Relevant bibliographies by topics / Cytosine methylation

Academic literature on the topic 'Cytosine methylation'

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Published: 4 June 2021
Last updated: 10 March 2023

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Journal articles on the topic "Cytosine methylation"

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Halla-aho, Viivi, and Harri Lähdesmäki. "LuxUS: DNA methylation analysis using generalized linear mixed model with spatial correlation." Bioinformatics 36, no. 17 (June 2, 2020): 4535–43. http://dx.doi.org/10.1093/bioinformatics/btaa539.

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Abstract Motivation DNA methylation is an important epigenetic modification, which has multiple functions. DNA methylation and its connections to diseases have been extensively studied in recent years. It is known that DNA methylation levels of neighboring cytosines are correlated and that differential DNA methylation typically occurs rather as regions instead of individual cytosine level. Results We have developed a generalized linear mixed model, LuxUS, that makes use of the correlation between neighboring cytosines to facilitate analysis of differential methylation. LuxUS implements a likelihood model for bisulfite sequencing data that accounts for experimental variation in underlying biochemistry. LuxUS can model both binary and continuous covariates, and mixed model formulation enables including replicate and cytosine random effects. Spatial correlation is included to the model through a cytosine random effect correlation structure. We show with simulation experiments that using the spatial correlation, we gain more power to the statistical testing of differential DNA methylation. Results with real bisulfite sequencing dataset show that LuxUS is able to detect biologically significant differentially methylated cytosines. Availability and implementation The tool is available at https://github.com/hallav/LuxUS. Supplementary information Supplementary data are available at Bioinformatics online.
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Thompson, Reid F., Maria E. Figueroa, Ari M. Melnick, and John M. Greally. "Epigenetic Dysregulation of Candidate Cis-Regulatory Sequences in Hematological Malignancies." Blood 108, no. 11 (November 1, 2006): 2229. http://dx.doi.org/10.1182/blood.v108.11.2229.2229.

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Abstract Epigenetic changes (in particular, altered cytosine methylation) have been described in a variety of tumors. The CpG Island Methylator Phenotype (CIMP) is a well-known instance of this phenomenon wherein cytosine methylation is markedly dysregulated (normally hypomethylated loci shift to a methylated state). CIMP has been demonstrated in a number of different cancer types including hematological malignancies like AML. While methylation status has been studied predominantly at CpG islands, we used a novel assay (HELP; Khulan et al., Genome Res. 2006) to look for changes in cytosine methylation in large contiguous regions of the genome. We assessed global patterns of cytosine methylation by HELP analysis in a variety of tumor samples including leukemias and lymphomas. We found significant changes in the global methylation patterns of malignant cells, confirming prior observations of epigenetic dysregulation in these tumor types. We also discovered that the majority of the changes in cytosine methylation are occurring not at CpG islands but at other loci in the genome, including constitutively hypomethylated loci that we are finding to be candidate cis-regulatory sequences. We conclude that cytosine methylation changes in cancer occur much more extensively than analysis of CpG islands alone would indicate, and that the epigenetic dysregulation in cancer may be predominantly targeted to cis-regulatory sequences rather than to promoters.
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Kusmartsev, Vassili, Magdalena Drożdż, Benjamin Schuster-Böckler, and Tobias Warnecke. "Cytosine Methylation Affects the Mutability of Neighboring Nucleotides in Germline and Soma." Genetics 214, no. 4 (February 20, 2020): 809–23. http://dx.doi.org/10.1534/genetics.120.303028.

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Methylated cytosines deaminate at higher rates than unmethylated cytosines, and the lesions they produce are repaired less efficiently. As a result, methylated cytosines are mutational hotspots. Here, combining rare polymorphism and base-resolution methylation data in humans, Arabidopsis thaliana, and rice (Oryza sativa), we present evidence that methylation state affects mutation dynamics not only at the focal cytosine but also at neighboring nucleotides. In humans, contrary to prior suggestions, we find that nucleotides in the close vicinity (±3 bp) of methylated cytosines mutate less frequently. Reduced mutability around methylated CpGs is also observed in cancer genomes, considering single nucleotide variants alongside tissue-of-origin-matched methylation data. In contrast, methylation is associated with increased neighborhood mutation risk in A. thaliana and rice. The difference in neighborhood mutation risk is less pronounced further away from the focal CpG and modulated by regional GC content. Our results are consistent with a model where altered risk at neighboring bases is linked to lesion formation at the focal CpG and subsequent long-patch repair. Our findings indicate that cytosine methylation has a broader mutational footprint than is commonly assumed.
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Jung, Seo-Hee, Sung-Ran Min, Soo-Young Lee, Ji-Young Park, S. Javad Davarpanah, Hwa-Jee Chung, Jae-Heung Jeon, Jang-Ryol Liu, and Won-Joong Jeong. "Gene Silencing Induced by Cytosine Methylation in Transgenic Tomato." Journal of Plant Biotechnology 34, no. 4 (December 31, 2007): 323–29. http://dx.doi.org/10.5010/jpb.2007.34.4.323.

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Kalinka, Anna, Magdalena Achrem, and Paulina Poter. "The DNA methylation level against the background of the genome size and t-heterochromatin content in some species of the genusSecale L." PeerJ 5 (January 24, 2017): e2889. http://dx.doi.org/10.7717/peerj.2889.

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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 genusSecale. 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. MSAP analysis showed thatS. sylvestrewas the most distinct species among the studied rye taxa; however, the results clearly indicated that these differences were not statistically significant. The total methylation level of the studied loci was very similar in all taxa and ranged from 60% inS. strictumssp.africanumto 66% inS. cerealessp.segetale, which confirmed the lack of significant differences in the sequence methylation pattern between the pairs of rye taxa. The level of global cytosine methylation in the DNA was not significantly associated with the content of t-heterochromatin and did not overlap with the existing taxonomic rye relationships. The highest content of 5-methylcytosine was found inS. cerealessp.segetale(83%), while very low inS. strictumssp.strictum(53%), which was significantly different from the methylation state of all taxa, except forS. sylvestre. The other studied taxa of rye had a similar level of methylated cytosine ranging from 66.42% (S. vavilovii) to 74.41% in (S. cerealessp.afghanicum). The results obtained in this study are evidence that the percentage of methylated cytosine cannot be inferred solely based on the genome size or t-heterochromatin. This is a significantly more complex issue.
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Bernstein, Carol. "DNA Methylation and Establishing Memory." Epigenetics Insights 15 (January 2022): 251686572110724. http://dx.doi.org/10.1177/25168657211072499.

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A single event can cause a life-long memory. Memories physically reside in neurons, and changes in neuronal gene expression are considered to be central to memory. Early models proposed that specific DNA methylations of cytosines in neuronal DNA encode memories in a stable biochemical form. This review describes recent research that elucidates the molecular mechanisms used by the mammalian brain to form DNA methylcytosine encoded memories. For example, neuron activation initiates cytosine demethylation by stimulating DNA topoisomerase II beta (TOP2B) protein to make a temporary DNA double-strand break (repaired within about 2 hours) at a promoter of an immediate early gene, EGR1, allowing expression of this gene. The EGR1 proteins then recruit methylcytosine dioxygenase TET1 proteins to initiate demethylation at several hundred genes, facilitating expression of those genes. Initiation of demethylation of cytosine also occurs when OGG1 localizes at oxidized guanine in a methylated CpG site and recruits TET1 for initiation of demethylation at that site. DNMT3A2 is another immediate early gene upregulated by synaptic activity. DNMT3A2 protein catalyzes de novo DNA methylations. These several mechanisms convert external experiences into DNA methylations and initiated demethylations of neuronal DNA cytosines, causing changes in gene expression that are the basis of long-term memories.
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Tillo, Desiree, Sanjit Mukherjee, and Charles Vinson. "Inheritance of Cytosine Methylation." Journal of Cellular Physiology 231, no. 11 (March 15, 2016): 2346–52. http://dx.doi.org/10.1002/jcp.25350.

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Ooi, Steen K. T., and Timothy H. Bestor. "Cytosine Methylation: Remaining Faithful." Current Biology 18, no. 4 (February 2008): R174—R176. http://dx.doi.org/10.1016/j.cub.2007.12.045.

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Peñuela, Mauricio, Jenny Johana Gallo-Franco, Jorge Finke, Camilo Rocha, Anestis Gkanogiannis, Thaura Ghneim-Herrera, and Mathias Lorieux. "Methylation in the CHH Context Allows to Predict Recombination in Rice." International Journal of Molecular Sciences 23, no. 20 (October 19, 2022): 12505. http://dx.doi.org/10.3390/ijms232012505.

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DNA methylation is the most studied epigenetic trait. It is considered a key factor in regulating plant development and physiology, and has been associated with the regulation of several genomic features, including transposon silencing, regulation of gene expression, and recombination rates. Nonetheless, understanding the relation between DNA methylation and recombination rates remains a challenge. This work explores the association between recombination rates and DNA methylation for two commercial rice varieties. The results show negative correlations between recombination rates and methylated cytosine counts for all contexts tested at the same time, and for CG and CHG contexts independently. In contrast, a positive correlation between recombination rates and methylated cytosine count is reported in CHH contexts. Similar behavior is observed when considering only methylated cytosines within genes, transposons, and retrotransposons. Moreover, it is shown that the centromere region strongly affects the relationship between recombination rates and methylation. Finally, machine learning regression models are applied to predict recombination using the count of methylated cytosines in the CHH context as the entrance feature. These findings shed light on the understanding of the recombination landscape of rice and represent a reference framework for future studies in rice breeding, genetics, and epigenetics.
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Bian, Rujin, Dandan Nie, Fu Xing, Xiaoling Zhou, Ying Gao, Zhenjian Bai, and Bao Liu. "Adaptational significance of variations in DNA methylation in clonal plant Hierochloe glabra (Poaceae) in heterogeneous habitats." Australian Journal of Botany 61, no. 4 (2013): 274. http://dx.doi.org/10.1071/bt12242.

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As a prominent epigenetic modification, cytosine methylation may play a critical role in the adaptation of plants to different environments. The present study sought to investigate possible impacts of differential levels of nitrogen (N) supply on cytosine-methylation levels of a clonal plant, Hierochloe glabra Trin. (Poaceae). For this purpose, nitrate was applied at concentrations of 0, 0.15, 0.30 and 0.45 g N kg–1 soil, and ecologically important morphological traits were measured. The methylation-sensitive amplification polymorphism method was also conducted to analyse the variations in DNA cytosine methylation. Our results showed that N addition reduced CHG cytosine-methylation levels markedly compared with control plants growing in homogeneous pots (P = 0.026). No substantial differences were observed in morphological traits at the end of the growing stage, except for the highest ratio of leaf area to leaf dry mass in the medium-N patch (P = 0.008). However, significant linear regression relationships were found between cytosine-methylation levels and morphological traits, such as bud number and rhizome length and biomass. In conclusion, the higher cytosine-methylation level may activate asexual reproduction to produce more offspring and expand plant populations, possibly helping clonal plants to adapt to heterogeneous habitats.
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Dissertations / Theses on the topic "Cytosine methylation"

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Currie, Graeme M. "DNA methylation at cytosine position 5." Thesis, Aston University, 1992. http://publications.aston.ac.uk/12603/.

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DNA methylation appears to be involved in the regulation of gene expression. Transcriptionally inactive (silenced) genes normally contain a high proportion of 5-methyl-2'-deoxycytosine residues whereas transcriptionally active genes show much reduced levels. There appears good reason to believe that chemical agents capable of methylating 2'-deoxycytosine might affect gene expression and as a result of hypermethylating promoter regions of cytosine-guanine rich oncogenic sequences, cancer related genes may be silenced. This thesis describes the synthesis of a number of `electrophilic' S-methylsulphonium compounds and assesses their ability to act as molecules capable of methylating cytosine at position 5 and also considers their potential as cytotoxic agents. DNA is methylated in vivo by DNA methyltransferase utilising S-adenoxylmethionine as the methyl donor. This thesis addresses the theory that S-adenoxylmethionine may be replaced as the methyl donor for DNA methytransferase by other sulphonium compounds. S-[3H-methyl]methionine sulphonium iodide was synthesised and experiments to assess the ability of this compounds to transfer methyl groups to cytosine in the presence of DNA methyltransferase were unsuccessful. A proline residue adjacent to a cysteine residue has been identified to a highly conserved feature of the active site region of a large number of prokaryotic DNA methyltransferases. The thesis examines the possibility that short peptides containing the Pro-Cys fragment may be able to facilitate the alkylation of cytosine position 5 by sulphonium compounds. Peptides were synthesised up to 9 amino acids in length but none were shown to exhibit significant activity. Molecular modelling techniques, including Chem-X, Quanta, BIPED and protein structure prediction programs were used to assess any structural similarities that may exist between short peptides containing a Pro-Cys fragment and similar sequences present in proteins. A number of similar structural features were observed.
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Al-Azzawi, Haneen. "Cytosine methylation and hydroxymethylation at the leptin promoter." Thesis, University of Nottingham, 2013. http://eprints.nottingham.ac.uk/13843/.

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Leptin is an important hormone well known for its role in regulating energy intake and expenditure. DNA methylation levels at the leptin promoter in adult tissues appear to correlate with environmental stresses experienced during early life. This suggests that, once established in early life, DNA methylation is stably transmitted over successive cell generations. The aim of the work presented in this thesis was to determine factors that contribute to the establishment and maintenance of this epigenetic mark at the leptin promoter and to investigate the individual roles of cytosine methylation and cytosine hydroxymethylation at this genomic locus. No effect of a high fat prenatal diet was observed on leptin promoter DNA methylation levels in the adipose tissue of pigs. However, this genomic region exhibited intermediate levels of DNA methylation, which is usually associated with gene silencing, even though adipose tissue is the primary site of leptin expression. Double stranded methylation data obtained from DNA methyltransferase (DNMT) mutant mouse embryonic stem cells (mESCs) was used to investigate the contributions of the three catalytically active DNMT enzymes to leptin promoter DNA methylation patterns. Depletion of DNMT3b resulted in increased methylation levels at the leptin promoter, consistent with preliminary data from mutant DNMT3b mouse tissues where similar increases in methylation levels were observed at specific CpG dinucleotides. Two mESC lines, either hypomethylated or hypermethylated at the leptin promoter, were tested for leptin mRNA expression and neither cell line expressed leptin mRNA, suggesting that some form of methylation may be required for leptin expression. To further investigate the relationship between DNA methylation and leptin expression, in vitro differentiated adipocytes were analysed. 3T3-L1 preadipocytes, which do not express leptin, exhibit high levels of DNA methylation and these high methylation levels are maintained after the cells differentiate into leptin-expressing adipocytes. Induction of cytosine hydroxymethylation at the leptin promoter was detected in differentiating and mature adipocytes and evidence is presented to suggest that cytosine hydroxymethylation at the leptin promoter correlates with leptin expression.
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Genger, Ruth Kathleen, and Ruth Genger@csiro au. "Cytosine methylation, methyltransferases and flowering time in Arabidopsis thaliana." The Australian National University. Faculty of Science, 2000. http://thesis.anu.edu.au./public/adt-ANU20011127.115231.

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Environmental signals such as photoperiod and temperature provide plants with seasonal information, allowing them to time flowering to occur in favourable conditions. Most ecotypes of the model plant Arabidopsis thaliana flower earlier in long photoperiods and after prolonged exposure to cold (vernalization). The vernalized state is stable through mitosis, but is not transmitted to progeny, suggesting that the vernalization signal may be transmitted via a modification of DNA such as cytosine methylation. The role of methylation in the vernalization response is investigated in this thesis. ¶ Arabidopsis plants transformed with an antisense construct to the cytosine methyltransferase METI (AMT) showed significant decreases in methylation. AMT plants flowered significantly earlier than unvernalized wildtype plants, and the promotion of flowering correlated with the extent of demethylation. The flowering time of mutants with decreased DNA methylation (ddm1) was promoted only in growth conditions in which wildtype plants showed a vernalization response, suggesting that the early flowering response to demethylation operated specifically through the vernalization pathway. ¶ The AMT construct was crossed into two late flowering mutants that differed in vernalization responsiveness. Demethylation promoted flowering of the vernalization responsive mutant fca, but not of the fe mutant, which has only a slight vernalization response. This supports the hypothesis that demethylation is a step in the vernalization pathway. ¶ The role of gibberellic acid (GA) in the early flowering response to demethylation was investigated by observing the effect of the gai mutation, which disrupts the GA signal transduction pathway, on flowering time in plants with demethylated DNA. The presence of a single gai allele delayed flowering, suggesting that the early flowering response to demethylation requires a functional GA signal transduction pathway, and that demethylation increases GA levels or responses, directly or indirectly. ¶ In most transgenic lines, AMT-mediated demethylation did not fully substitute for vernalization. This indicates that part of the response is not affected by METI-mediated methylation, and may involve a second methyltransferase or a factor other than methylation. A second Arabidopsis methyltransferase, METIIa, was characterized and compared to METI. The two genes are very similar throughout the coding region, and share the location of their eleven introns, indicating that they diverged relatively recently. Both are transcribed in all tissues and at all developmental stages assayed, but the level of expression of METI is significantly higher than that of METIIa. The possible functions of METI, METIIa, and other Arabidopsis cytosine methyltransferase genes recently identified are discussed.
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Voss, Karl O. "Capillary electrophoresis for DNA sequencing and cytosine methylation analysis." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp02/NQ29120.pdf.

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Spangler, Maribeth. "Cytosine Methylation of Phytophthora sojae by Methylated DNA Immunoprecipitation." Bowling Green State University / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1339451917.

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Cull, Rebecca M. "Analysis of Cytosine Methylation in Soybean Pathogen Phytophthora sojae." Bowling Green State University / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1404745644.

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Schmidt, Martin, Sarah Hense, André E. Minoche, Juliane C. Dohm, Heinz Himmelbauer, Thomas Schmidt, and Falk Zakrzewski. "Cytosine Methylation of an Ancient Satellite Family in the Wild Beet Beta procumbens." Karger, 2014. https://tud.qucosa.de/id/qucosa%3A70576.

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DNA methylation is an essential epigenetic feature for the regulation and maintenance of heterochromatin. Satellite DNA is a repetitive sequence component that often occurs in large arrays in heterochromatin of subtelomeric, intercalary and centromeric regions. Knowledge about the methylation status of satellite DNA is important for understanding the role of repetitive DNA in heterochromatization. In this study, we investigated the cytosine methylation of the ancient satellite family pEV in the wild beet Beta procumbens. The pEV satellite is widespread in species-specific pEV subfamilies in the genus Beta and most likely originated before the radiation of the Betoideae and Chenopodioideae. In B. procumbens , the pEV subfamily occurs abundantly and spans intercalary and centromeric regions. To uncover its cytosine methylation, we performed chromosome-wide immunostaining and bisulfite sequencing of pEV satellite repeats. We found that CG and CHG sites are highly methylated while CHH sites show only low levels of methylation. As a consequence of the low frequency of CG and CHG sites and the preferential occurrence of most cytosines in the CHH motif in pEV monomers, this satellite family displays only low levels of total cytosine methylation.
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Shock, Lisa. "Functional consequences of cytosine methylation in mitochondrial DNA catalyzed by DNA methyltransferase 1." VCU Scholars Compass, 2011. http://scholarscompass.vcu.edu/etd/271.

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Cytosine methylation of mitochondrial DNA (mtDNA) was first described several decades ago, but neither the mechanism generating this modification nor its functional significance was known. Because mitochondrial dysfunction is a hallmark characteristic of numerous human diseases, including neurological and cardiovascular disease, aging and cancer, this dissertation addressed whether epigenetic modification of mtDNA regulates mitochondrial function. We show that mtDNA contains not only 5-methylcytosine (5mC), but also 5-hydroxymethylcytosine (5hmC), suggesting that previous reports likely underestimated the degree of epigenetic modification within the mitochondrial genome. We questioned how these modifications were generated by looking for mitochondrial isoforms of the nuclear-encoded DNA methyltransferases. We found that an isoform of the most abundant mammalian methyltransferase, DNA methyltransferase 1 (DNMT1) translocates to mitochondria, driven by an in-frame mitochondrial targeting sequence (MTS) located upstream of the nuclear DNMT1 translational start site. This MTS is highly conserved across mammalian species, and directs a heterologous protein to the mitochondria. To investigate the function of mitochondrial DNMT1 (mtDNMT1), we created a cell line that carries a tandem-affinity purification (TAP) tag at the C-terminus of a single endogenous human DNMT1 allele. Using the DNMT1-TAP cell line, we showed that mtDNMT1 specifically binds mtDNA in a manner that is proportional to CpG density, proving its presence in the mitochondrial matrix. mtDNMT1 exhibits CpG-specific methyltransferase activity in vitro that is resistant to trypsin-treatment of intact mitochondria, but moderately susceptible to pharmacologic inhibition by the nucleoside analog 5-aza-2’-deoxycytidine (5-aza-dC). NRF1 and PGC1α, transcription factors that activate nuclear-encoded mitochondrial proteins in response to oxidative stress, were observed to up-regulate expression of mtDNMT1. Loss of p53, a tumor suppressor gene known to help control mitochondrial metabolism, also results in a striking increase in mtDNMT1 expression, and this up-regulation of mtDNMT1 appears to modify mitochondrial transcription in a gene-specific fashion. Our data suggests roles for mtDNMT1 in both the establishment and maintenance of cytosine methylation (from which 5hmC is presumably derived) and in the regulation of mitochondrial transcription. We propose that the enzymes responsible for epigenetic modification of mtDNA have potential as therapeutic targets, with relevance to a broad spectrum of human disorders.
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Nicolini, Francesco. "Investigating the role of DNA (cytosine-5)-methyltransferase 1 in mitochondrial DNA methylation." Thesis, King's College London (University of London), 2018. https://kclpure.kcl.ac.uk/portal/en/theses/investigating-the-role-of-dna-cytosine5methyltransferase-1-in-mitochondrial-dna-methylation(4036df6a-90c7-4259-83fe-9470104d29d9).html.

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Mitochondrial DNA (mtDNA) that escapes from autophagy-mediated degradation after hemodynamic stress can cause inflammation in the heart by activating TLR9 signalling pathway, in which unmethylated CpG motifs bind to TLR9. DNA methyltransferases (DNMTs) such as DNMT1 and DNMT3A are involved in nuclear DNA methylation. It has also been reported that two additional potential transcription initiation codons exist at 5’ region to the original DNMT1 and that this 1st-to-3rd ATG sequence fused to GFP cDNA can localise in mitochondria, suggesting that DNMT1 might affect mtDNA methylation patterns. The aim of this study is to elucidate the role of DNMT1 in mtDNA methylation. To achieve this aim, three different isoforms of mouse DNMT1 sequences (“nuclear DNMT1”, “whole DNMT1” and “mtDNMT1”) as well as a mouse DNMT3A isoform were generated through molecular cloning. Mitoprot II software analysis predicted a high chance of mitochondrial localization (>90%) for both whole DNMT1 and mtDNMT1 isoforms. Western blotting analysis confirmed overexpression of all DNMT1 constructs, and immunocytochemistry experiments confirmed the predicted localisation of DNMT1 isoforms. DNMT3A localisation was detected at nuclear level, but not at mitochondrial level. Adenoviral vectors for nuclear DNMT1 and mtDNMT1 were generated and the methylated-DNA immunoprecipitation/qPCR methylation analysis of the D-Loop showed a 3-to-5 fold increase in total methylation levels in mtDNMT1 overexpressed mouse cardiac endothelial cells. However, global percentage of methylation is low. CoIP-MS analysis after mtDNMT1 overexpression failed to highlight any candidates for mtDNMT1 co-interaction. These data suggest that the 1st-to-3rd ATG sequence contains the mitochondrial localisation signal for DNMT1, and that DNMT1 can localise to mitochondria through it and methylate mtDNA.
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Kan, Mun Seng. "Mutational analysis of M.HhaI to mimic #PSI#M.SpoI from Schizosaccharomyces pombe and Masc1 from Ascobolus immersus." Thesis, University of Sheffield, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.310873.

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Books on the topic "Cytosine methylation"

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Currie, Graeme Martin. DNA methylation at cytosine position 5. Birmingham: Aston University. Department of Pharmaceutical Sciences, 1992.

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V, Beck Stephen, and Olek A, eds. The epigenome: Molecular hide and seek. Weinheim: Wiley-VCH, 2003.

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Zhang, Xiaolin. Mutagenic mechanisms associated with DNA cytosine methylation, DNA base sequence context and DNA precursor pool asymmetry. 1995.

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The Epigenome: Molecular Hide and Seek. Wiley-VCH, 2003.

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Chess, Andrew, and Schahram Akbarian. The Human Brain and its Epigenomes. Edited by Dennis S. Charney, Eric J. Nestler, Pamela Sklar, and Joseph D. Buxbaum. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780190681425.003.0003.

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Conventional psychopharmacology elicits an insufficient therapeutic response in more than one half of patients diagnosed with schizophrenia, bipolar disorder, depression, anxiety, or related disorders. This underscores the need to further explore the neurobiology and molecular pathology of mental disorders in order to develop novel treatment strategies of higher efficacy. One promising avenue of research is epigenetics.Deeper understanding of genome organization and function in normal and diseased human brain will require comprehensive charting of neuronal and glial epigenomes. This includes DNA cytosine and adenine methylation, hundred(s) of residue-specific post-translational histone modifications and histone variants, transcription factor occupancies, and chromosomal conformations and loopings. Epigenome mappings provide an important avenue to assign function to many risk-associated DNA variants and mutations that do not affect protein-coding sequences. Powerful novel single cell technologies offer the opportunity to understand genome function in context of the vastly complex cellular heterogeneity and neuroanatomical diversity of the human brain.
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Book chapters on the topic "Cytosine methylation"

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Zacharias, Wolfgang. "Methylation of cytosine influences the DNA structure." In DNA Methylation, 27–38. Basel: Birkhäuser Basel, 1993. http://dx.doi.org/10.1007/978-3-0348-9118-9_3.

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Ortega-Recalde, Oscar, Julian R. Peat, Donna M. Bond, and Timothy A. Hore. "Estimating Global and Erasure Using Low-Coverage Whole-Genome Bisulfite (WGBS)." In Methods in Molecular Biology, 29–44. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1294-1_3.

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AbstractWhole-genome bisulfite sequencing (WGBS) is a popular method for characterizing cytosine methylation because it is fully quantitative and has base-pair resolution. While WGBS is prohibitively expensive for experiments involving many samples, low-coverage WGBS can accurately determine global methylation and erasure at similar cost to high-performance liquid chromatography (HPLC) or enzyme-linked immunosorbent assays (ELISA). Moreover, low-coverage WGBS has the capacity to distinguish between methylation in different cytosine contexts (e.g., CG, CHH, and CHG), can tolerate low-input material (<100 cells), and can detect the presence of overrepresented DNA originating from mitochondria or amplified ribosomal DNA. In addition to describing a WGBS library construction and quantitation approach, here we detail computational methods to predict the accuracy of low-coverage WGBS using empirical bootstrap samplers and theoretical estimators similar to those used in election polling. Using examples, we further demonstrate how non-independent sampling of cytosines can alter the precision of error calculation and provide methods to improve this.
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Tiedemann, Rochelle L., Hope E. Eden, Zhijun Huang, Keith D. Robertson, and Scott B. Rothbart. "Distinguishing Active Versus Passive Using Illumina MethylationEPIC BeadChip Microarrays." In Methods in Molecular Biology, 97–140. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1294-1_7.

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AbstractThe 5-carbon positions on cytosine nucleotides preceding guanines in genomic DNA (CpG) are common targets for DNA methylation (5mC). DNA methylation removal can occur through both active and passive mechanisms. Ten-eleven translocation enzymes (TETs) oxidize 5mC in a stepwise manner to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5mC can also be removed passively through sequential cell divisions in the absence of DNA methylation maintenance. In this chapter, we describe approaches that couple TET-assisted bisulfite (TAB) and oxidative bisulfite (OxBS) conversion to the Illumina MethylationEPIC BeadChIP (EPIC array) and show how these technologies can be used to distinguish active versus passive DNA demethylation. We also describe integrative bioinformatics pipelines to facilitate this analysis.
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Haque, Nazmul, and Masamichi Nishiguchi. "Bisulfite Sequencing for Cytosine-Methylation Analysis in Plants." In Methods in Molecular Biology, 187–97. Totowa, NJ: Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-123-9_13.

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Guevara, María Ángeles, Nuria de María, Enrique Sáez-Laguna, María Dolores Vélez, María Teresa Cervera, and José Antonio Cabezas. "Analysis of DNA Cytosine Methylation Patterns Using Methylation-Sensitive Amplification Polymorphism (MSAP)." In Plant Epigenetics, 99–112. Boston, MA: Springer US, 2016. http://dx.doi.org/10.1007/978-1-4899-7708-3_9.

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Suzuki, Masako, and John M. Greally. "HELP-Tagging: Tag-Based Genome-Wide Cytosine Methylation Profiling." In Tag-Based Next Generation Sequencing, 299–309. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2012. http://dx.doi.org/10.1002/9783527644582.ch18.

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Mallik, Saurav, and Ujjwal Maulik. "Module-Based Knowledge Discovery for Multiple-Cytosine-Variant Methylation Profile." In Soft Computing for Biological Systems, 169–86. Singapore: Springer Singapore, 2018. http://dx.doi.org/10.1007/978-981-10-7455-4_10.

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Arita, Kyohei, Tatsuo Kanno, Manabu Yoshikawa, and Yoshiki Habu. "Mechanisms Linking Cytosine Methylation to Histone Modification in Arabidopsis thaliana." In Non Coding RNAs in Plants, 237–49. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-19454-2_15.

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Bilichak, Andriy, and Igor Kovalchuk. "Analysis of Global Genome Methylation Using the Cytosine-Extension Assay." In Plant Epigenetics, 73–79. Boston, MA: Springer US, 2016. http://dx.doi.org/10.1007/978-1-4899-7708-3_6.

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Zannino, Lorena, Stella Siciliani, and Marco Biggiogera. "Timing of Cytosine Methylation on Newly Synthesized RNA by Electron Microscopy." In The Nucleus, 197–205. New York, NY: Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-0763-3_14.

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Conference papers on the topic "Cytosine methylation"

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Sanchez, Robersy, and Sally Mackenzie. "Genome-wide Discriminatory Information Patterns of Cytosine DNA Methylation." In MOL2NET. Basel, Switzerland: MDPI, 2016. http://dx.doi.org/10.3390/mol2net-1-e001.

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Sanchez, Robersy, and Sally Mackenzie. "Genome-wide Discriminatory Information Patterns of Cytosine DNA Methylation." In MOL2NET, International Conference on Multidisciplinary Sciences. Basel, Switzerland: MDPI, 2015. http://dx.doi.org/10.3390/mol2net-1-e003.

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Vinarskaya, Alya, Alena Zuzina, and Pavel Balaban. "DNA CYTOSINE METHYLATION CONTRIBUTES TO LONG-TERM MEMORY MAINTENANCE IN SNAILS." In XV International interdisciplinary congress "Neuroscience for Medicine and Psychology". LLC MAKS Press, 2019. http://dx.doi.org/10.29003/m345.sudak.ns2019-15/121.

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Williams, Louise, V. K. Chaithanya Ponnaluri, Vaishnavi Panchapakesa, Romualdas Vaisvila, Matthew A. Campbell, Bradley W. Langhorst, Eileen T. Dimalanta, and Theodore B. Davis. "Abstract 2101: Enzymatic methyl-seq: Cytosine methylation detection using picograms of DNA." In Proceedings: AACR Annual Meeting 2021; April 10-15, 2021 and May 17-21, 2021; Philadelphia, PA. American Association for Cancer Research, 2021. http://dx.doi.org/10.1158/1538-7445.am2021-2101.

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Delgado-Cruzata, Lissette, Hui-Chen Wu, Jin Shen, Tiffany Thomas, Abby B. Siegel, Yu-Jing Zhang, Abhishek Goyal, Christine C. Hsu, Helen E. Remotti, and Regina M. Santella. "Abstract 4439: Relationship between DNA methylation of TET genes and levels of 5-methyl-cytosine and 5-hydroxymethyl-cytosine in hepatocellular carcinoma." In Proceedings: AACR 107th Annual Meeting 2016; April 16-20, 2016; New Orleans, LA. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1538-7445.am2016-4439.

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Lv, Jie, Yan Zhang, Yunfeng Qi, Hongbo Liu, Jiang Zhu, Jianzhong Su, and Ruijie Zhang. "ChIP-seq Data Plays an Important Role in a Cytosine-Based DNA Methylation Prediction Model." In 2009 Sixth International Conference on Fuzzy Systems and Knowledge Discovery. IEEE, 2009. http://dx.doi.org/10.1109/fskd.2009.708.

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Cote, Michele L., Justin A. Colacino, Shejie Sheng, Fulvio Lonardo, Mark Stewart, Dana C. Dolinoy, Tamara R. Jones, Ann G. Schwartz, and Laura S. Rozek. "Abstract LB-383: Methylation profiles using 480,000 cytosine markers of early stage adenocarcinomas of the lung." In Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.am2012-lb-383.

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Ahsan, Sama, Eric Raabe, Michael C. Haffner, Javad Nazarian, Katherine Warren, Leo Ballester, Martha Quezado, Charles Eberhart, and Fausto J. Rodriguez. "Abstract 384: Epigenetic derangements in histone and cytosine methylation are unique to diffuse intrinsic pontine glioma (DIPG)." In Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA. American Association for Cancer Research, 2014. http://dx.doi.org/10.1158/1538-7445.am2014-384.

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Wiley, Dorothy J., Emmanuel V. Masongsong, Provaboti Barman, Mina Kalantari, Hans Ullrich Bernard, Francois Coutlee, and David A. Elashoff. "Abstract LB-177: HPV16 CpG and de novo-cytosine methylation is differentially associated with low-grade versus high-grade anal intraepithelial neoplasia in HIV-infected men." In Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL. American Association for Cancer Research, 2011. http://dx.doi.org/10.1158/1538-7445.am2011-lb-177.

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Ivanov, Maxim, Magnus Ingelman-Sundberg, Mart Kals, and Lili Milani. "Targeted profiling of 5-(hydroxy)methylcytosine in genomic DNA from human livers: Next-generation sequencing of target enriched DNA reveals unexpectedly high interindividual variability of cytosine methylation and hydroxymethylation." In 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2014. http://dx.doi.org/10.1109/bibm.2014.6999389.

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