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Cytosine methylation

Te-Sha Tsai, Sonika Tyagi, Justin C St John
STUDY QUESTION: What are the molecular differences between mitochondrial DNA (mtDNA)-deficient and mtDNA-normal oocytes and how does mitochondrial supplementation alter these? SUMMARY ANSWER: Changes to DNA methylation in a 5' cytosine-phosphate-guanine 3' (CpG) island in the mtDNA-specific replication factor (DNA polymerase gamma (POLG)) of mtDNA-deficient oocytes mediates an increase in mtDNA copy number by the 2-cell stage that positively modulates the expression of nuclear genes, which affect cellular and metabolic processes, following autologous mitochondrial supplementation...
March 13, 2018: Human Reproduction
Graziela de Sá Machado Araújo, Ronaldo da Silva Francisco Junior, Cristina Dos Santos Ferreira, Pedro Thyago Mozer Rodrigues, Douglas Terra Machado, Thais Louvain de Souza, Jozimara Teixeira de Souza, Cleiton Figueiredo Osorio da Silva, Antônio Francisco Alves da Silva, Claudia Caixeta Franco Andrade, Alan Tardin da Silva, Victor Ramos, Ana Beatriz Garcia, Filipe Brum Machado, Enrique Medina-Acosta
A hallmark of imprinted genes in mammals is the occurrence of parent-of-origin-dependent asymmetry of DNA cytosine methylation (5m C) of alleles at CpG islands (CGIs) in their promoter regions. This 5m CpG asymmetry between the parental alleles creates allele-specific imprinted differentially methylated regions (iDMRs). iDMRs are often coupled to the transcriptional repression of the methylated allele and the activation of the unmethylated allele in a tissue-specific, developmental-stage-specific and/or isoform-specific fashion...
2018: Frontiers in Genetics
Omar Ramos-Lopez, Mirian Samblas, Fermin I Milagro, M Angeles Zulet, Maria L Mansego, Jose I Riezu-Boj, J Alfredo Martinez
Folate deficiency has been putatively implicated in the onset of diverse metabolic abnormalities, including insulin resistance, by altering epigenetic processes on key regulatory genes. The calcium/calmodulin-dependent protein kinase kinase 2 (CAMKK2) is involved in the regulation of critical metabolic processes such as adiposity and glucose homeostasis. This study hypothesized associations between low folate intakes and lower methylation levels of the CAMKK2 gene, with the presence of metabolic alterations in subjects with obesity...
February 2018: Nutrition Research
Sumith Kumar, Bipul C Karmakar, Deepesh Nagarajan, Asish K Mukhopadhyay, Richard D Morgan, Desirazu N Rao
No abstract text is available yet for this article.
March 10, 2018: Nucleic Acids Research
Emily C Sheppard, Rikke Brandstrup Morrish, Michael J Dillon, Rebecca Leyland, Richard Chahwan
Epigenetic modifications, such as histone modifications, DNA methylation status, and non-coding RNAs (ncRNA), all contribute to antibody maturation during somatic hypermutation (SHM) and class-switch recombination (CSR). Histone modifications alter the chromatin landscape and, together with DNA primary and tertiary structures, they help recruit Activation-Induced Cytidine Deaminase (AID) to the immunoglobulin (Ig) locus. AID is a potent DNA mutator, which catalyzes cytosine-to-uracil deamination on single-stranded DNA to create U:G mismatches...
2018: Frontiers in Immunology
Jocelyn Charlton, Timothy L Downing, Zachary D Smith, Hongcang Gu, Kendell Clement, Ramona Pop, Veronika Akopian, Sven Klages, David P Santos, Alexander M Tsankov, Bernd Timmermann, Michael J Ziller, Evangelos Kiskinis, Andreas Gnirke, Alexander Meissner
Cytosine methylation is widespread among organisms and essential for mammalian development. In line with early postulations of an epigenetic role in gene regulation, symmetric CpG methylation can be mitotically propagated over many generations with extraordinarily high fidelity. Here, we combine BrdU labeling and immunoprecipitation with genome-wide bisulfite sequencing to explore the inheritance of cytosine methylation onto newly replicated DNA in human cells. Globally, we observe a pronounced lag between the copying of genetic and epigenetic information in embryonic stem cells that is reconsolidated within hours to accomplish faithful mitotic transmission...
March 12, 2018: Nature Structural & Molecular Biology
Jiang Li, Caili Li, Shanfa Lu
Cytosine DNA methylation is highly conserved epigenetic modification involved in a wide range of biological processes in eukaryotes. It was established and maintained by cytosine-5 DNA methyltransferases (C5-MTases) in plants. Through genome-wide identification, eight putative SmC5-MTase genes were identified from the genome of Salvia miltiorrhiza , a well-known traditional Chinese medicine material and an emerging model medicinal plant. Based on conserved domains and phylogenetic analysis, eight SmC5-MTase genes were divided into four subfamilies, including MET , CMT , DRM and DNMT2 ...
2018: PeerJ
Weiwen Kong, Bin Li, Qianqian Wang, Bin Wang, Xiaoke Duan, Li Ding, Yanke Lu, Li-Wei Liu, Honggui La
The relationships between transcription and methylation were revealed in Arabidopsis thaliana NB-LRR-encoding genes in wild type (Col-0) and different mutants. Plant nucleotide-binding, leucine-rich repeat (NB-LRR) proteins constitute a large family that plays predominant roles in disease resistance. However, the regulation of NB-LRR-encoding genes at the transcriptional level is still poorly understood. Recently, DNA cytosine methylation in eukaryotes has been described as serving an important function in regulating gene expression...
March 10, 2018: Plant Molecular Biology
Pavel Bashtrykov, Albert Jeltsch
Methylation of cytosine bases in DNA is one of the main epigenetic signals regulating gene expression and chromatin structure. The distribution of DNA methylation in the genome has a cell-type-specific pattern and can be modulated by internal or external stimuli. One of the most powerful approaches to investigate DNA methylation patterns is bisulfite conversion of the DNA followed by DNA sequencing, which allows to determine methylation patterns at a single-cytosine resolution. Here, we present a protocol for bisulfite DNA methylation analysis of targeted genomic regions using amplicon-based next-generation sequencing (NGS) on an Illumina sequencing system...
2018: Methods in Molecular Biology
Elsa Leitão, Jasmin Beygo, Michael Zeschnigk, Ludger Klein-Hitpass, Marcel Bargull, Sven Rahmann, Bernhard Horsthemke
DNA methylation, i.e., the methylation of cytosine at carbon atom C5, has an important role in the regulation of gene expression. The methylation status of each cytosine in a specific genomic region can be determined by targeted deep bisulfite sequencing at single-molecule resolution. Here we describe the design of PCR primers that are used to amplify specific sequences from bisulfite-converted DNA, the preparation of sequencing libraries, the sequencing of these libraries on the MiSeq system, as well as the analysis of the sequence reads...
2018: Methods in Molecular Biology
Magali Kernaleguen, Christian Daviaud, Yimin Shen, Eric Bonnet, Victor Renault, Jean-François Deleuze, Florence Mauger, Jörg Tost
The analysis of genome-wide epigenomic alterations including DNA methylation and hydroxymethylation has become a subject of intensive research for many biological and disease-associated investigations. Whole-genome bisulfite sequencing (WGBS) using next-generation sequencing technologies is currently considered as the gold standard for a comprehensive and quantitative analysis of DNA methylation throughout the genome. However, bisulfite conversion does not allow distinguishing between cytosine methylation and hydroxymethylation requiring an additional chemical or enzymatic step to identify hydroxymethylated cytosines...
2018: Methods in Molecular Biology
Tim Stuart, Sam Buckberry, Ryan Lister
DNA methylation is a covalent modification of DNA that plays important roles in processes such as the regulation of gene expression, transcription factor binding, and suppression of transposable elements. The use of whole genome bisulfite sequencing (WGBS) enables the genome-wide identification and quantification of DNA methylation patterns at single-base resolution and is the gold standard for analysis of DNA methylation. Computational analysis of WGBS data can be particularly challenging, as many computationally intensive steps are required...
2018: Methods in Molecular Biology
Dulce B Vargas-Landin, Jahnvi Pflüger, Ryan Lister
Whole genome bisulfite sequencing (WGBS) enables the detection of DNA methylation at single base-pair resolution. The treatment of DNA with sodium bisulfite allows the discrimination of methylated and unmethylated cytosines, but the power of this technology can be limited by the input amounts of DNA and the length of DNA fragments due to DNA damage caused by the desulfonation process. Here, we describe a WGBS library preparation protocol that minimizes the loss and damage of DNA, generating high quality libraries amplified with fewer PCR cycles, and hence data with fewer PCR duplicates, from lower amounts of input material...
2018: Methods in Molecular Biology
Haiyan Wang, Huanshun Yin, Hua Huang, Kelin Li, Yunlei Zhou, Geoffrey I N Waterhouse, Hai Lin, Shiyun Ai
Herein, a novel dual-signal amplified photoelectrochemical (PEC) biosensor was successfully developed for the highly selective detection of N6 -methyladenosine (m6 A) methylated RNA. The PEC biosensor comprised BiVO4 -110-TiO2 heterojunction and gold nanoparticle decorated MoS2 (MoS2 -AuNPs) as the photoactive materials, horseradish peroxidase conjugated biotin (HRP-Biotin) as the enzymatic unit, Ag+ -mediated cytosine pairs (C-Ag+ -C) as the signal amplification unit, and the anti-m6 A antibody as the m6 A methylated RNA recognition unit...
February 27, 2018: Biosensors & Bioelectronics
Chantriolnt-Andreas Kapourani, Guido Sanguinetti
Motivation: High-throughput measurements of DNA methylation are increasingly becoming a mainstay of biomedical investigations. While the methylation status of individual cytosines can sometimes be informative, several recent papers have shown that the functional role of DNA methylation is better captured by a quantitative analysis of the spatial variation of methylation across a genomic region. Results: Here we present BPRMeth, a Bioconductor package which quantifies methylation profiles by generalised linear model regression (Kapourani and Sanguinetti, 2016)...
March 7, 2018: Bioinformatics
Takuya Yotani, Yuriko Yamada, Eri Arai, Ying Tian, Masahiro Gotoh, Motokiyo Komiyama, Hiroyuki Fujimoto, Michiie Sakamoto, Yae Kanai
The aim of this study was to develop a new methodology that is suitable for DNA methylation diagnostics and to demonstrate its clinical applicability. We developed a new anion-exchange column for high-performance liquid chromatography (HPLC) with electrostatic and hydrophobic properties. Both cytosine and thymine, corresponding to methylated and unmethylated cytosine after bisulfite modification, respectively, are captured by electrostatic interaction and then discriminated from each other by their hydrophobic interactions...
March 9, 2018: Cancer Science
Marketa Tomkova, Michael McClellan, Skirmantas Kriaucionis, Benjamin Schuster-Böckler
No abstract text is available yet for this article.
February 27, 2018: DNA Repair
Vikas Yadav, Sheng Sun, R Blake Billmyre, Bhagya C Thimmappa, Terrance Shea, Robert Lintner, Guus Bakkeren, Christina A Cuomo, Joseph Heitman, Kaustuv Sanyal
The centromere DNA locus on a eukaryotic chromosome facilitates faithful chromosome segregation. Despite performing such a conserved function, centromere DNA sequence as well as the organization of sequence elements is rapidly evolving in all forms of eukaryotes. The driving force that facilitates centromere evolution remains an enigma. Here, we studied the evolution of centromeres in closely related species in the fungal phylum of Basidiomycota. Using ChIP-seq analysis of conserved inner kinetochore proteins, we identified centromeres in three closely related Cryptococcus species: two of which are RNAi-proficient, while the other lost functional RNAi...
March 5, 2018: Proceedings of the National Academy of Sciences of the United States of America
Rachael M Taylor, Roger Smith, Clare E Collins, David Mossman, Michelle W Wong-Brown, Eng-Cheng Chan, Tiffany-Jane Evans, John R Attia, Tenele Smith, Trent Butler, Alexis J Hure
BACKGROUND: During the early postnatal period, the impact of nutrition on DNA methylation has not been well studied in humans. The aim was to quantify the relationship between one-carbon metabolism nutrient intake during the first three years of life and global DNA methylation levels at four years. DESIGN: Childhood dietary intake was assessed using infant feeding questionnaires, food frequency questionnaires, 4-day weighed food records and 24-h food records. The dietary records were used to estimate the intake of methionine, folate, vitamins B2, B6 and B12 and choline...
February 27, 2018: Nutrients
Matthew Ouellette, J Peter Gogarten, Jessica Lajoie, Andrea M Makkay, R Thane Papke
DNA methyltransferases (MTases), which catalyze the methylation of adenine and cytosine bases in DNA, can occur in bacteria and archaea alongside cognate restriction endonucleases (REases) in restriction-modification (RM) systems or independently as orphan MTases. Although DNA methylation and MTases have been well-characterized in bacteria, research into archaeal MTases has been limited. A previous study examined the genomic DNA methylation patterns (methylome) of the halophilic archaeon Haloferax volcanii , a model archaeal system which can be easily manipulated in laboratory settings, via single-molecule real-time (SMRT) sequencing and deletion of a putative MTase gene ( HVO_A0006 )...
February 27, 2018: Genes
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