil Qazi, Zhenzhen Quan, Asif Mir, Hong Qing
Research over the years has shown that causes of Alzheimer's disease are not well understood, but over the past years, the involvement of epigenetic mechanisms in the developing memory formation either under pathological or physiological conditions has become clear. The term epigenetics represents the heredity of changes in phenotype that are independent of altered DNA sequences. Different studies validated that cytosine methylation of genomic DNA decreases with age in different tissues of mammals, and therefore, the role of epigenetic factors in developing neurological disorders in aging has been under focus...
January 14, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28077169/distinct-5-methylcytosine-profiles-in-poly-a-rna-from-mouse-embryonic-stem-cells-and-brain
#2
Thomas Amort, Dietmar Rieder, Alexandra Wille, Daria Khokhlova-Cubberley, Christian Riml, Lukas Trixl, Xi-Yu Jia, Ronald Micura, Alexandra Lusser
BACKGROUND: Recent work has identified and mapped a range of posttranscriptional modifications in mRNA, including methylation of the N6 and N1 positions in adenine, pseudouridylation, and methylation of carbon 5 in cytosine (m5C). However, knowledge about the prevalence and transcriptome-wide distribution of m5C is still extremely limited; thus, studies in different cell types, tissues, and organisms are needed to gain insight into possible functions of this modification and implications for other regulatory processes...
January 5, 2017: Genome Biology
https://www.readbyqxmd.com/read/28070921/brm-smarca2-negative-clear-cell-renal-cell-carcinoma-is-associated-with-a-high-percentage-of-brm-somatic-mutations-deletions-and-promoter-methylation
#3
Qiu-Yuan Xia, Xue-Mei Zhan, Xiang-Shan Fan, Sheng-Bing Ye, Shan-Shan Shi, Rui Li, Xue Wei, Xuan Wang, Heng-Hui Ma, Zhen-Feng Lu, Xiao-Jun Zhou, Qiu Rao
AIMS: The aim of this study was to investigate potential molecular mechanisms associated with loss of BRM expression in poorly differentiated clear cell renal cell carcinoma (ccRCC). METHODS AND RESULTS: Nineteen previously selected BRM-negative RCC tissues were examined by DNA sequencing, fluorescence in-situ hybridization (FISH) and methylation-specific polymerase chain reaction (PCR) of the BRM gene. BRM mutation was identified in 78.9% (15 of 19) cases, chromosome 9 monosomy or BRM deletion in 43...
November 7, 2016: Histopathology
https://www.readbyqxmd.com/read/28069706/dna-sequence-properties-that-predict-susceptibility-to-epiallelic-switching
#4
Marco Catoni, Jayne Griffiths, Claude Becker, Nicolae Radu Zabet, Carlos Bayon, Mélanie Dapp, Michal Lieberman-Lazarovich, Detlef Weigel, Jerzy Paszkowski
Transgenerationally heritable epialleles are defined by the stable propagation of alternative transcriptional states through mitotic and meiotic cell cycles. Given that the propagation of DNA methylation at CpG sites, mediated in Arabidopsis by MET1, plays a central role in epigenetic inheritance, we examined genomewide DNA methylation in partial and complete loss-of-function met1 mutants. We interpreted the data in relation to transgenerational epiallelic stability, which allowed us to classify chromosomal targets of epigenetic regulation into (i) single copy and methylated exclusively at CpGs, readily forming epialleles, and (ii) transposon-derived, methylated at all cytosines, which may or may not form epialleles...
January 9, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28069330/top2a-hells-atad2-and-tet3-are-novel-prognostic-markers-in-renal-cell-carcinoma
#5
Dong Chen, Matthias Maruschke, Oliver Hakenberg, Wolfgang Zimmermann, Christian G Stief, Alexander Buchner
OBJECTIVE: To identify and validate novel prognostic marker genes in clear cell renal cell carcinoma (RCC) that are increasingly expressed during tumor progression. METHODS: Total RNA was isolated from normal renal tissue, primary G1 and G3 tumors, 14 samples each, and 32 metastases from RCC patients. Expression profiles were created using oligonucleotide microarrays. Significant gene expression differences (p<0.05) were identified between normal kidney, primary tumor and metastases...
January 6, 2017: Urology
https://www.readbyqxmd.com/read/28062751/transcriptome-wide-mapping-of-rna-5-methylcytosine-in-arabidopsis-mrnas-and-non-coding-rnas
#6
Rakesh David, Alice Burgess, Brian Parker, Jun Li, Kalinya Pulsford, Tennille Sibbritt, Thomas Preiss, Iain R Searle
Post-transcriptional methylation of RNA cytosine residues to 5-methylcytosine (m5C) is an important modification with diverse roles, such as regulating stress responses, stem cell proliferation, and RNA metabolism. Here, we used RNA bisulfite sequencing (bsRNA-seq) for transcriptome-wide quantitative mapping of m5C in the model plant, Arabidopsis thaliana. We discovered more than a thousand m5C sites in Arabidopsis mRNAs, long non-coding RNAs, and other non-coding RNAs across three tissue types (siliques, seedling shoots, and roots) and validated a number of these sites...
January 6, 2017: Plant Cell
https://www.readbyqxmd.com/read/28062506/wnt-signaling-pathway-inhibitor-sclerostin-inhibits-angiotensin-ii-induced-aortic-aneurysm-and-atherosclerosis
#7
Smriti Murali Krishna, Sai-Wang Seto, Roby J Jose, Jiaze Li, Susan K Morton, Erik Biros, Yutang Wang, Vianne Nsengiyumva, Jan H N Lindeman, Gabriela G Loots, Catherine M Rush, Jeffrey M Craig, Jonathan Golledge
OBJECTIVE: Sclerostin (SOST) has been identified as an important regulator of bone formation; however, it has not been previously implicated in arterial disease. The aim of this study was to assess the role of SOST in aortic aneurysm (AA) and atherosclerosis using human samples, a mouse model, and in vitro investigations. APPROACH AND RESULTS: SOST protein was downregulated in human and mouse AA samples compared with controls. Transgenic introduction of human SOST in apolipoprotein E-deficient (ApoE(-/-)) mice (SOST(Tg)...
December 22, 2016: Arteriosclerosis, Thrombosis, and Vascular Biology
https://www.readbyqxmd.com/read/28061462/identifying-genetic-hypomethylation-and-upregulation-of-toll-like-receptors-in-kawasaki-disease
#8
Ying-Hsien Huang, Sung-Chou Li, Lien-Hung Huang, Pao-Chun Chen, Yi-Yu Lin, Chiung-Chun Lin, Ho-Chang Kuo
Kawasaki disease (KD) is an acute febrile systemic vasculitis that occurs in children and is characterized by elevated levels of proinflammatory cytokines. Toll-like receptors (TLRs) serve as the sensor arm of the innate immune system and induce proinflammatory cytokine expressions.We recruited a total of 18 paired KD patients, before intravenous immunoglobulin (IVIG) and at least 3 weeks after IVIG treatment, 18 healthy controls, and 18 febrile controls. For TLR genes and their cytosine-phosphate-guanine (CpG) markers, we used Affymetrix GeneChip® Human Transcriptome Array 2...
January 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28060259/measurement-of-differentially-methylated-ins-dna-species-in-human-serum-samples-as-a-biomarker-of-islet-%C3%AE-cell-death
#9
Sarah A Tersey, Jennifer B Nelson, Marisa M Fisher, Raghavendra G Mirmira
The death of islet β cells is thought to underlie the pathogenesis of virtually all forms of diabetes and to precede the development of frank hyperglycemia, especially in type 1 diabetes. The development of sensitive and reliable biomarkers of β cell death may allow for early therapeutic intervention to prevent or delay the development of diabetes. Recently, several groups including our own have reported that cell-free, differentially methylated DNA encoding preproinsulin (INS) in the circulation is correlated to β cell death in pre-type 1 diabetes and new-onset type 1 diabetes...
December 21, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28056787/software-updates-in-the-illumina-hiseq-platform-affect-whole-genome-bisulfite-sequencing
#10
Hidehiro Toh, Kenjiro Shirane, Fumihito Miura, Naoki Kubo, Kenji Ichiyanagi, Katsuhiko Hayashi, Mitinori Saitou, Mikita Suyama, Takashi Ito, Hiroyuki Sasaki
BACKGROUND: Methylation of cytosine in genomic DNA is a well-characterized epigenetic modification involved in many cellular processes and diseases. Whole-genome bisulfite sequencing (WGBS), such as MethylC-seq and post-bisulfite adaptor tagging sequencing (PBAT-seq), uses the power of high-throughput DNA sequencers and provides genome-wide DNA methylation profiles at single-base resolution. However, the accuracy and consistency of WGBS outputs in relation to the operating conditions of high-throughput sequencers have not been explored...
January 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28054779/n6-adenosine-dna-methyltransferase-from-h-pylori-98-10-strain-in-complex-with-dna-and-adomet-structural-insights-from-in-silico-studies
#11
Swati Singh, Lalitha Guruprasad
Helicobacter pylori is a primitive Gram-negative bacterium that resides in the acidic environment of the human gastrointestinal tract, and some strains of this bacterium cause gastric ulcers and cancer. DNA methyltransferases (MTases) are promising drug targets for the treatment of cancer and other diseases that are also caused by epigenetic alternations of the genome. The N6-adenine-specific DNA MTase from H. pylori (M. Hpy N6mA) catalyzes the transfer of a methyl group from the cofactor S-adenosyl-l-methionine (AdoMet) to the flipped adenine of the substrate DNA...
January 5, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28053961/iron-supplementation-reverses-the-reduction-of-hydroxymethylcytosine-in-hepatic-dna-associated-with-chronic-alcohol-consumption-in-rats
#12
Stephanie A Tammen, Jung Eun Park, Phil Kyung Shin, Simonetta Friso, Jayong Chung, Sang-Woon Choi
BACKGROUND: Alcohol is known to affect two epigenetic phenomena, DNA methylation and DNA hydroxymethylation, and iron is a cofactor of ten-eleven translocation (TET) enzymes that catalyze the conversion from methylcytosine to hydroxymethylcytosine. In the present study we aimed to determine the effects of alcohol on DNA hydroxymethylation and further effects of iron on alcohol associated epigenetic changes. METHODS: Twenty-four male Sprague-Dawley rats were fed either Lieber-DeCarli alcohol diet (36% calories from ethanol) or Lieber-DeCarli control diet along with or without iron supplementation (0...
December 2016: Journal of Cancer Prevention
https://www.readbyqxmd.com/read/28053115/cytosine-methylation-at-cpcpg-sites-triggers-accumulation-of-non-cpg-methylation-in-gene-bodies
#13
Nicolae Radu Zabet, Marco Catoni, Filippo Prischi, Jerzy Paszkowski
Methylation of cytosine is an epigenetic mark involved in the regulation of transcription, usually associated with transcriptional repression. In mammals, methylated cytosines are found predominantly in CpGs but in plants non-CpG methylation (in the CpHpG or CpHpH contexts, where H is A, C or T) is also present and is associated with the transcriptional silencing of transposable elements. In addition, CpG methylation is found in coding regions of active genes. In the absence of the demethylase of lysine 9 of histone 3 (IBM1), a subset of body-methylated genes acquires non-CpG methylation...
January 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28053004/dna-methylation-profiles-of-selected-pro-inflammatory-cytokines-in-alzheimer-disease
#14
Vincenzina Nicolia, Rosaria A Cavallaro, Irene López-González, Mauro Maccarrone, Sigfrido Scarpa, Isidre Ferrer, Andrea Fuso
By means of functional genomics analysis, we recently described the mRNA expression profiles of various genes involved in the neuroinflammatory response in the brains of subjects with late-onset Alzheimer Disease (LOAD). Some of these genes, namely interleukin (IL)-1β and IL-6, showed distinct expression profiles with peak expression during the first stages of the disease and control-like levels at later stages. IL-1β and IL-6 genes are modulated by DNA methylation in different chronic and degenerative diseases; it is also well known that LOAD may have an epigenetic basis...
January 4, 2017: Journal of Neuropathology and Experimental Neurology
https://www.readbyqxmd.com/read/28052120/structural-analysis-of-g-quadruplex-formation-at-the-human-mest-promoter
#15
Aaron J Stevens, Martin A Kennedy
The promoter region of the imprinted gene MEST contains several motifs capable of forming G-quadruplex (G4) structures, which appear to contribute to consistent allelic dropout during polymerase chain reaction (PCR) analysis of this region. Here, we extend our previous analysis of MEST G4 structures by applying fluorescent footprinting techniques to assess non B-DNA structure and topology in dsDNA from the full MEST promoter region, under conditions that mimic PCR. We demonstrate that the buffer used for PCR provides an extremely favourable milieu for G4 formation, and that cytosine methylation helps maintain G4 structures during PCR...
2017: PloS One
https://www.readbyqxmd.com/read/28045988/differential-dna-methylation-patterns-are-related-to-phellogen-origin-and-quality-of-quercus-suber-cork
#16
Vera Inácio, Pedro M Barros, Augusta Costa, Cristóvão Roussado, Elsa Gonçalves, Rita Costa, José Graça, M Margarida Oliveira, Leonor Morais-Cecílio
DNA methylation is thought to influence Quercus suber cork quality, which is the main constraint for its economic valorisation. However, a deep knowledge of the cytosine methylation patterns disclosing the epigenetic variability of trees with different cork quality types is totally missing. This study investigates the hypothesis that variations in DNA methylation contribute to differences in cork cellular characteristics directly related to original or traumatic phellogen activity. We used MSAPs (Methylation Sensitive Amplified Polymorphism) to assess DNA methylation patterns of cork and leaf tissues of Q...
2017: PloS One
https://www.readbyqxmd.com/read/28043365/cooled-storage-of-equine-semen-does-not-induce-major-changes-in-sperm-dna-methylation
#17
Rodrigo Arruda de Oliveira, Dragos Scarlet, Natascha Ille, Christine Aurich
A decrease in fertility of equine semen during cooled-storage so far has mainly been attributed to changes in sperm membrane function. In the present study we hypothesized that cooled-storage also changes the sperm DNA methylation level. For this purpose, semen was collected from 10 fertile stallions and processed for cooled-storage at 5 °C. Two final concentrations, 50 × 10(6) and 100 × 10(6) cells/mL, were used. Semen was analyzed for total motility, progressive motility, membrane integrity, phosphatidylserine translocation (PST), mitochondrial membrane potential and chromatin condensation, immediately after processing and at 24 h-intervals until 72 h of storage...
February 2017: Theriogenology
https://www.readbyqxmd.com/read/28041877/cytosine-5-rna-methylation-regulates-neural-stem-cell-differentiation-and%C3%A2-motility
#18
Joana V Flores, Lucía Cordero-Espinoza, Feride Oeztuerk-Winder, Amanda Andersson-Rolf, Tommaso Selmi, Sandra Blanco, Jignesh Tailor, Sabine Dietmann, Michaela Frye
Loss-of-function mutations in the cytosine-5 RNA methylase NSUN2 cause neurodevelopmental disorders in humans, yet the underlying cellular processes leading to the symptoms that include microcephaly remain unclear. Here, we show that NSUN2 is expressed in early neuroepithelial progenitors of the developing human brain, and its expression is gradually reduced during differentiation of human neuroepithelial stem (NES) cells in vitro. In the developing Nsun2(-/-) mouse cerebral cortex, intermediate progenitors accumulate and upper-layer neurons decrease...
January 10, 2017: Stem Cell Reports
https://www.readbyqxmd.com/read/28040747/statistical-method-evaluation-for-differentially-methylated-cpgs-in-base-resolution-next-generation-dna-sequencing-data
#19
Yun Zhang, Saurabh Baheti, Zhifu Sun
High-throughput bisulfite methylation sequencing such as reduced representation bisulfite sequencing (RRBS), Agilent SureSelect Human Methyl-Seq (Methyl-seq) or whole-genome bisulfite sequencing is commonly used for base resolution methylome research. These data are represented either by the ratio of methylated cytosine versus total coverage at a CpG site or numbers of methylated and unmethylated cytosines. Multiple statistical methods can be used to detect differentially methylated CpGs (DMCs) between conditions, and these methods are often the base for the next step of differentially methylated region identification...
December 31, 2016: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28038990/putative-dna-modification-methylase-dr_c0020-of-deinococcus-radiodurans-is-an-atypical-sam-dependent-c-5-cytosine-dna-methylase
#20
Nayana A Patil, Bhakti Basu, Deepti D Deobagkar, Shree K Apte, Dileep N Deobagkar
BACKGROUND: Control of cellular processes by epigenetic modification of cytosine in DNA is widespread among living organisms, but, is hitherto unknown in the extremely radioresistant microbe D. radiodurans. METHODS: C-5 methyl cytosines (m(5)C) were detected by immuno-blotting with m(5)C-specific antibody. Site of cytosine methylation by DR_C0020 encoded protein was investigated by bisulfite sequencing. The DR_C0020 knockout mutant (Δdcm), constructed by site directed mutagenesis, was assessed for effect on growth, radiation resistance and proteome...
December 27, 2016: Biochimica et Biophysica Acta
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