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Cytosine methylation

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https://www.readbyqxmd.com/read/28214512/dynamics-and-context-dependent-roles-of-dna-methylation
#1
REVIEW
Christina Ambrosi, Massimiliano Manzo, Tuncay Baubec
DNA methylation is one of the most extensively studied epigenetic marks. It is involved in transcriptional gene silencing, it plays important roles during mammalian development and its perturbation is often associated with human diseases. In mammalian genomes, DNA methylation is a prevalent modification that decorates the majority of cytosines. It is found at the promoters and enhancers of inactive genes, at repetitive elements and within transcribed gene bodies. Its presence at promoters is dynamically linked to gene activity, suggesting that it could directly influence gene expression patterns and cellular identity...
February 15, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28213390/epigenetic-patterns-in-blood-associated-with-lipid-traits-predict-incident-coronary-heart-disease-events-and-are-enriched-for-results-from-genome-wide-association-studies
#2
Åsa K Hedman, Michael M Mendelson, Riccardo E Marioni, Stefan Gustafsson, Roby Joehanes, Marguerite R Irvin, Degui Zhi, Johanna K Sandling, Chen Yao, Chunyu Liu, Liming Liang, Tianxiao Huan, Allan F McRae, Serkalem Demissie, Sonia Shah, John M Starr, L Adrienne Cupples, Panos Deloukas, Timothy D Spector, Johan Sundström, Ronald M Krauss, Donna K Arnett, Ian J Deary, Lars Lind, Daniel Levy, Erik Ingelsson
BACKGROUND: Genome-wide association studies have identified loci influencing circulating lipid concentrations in humans; further information on novel contributing genes, pathways, and biology may be gained through studies of epigenetic modifications. METHODS AND RESULTS: To identify epigenetic changes associated with lipid concentrations, we assayed genome-wide DNA methylation at cytosine-guanine dinucleotides (CpGs) in whole blood from 2306 individuals from 2 population-based cohorts, with replication of findings in 2025 additional individuals...
January 2017: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/28208632/cross-talk-between-dnmt2-dependent-trna-methylation-and-queuosine-modification
#3
REVIEW
Ann E Ehrenhofer-Murray
Enzymes of the Dnmt2 family of methyltransferases have yielded a number of unexpected discoveries. The first surprise came more than ten years ago when it was realized that, rather than being DNA methyltransferases, Dnmt2 enzymes actually are transfer RNA (tRNA) methyltransferases for cytosine-5 methylation, foremost C38 (m5C38) of tRNAAsp. The second unanticipated finding was our recent discovery of a nutritional regulation of Dnmt2 in the fission yeast Schizosaccharomyces pombe. Significantly, the presence of the nucleotide queuosine in tRNAAsp strongly stimulates Dnmt2 activity both in vivo and in vitro in S...
February 10, 2017: Biomolecules
https://www.readbyqxmd.com/read/28204976/variation-in-whole-dna-methylation-in-red-maple-acer-rubrum-populations-from-a-mining-region-association-with-metal-contamination-and-cation-exchange-capacity-cec-in-podzolic-soils
#4
K N Kalubi, M Mehes-Smith, G Spiers, A Omri
Although a number of publications have provided convincing evidence that abiotic stresses such as drought and high salinity are involved in DNA methylation reports on the effects of metal contamination, pH, and cation exchange on DNA modifications are limited. The main objective of the present study is to determine the relationship between metal contamination and Cation exchange capacity (CEC) on whole DNA modifications. Metal analysis confirms that nickel and copper are the main contaminants in sampled sites within the Greater Sudbury Region (Ontario, Canada) and liming has increased soil pH significantly even after 30 years following dolomitic limestone applications...
February 15, 2017: Ecotoxicology
https://www.readbyqxmd.com/read/28203244/pistil-transcriptome-analysis-to-disclose-genes-and-gene-products-related-to-aposporous-apomixis-in-hypericum-perforatum-l
#5
Giulio Galla, Sara Zenoni, Linda Avesani, Lothar Altschmied, Paride Rizzo, Timothy F Sharbel, Gianni Barcaccia
Unlike sexual reproduction, apomixis encompasses a number of reproductive strategies, which permit maternal genome inheritance without genetic recombination and syngamy. The key biological features of apomixis are the circumvention of meiosis (i.e., apomeiosis), the differentiation of unreduced embryo sacs and egg cells, and their autonomous development in functional embryos through parthenogenesis, and the formation of viable endosperm either via fertilization-independent means or following fertilization with a sperm cell...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28195572/dna-methylation-as-a-putative-mechanism-for-reduced-dendritic-spine-density-in-the-superior-temporal-gyrus-of-subjects-with-schizophrenia
#6
B McKinney, Y Ding, D A Lewis, R A Sweet
Reduced dendritic spine density (DSD) in cortical layer 3 of the superior temporal gyrus (STG), and multiple other brain regions, is consistently observed in postmortem studies of schizophrenia (SZ). Elucidating the molecular mechanisms of this intermediate phenotype holds promise for understanding SZ pathophysiology, identifying SZ treatment targets and developing animal models. DNA methylation (DNAm), the addition of a methyl group to a cytosine nucleotide, regulates gene transcription and is a strong candidate for such a mechanism...
February 14, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28193886/improved-regulatory-element-prediction-based-on-tissue-specific-local-epigenomic-signatures
#7
Yupeng He, David U Gorkin, Diane E Dickel, Joseph R Nery, Rosa G Castanon, Ah Young Lee, Yin Shen, Axel Visel, Len A Pennacchio, Bing Ren, Joseph R Ecker
Accurate enhancer identification is critical for understanding the spatiotemporal transcriptional regulation during development as well as the functional impact of disease-related noncoding genetic variants. Computational methods have been developed to predict the genomic locations of active enhancers based on histone modifications, but the accuracy and resolution of these methods remain limited. Here, we present an algorithm, regulatory element prediction based on tissue-specific local epigenetic marks (REPTILE), which integrates histone modification and whole-genome cytosine DNA methylation profiles to identify the precise location of enhancers...
February 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28193703/methylation-in-the-matrix-metalloproteinase-2-gene-is-associated-with-cerebral-ischemic-stroke
#8
Hsiu-Fen Lin, Edward Hsi, Ling-Chun Huang, Yi-Chu Liao, Suh-Hang H Juo, Ruey-Tay Lin
Matrix metalloproteinase-2 (MMP-2) is involved in the pathophysiology of stroke. Previous studies have shown that MMP-2 activity is increased in stroke; however, evidence of epigenetic regulation of the MMP-2 in stroke is still limited. We examined methylation of the MMP-2 promoter in patients with ischemic stroke. This study included 298 patients with ischemic stroke and 258 age-matched and sex-matched controls. MMP-2 promoter methylation levels were measured by pyrosequencing at eight potential cytosine-guanine (CpG) sites...
February 13, 2017: Journal of Investigative Medicine: the Official Publication of the American Federation for Clinical Research
https://www.readbyqxmd.com/read/28187949/long-term-alterations-to-dna-methylation-as-a-biomarker-of-prenatal-alcohol-exposure-from-mouse-models-to-human-children-with-fetal-alcohol-spectrum-disorders
#9
REVIEW
Benjamin I Laufer, Eric J Chater-Diehl, Joachim Kapalanga, Shiva M Singh
Rodent models of Fetal Alcohol Spectrum Disorders (FASD) have revealed that prenatal alcohol exposure (PAE) results in differential DNA cytosine methylation in the developing brain. The resulting genome-wide methylation changes are enriched in genes with neurodevelopmental functions. The profile of differential methylation is dynamic and present in some form for life. The methylation changes are transmitted across subsequent mitotic divisions, where they are maintained and further modified over time. More recent follow up has identified a profile of the differential methylation in the buccal swabs of young children born with FASD...
November 22, 2016: Alcohol
https://www.readbyqxmd.com/read/28184257/an-empirically-driven-data-reduction-method-on-the-human-450k-methylation-array-to-remove-tissue-specific-non-variable-cpgs
#10
Rachel D Edgar, Meaghan J Jones, Wendy P Robinson, Michael S Kobor
BACKGROUND: Population based epigenetic association studies of disease and exposures are becoming more common with the availability of economical genome-wide technologies for interrogation of the methylome, such as the Illumina 450K Human Methylation Array (450K). Often, the expected small number of differentially methylated cytosine-guanine pairs (CpGs) in studies of the human methylome presents a statistical challenge, as the large number of CpGs measured on the 450K necessitates careful multiple test correction...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28176663/gsk3%C3%AE-5-flanking-dna-methylation-and-expression-in-alzheimer-s-disease-patients
#11
Vincenzina Nicolia, Viviana Ciraci, Rosaria A Cavallaro, Isidre Ferrer, Sigfrido Scarpa, Andrea Fuso
BACKGROUND: The GSK3β has been associated to pathological functions in neurodegenerative diseases. This kinase is involved in hyperphosphorylation of microtubule-associated tau protein, leading to aggregation andformation of NFTs.It has clearly been shown that GSK3β is regulated at post-translational level: phosphorylation at Tyr216 activates kinase while phosphorylation at Ser9 is essential to inhibit its activity. OBJECTIVES: At present, there are contradictory findings about the possibility that GSK3β may be regulated at gene level...
February 3, 2017: Current Alzheimer Research
https://www.readbyqxmd.com/read/28165867/hypermethylated-ltr-retrotransposon-exhibits-enhancer-activity
#12
Tianxiang Hu, Xingguo Zhu, Wenhu Pi, Miao Yu, Huidong Shi, Dorothy Tuan
LTR retrotransposons are repetitive DNA elements comprising ∼10% of the human genome. They are silenced by hypermethylation of cytosines in CpG dinucleotides and are considered parasitic DNA serving no useful function for the host genome. However, hypermethylated LTRs contain enhancer and promoter sequences and can promote tissue-specific transcription of cis-linked genes. To resolve the apparent paradox of hypermethylated LTRs possessing transcriptional activities, we studied the ERV-9 LTR retrotransposon located at the 5' border of the transcriptionally active β-globin gene locus in human erythroid progenitor and erythroleukemia K562 cells...
February 6, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28161170/maternal-supplementation-with-rumen-protected-methionine-increases-prepartal-plasma-methionine-concentration-and-alters-hepatic-mrna-abundance-of-1-carbon-methionine-and-transsulfuration-pathways-in-neonatal-holstein-calves
#13
C B Jacometo, Z Zhou, D Luchini, M N Corrêa, J J Loor
An important mechanism of nutritional "programming" induced by supplementation with methyl donors during pregnancy is the alteration of mRNA abundance in the offspring. We investigated the effects of rumen-protected Met (RPM) on abundance of 17 genes in the 1-carbon, Met, and transsulfuration pathways in calf liver from cows fed the same basal diet without (control, CON) or with RPM at 0.08% of diet dry matter/d (MET) from -21 through +30 d around calving. Biopsies (n = 8 calves per diet) were harvested on d 4, 14, 28, and 50 of age...
February 1, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28155687/subtype-specific-cpg-island-shore-methylation-and-mutation-patterns-in-30-breast-cancer-cell-lines
#14
Heejoon Chae, Sangseon Lee, Kenneth P Nephew, Sun Kim
BACKGROUND: Aberrant epigenetic modifications, including DNA methylation, are key regulators of gene activity in tumorigenesis. Breast cancer is a heterogeneous disease, and large-scale analyses indicate that tumor from normal and benign tissues, as well as molecular subtypes of breast cancer, can be distinguished based on their distinct genomic, transcriptomic, and epigenomic profiles. In this study, we used affinity-based methylation sequencing data in 30 breast cancer cell lines representing functionally distinct cancer subtypes to investigate methylation and mutation patterns at the whole genome level...
December 23, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/28155665/tea-the-epigenome-platform-for-arabidopsis-methylome-study
#15
Sheng-Yao Su, Shu-Hwa Chen, I-Hsuan Lu, Yih-Shien Chiang, Yu-Bin Wang, Pao-Yang Chen, Chung-Yen Lin
BACKGROUND: Bisulfite sequencing (BS-seq) has become a standard technology to profile genome-wide DNA methylation at single-base resolution. It allows researchers to conduct genome-wise cytosine methylation analyses on issues about genomic imprinting, transcriptional regulation, cellular development and differentiation. One single data from a BS-Seq experiment is resolved into many features according to the sequence contexts, making methylome data analysis and data visualization a complex task...
December 22, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28149679/the-dna-methylation-level-against-the-background-of-the-genome-size-and-t-heterochromatin-content-in-some-species-of-the-genus-secale-l
#16
Anna Kalinka, Magdalena Achrem, Paulina Poter
Methylation of cytosine in DNA is one of the most important epigenetic modifications in eukaryotes and plays a crucial role in the regulation of gene activity and the maintenance of genomic integrity. DNA methylation and other epigenetic mechanisms affect the development, differentiation or the response of plants to biotic and abiotic stress. This study compared the level of methylation of cytosines on a global (ELISA) and genomic scale (MSAP) between the species of the genus Secale. We analyzed whether the interspecific variation of cytosine methylation was associated with the size of the genome (C-value) and the content of telomeric heterochromatin...
2017: PeerJ
https://www.readbyqxmd.com/read/28149330/what-s-in-a-name-context-dependent-significance-of-global-methylation-measures-in-human-health-and-disease
#17
Regan Vryer, Richard Saffery
The study of DNA methylation in development and disease has 'exploded' as a field in recent years, with three major classes of measurement now routine. These encompass (i) locus-specific, (ii) genome-scale/wide and (iii) 'global' methylation approaches. Measures of global methylation refer to the level of 5-methylcytosine (5mC) content in a sample relative to total cytosine. Despite this, several other measures are often referred to as 'global', with the underlying assumption that they accurately reflect 5mC content...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28149329/improved-results-of-line-1-methylation-analysis-in-formalin-fixed-paraffin-embedded-tissues-with-the-application-of-a-heating-step-during-the-dna-extraction-process
#18
Xianyu Wen, Seorin Jeong, Younghoon Kim, Jeong Mo Bae, Nam Yun Cho, Jung Ho Kim, Gyeong Hoon Kang
BACKGROUND: Formalin-fixed, paraffin-embedded (FFPE) tissues are important resources for profiling DNA methylation changes and for studying a variety of diseases. However, formalin fixation introduces inter-strand crosslinking, which might cause incomplete bisulfite conversion of unmethylated cytosines, which might lead to falsely elevated measurements of methylation levels in pyrosequencing assays. Long interspersed nucleotide element-1 (LINE-1) is a major constituent of repetitive transposable DNA elements, and its methylation is referred to correlates with global DNA methylation...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28143949/allelic-drop-out-during-polymerase-chain-reaction-due-to-g-quadruplex-structures-and-dna-methylation-is-widespread-at-imprinted-human-loci
#19
Aaron J Stevens, Millie G Taylor, F Grant Pearce, Martin A Kennedy
Loss of one allele during polymerase chain reaction (PCR) amplification of DNA, known as allelic drop-out, can be caused by a variety of mechanisms. Allelic drop-out during PCR may have profound implications for molecular diagnostic and research procedures that depend on PCR and assume biallelic amplification has occurred. Complete allelic drop-out due to the combined effects of cytosine methylation and G-quadruplex formation was previously described for a differentially methylated region of the human imprinted gene, MEST We now demonstrate that this parent-of-origin specific allelic drop-out can potentially occur at several other genomic regions that display genomic imprinting and have propensity for G-quadruplex formation, including AIM1, BLCAP, DNMT1, PLAGL1, KCNQ1 and GRB10 These findings demonstrate that systematic allelic drop-out during PCR is a general phenomenon for regions of the genome where differential allelic methylation and G-quadruplex motifs coincide, and suggest that great care must be taken to ensure biallelic amplification is occurring in such situations...
January 30, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28143904/ampk-promotes-mitochondrial-biogenesis-and-function-by-phosphorylating-the-epigenetic-factors-dnmt1-rbbp7-and-hat1
#20
Traci L Marin, Brendan Gongol, Fan Zhang, Marcy Martin, David A Johnson, Han Xiao, Yinsheng Wang, Shankar Subramaniam, Shu Chien, John Y-J Shyy
Adenosine monophosphate (AMP)-activated protein kinase (AMPK) acts as a master regulator of cellular energy homeostasis by directly phosphorylating metabolic enzymes and nutrient transporters and by indirectly promoting the transactivation of nuclear genes involved in mitochondrial biogenesis and function. We explored the mechanism of AMPK-mediated induction of gene expression. We identified AMPK consensus phosphorylation sequences in three proteins involved in nucleosome remodeling: DNA methyltransferase 1 (DNMT1), retinoblastoma binding protein 7 (RBBP7), and histone acetyltransferase 1 (HAT1)...
January 31, 2017: Science Signaling
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