Journal articles: '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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Lan, Xi, Li-Juan Fu, Zhuo-Ying Hu, Qian Feng, Xue-Qing Liu, Xue Zhang, Xue-Mei Chen, Jun-Lin He, Ying-Xiong Wang, and Yu-Bin Ding. "Methylated oligonucleotide (MON)-induced promoter hypermethylation is associated with repression of CDH1 expression and contributes to the migration and invasion of human trophoblast cell lines." Reproduction, Fertility and Development 29, no. 8 (2017): 1509. http://dx.doi.org/10.1071/rd16031.

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DNA cytosine-5 methylation plays a vital role in regulating the expression of E-cadherin, which is encoded by the CDH1 gene. In this study, we characterised the DNA methylation and expression pattern of CDH1 in an extravillous trophoblast cell line (HTR-8/SVneo) and two trophoblast cell lines – JEG-3 and JAR. Promoter hypermethylation with reduced E-cadherin expression in HTR-8/SVneo cells and promoter hypomethylation with increased E-cadherin expression in JEG-3 and JAR cells were observed. Demethylation treatment significantly restored E-cadherin expression, contributing to decreases in the motility and invasiveness of HTR-8/SVneo cells. Sense-methylated oligonucleotides (MONs) labelled with Cy5 and complementary to a region of the human CDH1 promoter were designed, with the cytosines in 5′-cytosine-phosphate-guanine-3′ (CpG) dinucleotides being replaced by methylated cytosines. Following MON transfection into JEG-3 cells, the level of CDH1 promoter DNA methylation as well as cell motility and invasiveness were increased and gene expression was significantly repressed. Our results indicate that MON-mediated DNA methylation of the CDH1 promoter and subsequent alterations in gene expression may contribute to trophoblast motility and invasion, suggesting a potential method for controlling the biological function of trophoblasts in vitro through epigenetic modification.

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Liu, Zhuangzhuang, Pengpeng Tan, Youwang Liang, Yangjuan Shang, Kaikai Zhu, Fangren Peng, and Yongrong Li. "Grafting with Different Rootstocks Induced DNA Methylation Alterations in Pecan [Carya illinoinensis (Wangenh.) K. Koch]." Forests 14, no. 1 (December 20, 2022): 4. http://dx.doi.org/10.3390/f14010004.

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Rootstocks are well known to have important effects on scion growth performance. However, the involved mechanisms remain unclear. Recent studies provided some clues on the potential involvement of DNA methylation in grafting, which open up new horizons for exploring how rootstocks induce the growth changes. To better understand the involvement of DNA methylation in rootstock-induced growth alterations, whole-genome bisulfite sequencing (WGBS) was used to evaluate the methylation profiles of two sets of pecan grafts with different growth performances on different sizes of rootstocks. The results showed that methylated cytosines accounted for 24.52%–25.60% of all cytosines in pecan. Methylation levels in CG were the highest, with the lowest levels being in CHH (C= cytosine; G= guanine; H = adenine, thymine, or cytosine). Rootstocks induced extensive methylation alterations in scions with 934, 2864, and 15,789 differentially methylated regions (DMRs) determined in CG, CHG, and CHH contexts, respectively. DMR-related genes (DMGs) were found to participate in various processes associated with plant growth, among which 17 DMGs were found, most likely related to hormone response, that may play particularly important roles in graft growth regulation. This study revealed DNA methylomes throughout the pecan genome for the first time, and obtained abundant genes with methylation alterations that were potentially involved in rootstock-induced growth changes in pecan scions, which lays a good basis for further epigenetic studies on pecan and deeper understanding of grafting mechanisms in pecan grafts.

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Jackel, Jamie N., Jessica M. Storer, Tami Coursey, and David M. Bisaro. "Arabidopsis RNA Polymerases IV and V Are Required To Establish H3K9 Methylation, but Not Cytosine Methylation, on Geminivirus Chromatin." Journal of Virology 90, no. 16 (June 8, 2016): 7529–40. http://dx.doi.org/10.1128/jvi.00656-16.

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ABSTRACTIn plants, RNA-directed DNA methylation (RdDM) employs small RNAs to target enzymes that methylate cytosine residues. Cytosine methylation and dimethylation of histone 3 lysine 9 (H3K9me2) are often linked. Together they condition an epigenetic defense that results in chromatin compaction and transcriptional silencing of transposons and viral chromatin. Canonical RdDM (Pol IV-RdDM), involving RNA polymerases IV and V (Pol IV and Pol V), was believed to be necessary to establish cytosine methylation, which in turn could recruit H3K9 methyltransferases. However, recent studies have revealed that a pathway involving Pol II and RNA-dependent RNA polymerase 6 (RDR6) (RDR6-RdDM) is likely responsible for establishing cytosine methylation at naive loci, while Pol IV-RdDM acts to reinforce and maintain it. We used the geminivirusBeet curly top virus(BCTV) as a model to examine the roles of Pol IV and Pol V in establishing repressive viral chromatin methylation. As geminivirus chromatin is formedde novoin infected cells, these viruses are unique models for processes involved in the establishment of epigenetic marks. We confirm that Pol IV and Pol V are not needed to establish viral DNA methylation but are essential for its amplification. Remarkably, however, both Pol IV and Pol V are required for deposition of H3K9me2 on viral chromatin. Our findings suggest that cytosine methylation alone is not sufficient to triggerde novodeposition of H3K9me2 and further that Pol IV-RdDM is responsible for recruiting H3K9 methyltransferases to viral chromatin.IMPORTANCEIn plants, RNA-directed DNA methylation (RdDM) uses small RNAs to target cytosine methylation, which is often linked to H3K9me2. These epigenetic marks silence transposable elements and DNA virus genomes, but how they are established is not well understood. Canonical RdDM, involving Pol IV and Pol V, was thought to establish cytosine methylation that in turn could recruit H3K9 methyltransferases, but recent studies compel a reevaluation of this view. We used BCTV to investigate the roles of Pol IV and Pol V in chromatin methylation. We found that both are needed to amplify, but not to establish, DNA methylation. However, both are required for deposition of H3K9me2. Our findings suggest that cytosine methylation is not sufficient to recruit H3K9 methyltransferases to naive viral chromatin and further that Pol IV-RdDM is responsible.

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Warnecke, Peter M., and Timothy H. Bestor. "Cytosine methylation and human cancer." Current Opinion in Oncology 12, no. 1 (January 2000): 68–73. http://dx.doi.org/10.1097/00001622-200001000-00012.

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Walsh, C. P., and T. H. Bestor. "Cytosine methylation and mammalian development." Genes & Development 13, no. 1 (January 1, 1999): 26–34. http://dx.doi.org/10.1101/gad.13.1.26.

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Bestor, Timothy H. "Cytosine methylation mediates sexual conflict." Trends in Genetics 19, no. 4 (April 2003): 185–90. http://dx.doi.org/10.1016/s0168-9525(03)00049-0.

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Oshikawa, Daiki, Shintaro Inaba, Yudai Kitagawa, Kaori Tsukakoshi, and Kazunori Ikebukuro. "CpG Methylation Altered the Stability and Structure of the i-Motifs Located in the CpG Islands." International Journal of Molecular Sciences 23, no. 12 (June 9, 2022): 6467. http://dx.doi.org/10.3390/ijms23126467.

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Cytosine methylation within the 5′-C-phosphate-G-3′ sequence of nucleotides (called CpG methylation) is a well-known epigenetic modification of genomic DNA that plays an important role in gene expression and development. CpG methylation is likely to be altered in the CpG islands. CpG islands are rich in cytosine, forming a structure called the i-motif via cytosine-cytosine hydrogen bonding. However, little is known about the effect of CpG methylation on the i-motif. In this study, The CpG methylation-induced structural changes on the i-motif was examined by thermal stability, circular dichroism (CD) spectroscopy, and native-polyacrylamide gel electrophoresis (Native-PAGE) evaluation of five i-motif-forming DNAs from four cancer-related genes (VEGF, C-KIT, BCL2, and HRAS). This research shows that CpG methylation increased the transitional pH of several i-motif-forming DNAs and their thermal stability. When examining the effect of CpG methylation on the i-motif in the presence of opposite G4-forming DNAs, CpG methylation influenced the proportion of G4 and i-motif formation. This study showed that CpG methylation altered the stability and structure of the i-motif in CpG islands.

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Verma, Pratima, Amrita Singh, Supriya Purru, Kangila Venkataramana Bhat, and Suman Lakhanpaul. "Comparative DNA Methylome of Phytoplasma Associated Retrograde Metamorphosis in Sesame (Sesamum indicum L.)." Biology 11, no. 7 (June 23, 2022): 954. http://dx.doi.org/10.3390/biology11070954.

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Phytoplasma-associated diseases such as phyllody and little leaf are critical threats to sesame cultivation worldwide. The mechanism of the dramatic conversion of flowers to leafy structures leading to yield losses and the drastic reduction in leaf size due to Phytoplasma infection remains yet to be identified. Cytosine methylation profiles of healthy and infected sesame plants studied using Whole Genome Bisulfite Sequencing (WGBS) and Quantitative analysis of DNA methylation with the real-time PCR (qAMP) technique revealed altered DNA methylation patterns upon infection. Phyllody was associated with global cytosine hypomethylation, though predominantly in the CHH (where H = A, T or C) context. Interestingly, comparable cytosine methylation levels were observed between healthy and little leaf-affected plant samples in CG, CHG and CHH contexts. Among the different genomic fractions, the highest number of differentially methylated Cytosines was found in the intergenic regions, followed by promoter, exonic and intronic regions in decreasing order. Further, most of the differentially methylated genes were hypomethylated and were mainly associated with development and defense-related processes. Loci for STOREKEEPER protein-like, a DNA-binding protein and PP2-B15, an F-Box protein, responsible for plugging sieve plates to maintain turgor pressure within the sieve tubes were found to be hypomethylated by WGBS, which was confirmed by methylation-dependent restriction digestion and qPCR. Likewise, serine/threonine-protein phosphatase-7 homolog, a positive regulator of cryptochrome signaling involved in hypocotyl and cotyledon growth and probable O-methyltransferase 3 locus were determined to be hypermethylated. Phytoplasma infection-associated global differential methylation as well as the defense and development-related loci reported here for the first time significantly elucidate the mechanism of phytoplasma-associated disease development.

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Matoso, Daniele Aparecida. "Methylation Profile of 18S rDNA Gene in Brain and Muscle of Tambaqui Exposed to Parasiticide Trichlorfon." International Journal of Zoology and Animal Biology 6, no. 1 (2023): 1–7. http://dx.doi.org/10.23880/izab-16000445.

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Until recently, there were no reports on the methylation profile of Amazonian fish specimens employing restriction enzymes. The 18S rDNA methylation status of samples of captive tambaqui (Colossoma macropomum) exposed to the antiparasitic Trichlorfon was examined in the current study. The method performed makes use of the CCGG site's sensitivity to the presence of methylation in palindrome cytosines for the restriction enzymes HpaII and MspI. The cleavage occurs by the detection or non-detection of the methyl radical in the inner (C5mCGG) or outer (5mCCGG) cytosine, which makes it possible to compare the DNA methylation profile. When compared to the specimens examined as the control group, the results obtained revealed an increase in methylated fragments of the 18S rDNA gene at LC concentrations of 30% and 50%.

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Chen, Longzheng, and Jinfeng Chen. "Changes of cytosine methylation induced by wide hybridization and allopolyploidy in Cucumis." Genome 51, no. 10 (October 2008): 789–99. http://dx.doi.org/10.1139/g08-063.

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We previously demonstrated that allopolyploidization could induce phenotypic variations and genome changes in a newly synthesized allotetraploid in Cucumis . To explore the molecular involvement of epigenetic phenomena, we investigated cytosine methylation in Cucumis by using methylation-sensitive amplified polymorphism (MSAP). Results revealed a twofold difference in the level of cytosine methylation between the reciprocal F1 hybrids and the allotetraploid. Analysis of the methylation pattern indicated that methylation changed at 2.0% to 6.4% of total sites in both the F1 hybrids and the allotetraploid compared with their corresponding parents. Furthermore, 68.2% to 80.0% of the changed sites showed an increase in cytosine methylation and a majority of the methylated sites were from the maternal parent. Observations in different generations of the allotetraploid found that the extent of change in cytosine methylation pattern between the S1 and S2 was significantly higher than that between the S2 and S3, suggesting stability in advanced generations. Analysis of 7 altered sequences indicated their similarity to known functional genes or genes involved in regulating gene expression. Reverse transcription – polymerase chain reaction analysis suggested that at least two of the methylation changes might be related to gene expression changes, which further supports the hypothesis that DNA methylation plays a significant role in allopolyploidization.

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Sun, Hailin, Yanxin Zheng, Chunnuan Zhao, Tao Yu, and Jianguo Lin. "Study on the Heterosis of the First Generation of Hybrid between Chinese and Korean Populations of Scapharca broughtonii using Methylation-Sensitive Amplification Polymorphism (MSAP)." Journal of Molecular Biology Research 5, no. 1 (November 6, 2015): 56. http://dx.doi.org/10.5539/jmbr.v5n1p56.

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DNA methylation is known to play an important role in the regulation of gene expression in eukaryotes. In this study, the author assessed the extent and pattern of cytosine methylation in the Scapharca broughtonii genome using the technique of methylation-sensitive amplified polymorphism (MSAP).The results showed that, DNA methylation rate was negatively related to the shell length, the gross weight and the weight of soft body, but positively related to the shell broadness and the shell height; there was significantly different between the parents and the offspring: 31.6% of 5'-CCGG sites in the Patinopecten yessoensis of Korean populations genome were cytosine methylated, and in the Patinopecten yessoensis of Chinese populations were 33%, the methylation rates of F1 was 29.98%; four classes of patterns were identified in a comparative assay of cytosine methylation in the parents and hybrid, increased methylation was detected in the hybrid compared to the parents at some of the recognition sites, while decreased methylation in the hybrid was detected at other sites. It indicated that the alteration of methylation resulted from cross-breeding, and the inbreeding did not change the methylation ratio and patterns; The DNA cytosine methylation has a relationship with the heterosis.

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Lei, H., S. P. Oh, M. Okano, R. Juttermann, K. A. Goss, R. Jaenisch, and E. Li. "De novo DNA cytosine methyltransferase activities in mouse embryonic stem cells." Development 122, no. 10 (October 1, 1996): 3195–205. http://dx.doi.org/10.1242/dev.122.10.3195.

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It has been a controversial issue as to how many DNA cytosine methyltransferase mammalian cells have and whether de novo methylation and maintenance methylation activities are encoded by a single gene or two different genes. To address these questions, we have generated a null mutation of the only known mammalian DNA methyltransferase gene through homologous recombination in mouse embryonic stem cells and found that the development of the homozygous embryos is arrested prior to the 8-somite stage. Surprisingly, the null mutant embryonic stem cells are viable and contain low but stable levels of methyl cytosine and methyltransferase activity, suggesting the existence of a second DNA methyltransferase in mammalian cells. Further studies indicate that de novo methylation activity is not impaired by the mutation as integrated provirus DNA in MoMuLV-infected homozygous embryonic stem cells become methylated at a similar rate as in wild-type cells. Differentiation of mutant cells results in further reduction of methyl cytosine levels, consistent with the de novo methylation activity being down regulated in differentiated cells. These results provide the first evidence that an independently encoded DNA methyltransferase is present in mammalian cells which is capable of de novo methylating cellular and viral DNA in vivo.

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Liu, Xu, Emily R. Weikum, Desiree Tilo, Charles Vinson, and Eric A. Ortlund. "Structural basis for glucocorticoid receptor recognition of both unmodified and methylated binding sites, precursors of a modern recognition element." Nucleic Acids Research 49, no. 15 (July 21, 2021): 8923–33. http://dx.doi.org/10.1093/nar/gkab605.

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Abstract The most common form of DNA methylation involves the addition of a methyl group to a cytosine base in the context of a cytosine–phosphate–guanine (CpG) dinucleotide. Genomes from more primitive organisms are more abundant in CpG sites that, through the process of methylation, deamination and subsequent mutation to thymine–phosphate–guanine (TpG) sites, can produce new transcription factor binding sites. Here, we examined the evolutionary history of the over 36 000 glucocorticoid receptor (GR) consensus binding motifs in the human genome and identified a subset of them in regulatory regions that arose via a deamination and subsequent mutation event. GR can bind to both unmodified and methylated pre-GR binding sequences (GBSs) that contain a CpG site. Our structural analyses show that CpG methylation in a pre-GBS generates a favorable interaction with Arg447 mimicking that made with a TpG in a GBS. This methyl-specific recognition arose 420 million years ago and was conserved during the evolution of GR and likely helps fix the methylation on the relevant cytosines. Our study provides the first genetic, biochemical and structural evidence of high-affinity binding for the likely evolutionary precursor of extant TpG-containing GBS.

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Cai, Qinyin, Charles L. Guy, and Gloria A. Moore. "Detection of cytosine methylation and mapping of a gene influencing cytosine methylation in the genome ofCitrus." Genome 39, no. 2 (April 1, 1996): 235–42. http://dx.doi.org/10.1139/g96-032.

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A new method was developed to detect DNA methylation in the Citrus genome using random amplification coupled with restriction enzyme digestion. Genomic DNA from Citrus grandis (L.) Osb., Poncirus trifoliata (L.) Raf., and their F1hybrid was amplified using 7 individual 10-mer random primers. Prior to amplification the DNA templates were digested with 2 pairs of restriction endonucleases (HpaII–MspI and (or) Sau3AI–NdeII) with different sensitivities to cytosine methylation and after PCR amplification their amplified products were further digested with the same enzymes. Using this method, it was possible to detect 28 methylation events involving 23 amplified bands with the 7 random primers and 2 pairs of enzymes. A methylation polymorphism was found at a Sau3AI site in a 1.2-kb band amplified with one primer. One locus influencing cytosine methylation at this restriction site was identified through genetic analysis of a BC1population between C. grandis and P. trifoliata and was mapped to linkage group IV using an already developed core map. This technique for detecting methylation and methylation polymorphisms is simple and should be applicable to any eukaryotic species and to many situations where it is desirable to determine whether a sequence is methylated. Key words : Citrus grandis, Poncirus trifoliata, restriction endonuclease, polymerase chain reaction, RAPD.

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Ramasamy, Deepa, Arunagiri Kuha Deva Magendhra Rao, Thangarajan Rajkumar, and Samson Mani. "Experimental and Computational Approaches for Non-CpG Methylation Analysis." Epigenomes 6, no. 3 (August 16, 2022): 24. http://dx.doi.org/10.3390/epigenomes6030024.

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Cytosine methylation adjacent to adenine, thymine, and cytosine residues but not guanine of the DNA is distinctively known as non-CpG methylation. This CA/CT/CC methylation accounts for 15% of the total cytosine methylation and varies among different cell and tissue types. The abundance of CpG methylation has largely concealed the role of non-CpG methylation. Limitations in the early detection methods could not distinguish CpG methylation from non-CpG methylation. Recent advancements in enrichment strategies and high throughput sequencing technologies have enabled the detection of non-CpG methylation. This review discusses the advanced experimental and computational approaches to detect and describe the genomic distribution and function of non-CpG methylation. We present different approaches such as enzyme-based and antibody-based enrichment, which, when coupled, can also improve the sensitivity and specificity of non-CpG detection. We also describe the current bioinformatics pipelines and their specific application in computing and visualizing the imbalance of CpG and non-CpG methylation. Enrichment modes and the computational suites need to be further developed to ease the challenges of understanding the functional role of non-CpG methylation.

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Flavell, R. B., and M. O'Dell. "Variation and inheritance of cytosine methylation patterns in wheat at the high molecular weight glutenin and ribosomal RNA gene loci." Development 108, Supplement (April 1, 1990): 15–20. http://dx.doi.org/10.1242/dev.108.supplement.15.

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Chromosome marking by cytosine methyiation has been examined in two gene systems in wheat – at the loci encoding high molecular weight (HMW) glutenin subunits (seed proteins) and ribosomai RNA. Variation in cytosine methyiation occurs between progeny in highly inbred lines around the HMW glutenin locus. The variation is inherited through meiosis to F1, and F2 generations but occasionally a new variant arises. Specific cytosine residues lose their methyl group in the seed, the organ where the genes are expressed. Within the multigene family of ribosomai RNA genes, several subsets of genes can be defined based upon the cytosine methylation patterns. High activity of a ribosomai RNA gene locus is correlated with loss of methylation at specific cytosine residues, especially in the promoter and upstream regulatory regions. A model is described in which the subset of genes selected to be used are those to which specific regulatory proteins and transcription complexes bind most favourably. Binding of such proteins inhibits cytosine methylation and so marks the subset of genes for expression in subsequent cell generations. Examples are described where new types of RNA genes are introduced via sexual crosses that result in changes to the methylation patterns of the ribosomai RNA genes. The processes determining the changes begin, it is believed, in the fertilised egg.

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Poudel, Shyaron, Brett Hale, and Asela J. Wijeratne. "Evaluation of cytosine conversion methods for whole-genome DNA methylation profiling." F1000Research 11 (December 7, 2022): 1450. http://dx.doi.org/10.12688/f1000research.128391.1.

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Background: DNA methylation, the most common epigenetic modification, is defined as the removal or addition of methyl groups to cytosine bases. Studying DNA methylation provides insight into the regulation of gene expression, transposon mobility, genomic stability, and genomic imprinting. Whole-genome DNA methylation profiling (WGDM) is a powerful tool to find DNA methylation. This technique combines standard whole-genome sequencing methodology (e.g., Illumina high-throughput sequencing) with additional steps where unmethylated cytosine is converted to uracil. However, factors such as low cytosine conversion efficiency and inadequate DNA recovery during sample preparation oftentimes render poor-quality data. It is therefore imperative to benchmark sample preparation protocols to increase sequencing data quality and reduce false positives in methylation detection. Methods: A survey analysis was performed to investigate the efficiency of the following commercially available cytosine conversion kits when coupled with the NEBNext® Ultra™ DNA Library Prep Kit for Illumina (NEB): Zymo Research EZ DNA Methylation™ kit (hereafter known as Zymo Conversion kit), QIAGEN EpiTect Bisulfite kit (hereafter known as QIAGEN Conversion kit), and NEBNext® Enzymatic Methyl-seq Conversion Module (hereafter known as NEB EM-seq kit). Input DNA was derived from soybean (Glycine max [L.] Merrill) leaf tissue. Results: Of those tested, the QIAGEN Conversion kit provided the best sample recovery and the highest number of sequencing reads, whereas the Zymo Conversion kit had the best cytosine conversion efficiency and the least duplication. The sequence library obtained with the NEB EM-seq kit had the highest mapping efficiency (percentage of reads mapped to the genome). The data quality (defined by Phred score) and methylated cytosine call were similar between kits. Conclusions: This study offers the groundwork for selecting an effective DNA methylation detection kit for crop genome research.

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Bestor, Timothy H., and Angela Coxon. "Cytosine methylation The pros and cons of DNA methylation." Current Biology 3, no. 6 (June 1993): 384–86. http://dx.doi.org/10.1016/0960-9822(93)90209-7.

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Garrett-Bakelman, Francine E., Sheng Li, Todd Hricik, Stephen S. Chung, Haim Bar, Anna L. Brown, Jay P. Patel, et al. "Epigenetic Deregulation In Relapsed Acute Myeloid Leukemia." Blood 122, no. 21 (November 15, 2013): 2499. http://dx.doi.org/10.1182/blood.v122.21.2499.2499.

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Abstract Treatment failure in Acute Myeloid Leukemia (AML) is attributed in many cases to relapsed disease. Relapsed AML is a fundamental clinical challenge since most patients have poor clinical outcomes. The exact biological basis of AML relapse remains unclear. Genetic clonal evolution is widely believed to underlie the emergence of chemotherapy resistant clones. However, only limited, predominantly non-overlapping, somatic mutations and copy number aberrations were found to occur upon AML relapse. Furthermore, in a subset of cases, no relapse specific somatic mutations or copy number aberrations were identified. This suggests a role for other mechanisms in relapsed AML. We hypothesize that epigenetic plasticity and deregulation contributes to the pathogenesis of relapse in AML. To explore this notion, we performed a genome scale epigenetic and genetic analysis of thirty-nine paired diagnosis and relapsed AML human patient samples using exome capture, RNA-seq and ERRBS for DNA methylation sequencing. Exome capture was performed on each patient’s germline DNA as well. Exome capture revealed only a limited number of known recurrent somatic mutations acquired upon disease relapse, in agreement with previous reports. In contrast, upon disease relapse we identified thousands of statistically significant changes in cytosine methylation patterns. Globally, the majority of patients (85%) displayed striking predominance of DNA hypermethylation (p= 1.00433e-05, binomial test for equality of proportions) upon disease relapse. Notably a smaller set of patients displayed the opposite epigenetic phenotype with prominent loss of cytosine methylation. While differential methylation in the hypermethylated group of patients localized predominantly to CpG islands, the majority of differential methylation in the hypomethylated group localized to regions lacking both CpG islands and shores. In spite of these two distinct overall cytosine methylation patterns, the majority of differentially methylated cytosines are located in intergenic regions in all cases, and a subset of promoters were hypermethylated in almost all patients at relapse. A pathway analysis indicated that the commonly hypermethylated gene promoters at relapse are involved in the Hedghog, Wnt and calcium signaling pathways (p<0.05, modified Fisher Exact test). Integration of these findings with mutational and transcriptional profiles is underway. In order to determine whether epigenetic events linked to AML relapse could be modeled experimentally we performed a pilot study of a human AML xenograft in immunocompromised mice. Engrafted mice were treated with Ara-C at a clinically relevant dose (60mg/Kg; n=2) or vehicle alone (n=3) for five consecutive days. Human AML cells were collected at various timepoints including 28 days after Ara-C treatment where the AML had frankly relapsed in mice. Cytosine methylation profiles obtained through ERRBS revealed predominantly hypermethylated cytosines when compared to the xenotransplanted diagnostic sample (72% hypermethylated versus 28% hypomethylated). Remarkably, there was a strong overlap with gene promoters that are also aberrantly methylated in relapsed AML patients (p<0.01, hypergeometric test), including members of the Wnt signaling pathway. We conclude that there are epigenetically distinct forms of relapsed AML. Nonetheless, there is convergent epigenetic regulation of specific gene pathways that may contribute to relapsed AML pathogenesis and xenotransplanted AML mice can serve as experimental models for further study. Finally, the genomic distribution of reprogrammed methylation suggests a role for epigenetic plasticity at distal regulatory elements. Whereas it remains unclear whether these changes represent clonal selection, their extensive and dynamic range suggest that exposure to chemotherapy may alter the fidelity of mechanisms that control cytosine methylation distribution thus permitting widespread and distant epigenetic reprogramming and contributing to disease relapse. Disclosures: No relevant conflicts of interest to declare.

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Liu, Zhuang-Zhuang, Tao Chen, Fang-Ren Peng, You-Wang Liang, Peng-Peng Tan, Zheng-Hai Mo, Fan Cao, Yang-Juan Shang, Rui Zhang, and Yong-Rong Li. "Variation in Cytosine Methylation among Pecan Cultivars at Different Developmental Stages." Journal of the American Society for Horticultural Science 143, no. 3 (May 2018): 173–83. http://dx.doi.org/10.21273/jashs04343-18.

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Cytosine methylation plays important roles in regulating gene expression and modulating agronomic traits. In this study, the fluorescence-labeled methylation-sensitive amplified polymorphism (F-MSAP) technique was used to study variation in cytosine methylation among seven pecan (Carya illinoinensis) cultivars at four developmental stages. In addition, phenotypic variations in the leaves of these seven cultivars were investigated. Using eight primer sets, 22,796 bands and 950 sites were detected in the pecan cultivars at four stages. Variation in cytosine methylation was observed among the pecan cultivars, with total methylation levels ranging from 51.18% to 56.58% and polymorphism rates of 82.29%, 81.73%, 78.64%, and 79.09% being recorded at the four stages. Sufficiently accompanying the polymorphism data, significant differences in phenotypic traits were also observed among the pecan cultivars, suggesting that cytosine methylation may be an important factor underlying phenotypic variation. Hypermethylation was the dominant type of methylation among the four types observed, and full methylation occurred at higher levels than did hemimethylation in the pecan genomes. Cluster analysis and principal coordinate analysis (PCoA) identified Dice coefficients ranging from 0.698 to 0.778, with an average coefficient of 0.735, and the variance contribution rates of the previous three principal coordinates were 19.6%, 19.0%, and 18.2%, respectively. Among the seven pecan cultivars, four groups were clearly classified based on a Dice coefficient of 0.75 and the previous three principal coordinates. Tracing dynamic changes in methylation status across stages revealed that methylation patterns changed at a larger proportion of CCGG sites from the 30% of final fruit-size (30%-FFS) stage to the 70%-FFS stage, with general decreases in the total methylation level, the rate of polymorphism, and specific sites being observed in each cultivar. These results demonstrated that the F-MSAP technique is a powerful tool for quantitatively detecting cytosine methylation in pecan genomes and provide a new perspective for studying many important life processes in pecan.

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Hardin, Charles C., Matthew Corregan, Bernard A. Brown, and Lori N. Frederick. "Cytosine-cytosine+ base pairing stabilizes DNA quadruplexes and cytosine methylation greatly enhances the effect." Biochemistry 32, no. 22 (June 8, 1993): 5870–80. http://dx.doi.org/10.1021/bi00073a021.

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Cheng, X. "Enzymatic C5-cytosine methylation of DNA." Acta Crystallographica Section A Foundations of Crystallography 52, a1 (August 8, 1996): C95. http://dx.doi.org/10.1107/s0108767396095293.

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Severin, Philip M. D., Xueqing Zou, Hermann E. Gaub, and Klaus Schulten. "Cytosine methylation alters DNA mechanical properties." Nucleic Acids Research 39, no. 20 (July 20, 2011): 8740–51. http://dx.doi.org/10.1093/nar/gkr578.

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Zhang, Meishan, Josphert N. Kimatu, Kezhang Xu, and Bao Liu. "DNA cytosine methylation in plant development." Journal of Genetics and Genomics 37, no. 1 (January 2010): 1–12. http://dx.doi.org/10.1016/s1673-8527(09)60020-5.

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Ooi, S. K. T., A. H. O'Donnell, and T. H. Bestor. "Mammalian cytosine methylation at a glance." Journal of Cell Science 122, no. 16 (August 5, 2009): 2787–91. http://dx.doi.org/10.1242/jcs.015123.

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Sanchez, Robersy, and Sally A. Mackenzie. "Information Thermodynamics of Cytosine DNA Methylation." PLOS ONE 11, no. 3 (March 10, 2016): e0150427. http://dx.doi.org/10.1371/journal.pone.0150427.

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Millard, Julie T., and Tina M. Beachy. "Cytosine methylation enhances mitomycin C crosslinking." Biochemistry 32, no. 47 (November 1993): 12850–56. http://dx.doi.org/10.1021/bi00210a038.

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Chomet, Paul S. "Cytosine methylation in gene-silencing mechanisms." Current Opinion in Cell Biology 3, no. 3 (June 1991): 438–43. http://dx.doi.org/10.1016/0955-0674(91)90071-6.

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Cencioni, Chiara, Carlo Gaetano, and Francesco Spallotta. "Dissecting cytosine methylation mechanics of dysmetabolism." Aging 11, no. 3 (January 23, 2019): 837–38. http://dx.doi.org/10.18632/aging.101788.

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Gissot, Mathieu, Sang-Woon Choi, Reid F. Thompson, John M. Greally, and Kami Kim. "Toxoplasma gondii and Cryptosporidium parvum Lack Detectable DNA Cytosine Methylation." Eukaryotic Cell 7, no. 3 (January 4, 2008): 537–40. http://dx.doi.org/10.1128/ec.00448-07.

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ABSTRACT Epigenetic factors play a role in the expression of virulence traits in Apicomplexa. Apicomplexan genomes encode putative DNA cytosine methylation enzymes. To assess the presence of cytosine methylation of Toxoplasma gondii and Cryptosporidium parvum DNA, we used mass spectrometry analysis and confirmed that these organisms lack detectable methylcytosine in their DNA.

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Lin, Chien-Chu, Yi-Ping Chen, Wei-Zen Yang, James C. K. Shen, and Hanna S. Yuan. "Structural insights into CpG-specific DNA methylation by human DNA methyltransferase 3B." Nucleic Acids Research 48, no. 7 (February 21, 2020): 3949–61. http://dx.doi.org/10.1093/nar/gkaa111.

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Abstract DNA methyltransferases are primary enzymes for cytosine methylation at CpG sites of epigenetic gene regulation in mammals. De novo methyltransferases DNMT3A and DNMT3B create DNA methylation patterns during development, but how they differentially implement genomic DNA methylation patterns is poorly understood. Here, we report crystal structures of the catalytic domain of human DNMT3B–3L complex, noncovalently bound with and without DNA of different sequences. Human DNMT3B uses two flexible loops to enclose DNA and employs its catalytic loop to flip out the cytosine base. As opposed to DNMT3A, DNMT3B specifically recognizes DNA with CpGpG sites via residues Asn779 and Lys777 in its more stable and well-ordered target recognition domain loop to facilitate processive methylation of tandemly repeated CpG sites. We also identify a proton wire water channel for the final deprotonation step, revealing the complete working mechanism for cytosine methylation by DNMT3B and providing the structural basis for DNMT3B mutation-induced hypomethylation in immunodeficiency, centromere instability and facial anomalies syndrome.

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Do, Hongdo, Ramyar Molania, Paul L. Mitchell, Rita Vaiskunaite, John D. Murdoch, and Alexander Dobrovic. "Reducing Artifactual EGFR T790M Mutations in DNA from Formalin-Fixed Paraffin-Embedded Tissue by Use of Thymine-DNA Glycosylase." Clinical Chemistry 63, no. 9 (September 1, 2017): 1506–14. http://dx.doi.org/10.1373/clinchem.2017.271932.

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Abstract BACKGROUND False-positive EGFR T790M mutations have been reported in formalin-fixed lung tumors, but the cause of the false positives has not been identified. The T790M mutation results from a C>T change at the cytosine of a CpG dinucleotide. The presence or absence of methylation at this cytosine has different consequences following deamination, resulting in a thymine or uracil, respectively, both of which however result in an artifactual change. Uracil-DNA glycosylase (UDG) can be used to eliminate DNA templates with uracil residues but is not active against artifactual thymines. We therefore investigated the use of thymine-DNA glycosylase (TDG) to reduce artifactual T790M mutations. METHODS Formalin-fixed normal lung tissues and lung squamous cell carcinomas were tested to measure the frequency of false-positive EGFR mutations by use of droplet digital PCR before and after treatment with either UDG or TDG. Methylation at the cytosine at EGFR T790 was assessed by pyrosequencing and by analysis of public databases. RESULTS Artifactual EGFR T790M mutations were detected in all of the archival formalin-fixed normal lung and lung squamous cell carcinomas at mutant allele frequencies of 1% or lower. The cytosine at EGFR T790 showed high levels of methylation in all lung cancer samples and normal tissues. Pretreatment of the formalin-fixed DNA with either UDG or TDG reduced the false EGFR T790M mutations, but a greater reduction was seen with the TDG treatment. CONCLUSIONS Both U:G and T:G lesions in formalin-fixed tissue are sources of false-positive EGFR T790M mutations. This is the first report of the use of TDG to reduce sequence artifacts in formalin-fixed DNA and is applicable to the accurate detection of mutations arising at methylated cytosines.

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Riddle, Nicole C., and Eric J. Richards. "The Control of Natural Variation in Cytosine Methylation in Arabidopsis." Genetics 162, no. 1 (September 1, 2002): 355–63. http://dx.doi.org/10.1093/genetics/162.1.355.

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Abstract We explore the extent and sources of epigenetic variation in cytosine methylation in natural accessions of the flowering plant, Arabidopsis thaliana, by focusing on the methylation of the major rRNA gene repeats at the two nucleolus organizer regions (NOR). Our findings indicate that natural variation in NOR methylation results from a combination of genetic and epigenetic mechanisms. Genetic variation in rRNA gene copy number and trans-acting modifier loci account for some of the natural variation in NOR methylation. Our results also suggest that divergence and inheritance of epigenetic information, independent of changes in underlying nucleotide sequence, may play an important role in maintaining natural variation in cytosine methylation.

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Crouse, Matthew S., Wellison Jarles Da Silva Diniz, Joel Caton, Carl R. Dahlen, Lawrence P. Reynolds, Pawel P. Borowicz, and Alison K. Ward. "82 Methyl Donor Supplementation Alters Cytosine Methylation and Biological Processes of Cells Cultured in Divergent Glucose Media Reflecting Improvements in Mitochondrial Respiration and Cell Growth Rate." Journal of Animal Science 99, Supplement_1 (May 1, 2021): 109. http://dx.doi.org/10.1093/jas/skab054.178.

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Abstract We hypothesized that supplementation of one-carbon metabolites (OCM: methionine, folate, choline, and vitamin B12) to bovine embryonic tracheal fibroblasts in divergent glucose media would alter cytosine methylation, and alterations in cytosine methylation will reflect biological processes matching previously improved mitochondrial respiration, cell proliferation, and cell growth rate data. Cells were cultured with 1g/L glucose (Low) or 4.5g/L glucose (High). Control medium (CON) contained basal concentrations of folate (0.001g/L), choline (0.001g/L), vitamin B12 (4µg/L), and methionine (0.015g/L). The OCM were supplemented at 2.5 and 5 times (2.5X and 5X, respectively) the CON media, except methionine was limited to 2X across all supplemented treatments. Cells were passaged three times in their treatment media before DNA extraction. Reduced representation bisulfite sequencing was adopted to analyze and compare the genomic methylation patterns within and across treatments using edgeR. Biological processes (BP) were retrieved based on the nearest genes of differentially methylated cytosines (P < 0.01) for each comparison between treatments. In both Low and High treatments, greater OCM increased the proportion of hypomethylated vs. hypermethylated cytosines. Functional analyses pointed out positive regulation of BP related to energy metabolism, except for the contrasts within the High group. Among the BP, we can highlight positive regulation of: GTPase activity, catalytic activity, molecular function, protein modification processes, phosphorylation, protein phosphorylation, cellular protein metabolic processes, MAPK cascade, and metabolic processes. These data support previously reported results from this experiment that showed increased mitochondrial respiration, cell proliferation, and growth rates with increasing OCM levels. We interpret these data to imply that when energy and OCM requirements are met for growth and basal methylation levels, DNA methylation levels decrease which may allow for greater transcription. Thus, OCM can be utilized for other functions such as polyamine synthesis, nucleotide synthesis, energetic metabolites, and phosphatidylcholine synthesis. USDA is an equal opportunity provider and employer.

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Tsuruta, Mitsuki, Yui Sugitani, Naoki Sugimoto, and Daisuke Miyoshi. "Combined Effects of Methylated Cytosine and Molecular Crowding on the Thermodynamic Stability of DNA Duplexes." International Journal of Molecular Sciences 22, no. 2 (January 19, 2021): 947. http://dx.doi.org/10.3390/ijms22020947.

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Methylated cytosine within CpG dinucleotides is a key factor for epigenetic gene regulation. It has been revealed that methylated cytosine decreases DNA backbone flexibility and increases the thermal stability of DNA. Although the molecular environment is an important factor for the structure, thermodynamics, and function of biomolecules, there are few reports on the effects of methylated cytosine under a cell-mimicking molecular environment. Here, we systematically investigated the effects of methylated cytosine on the thermodynamics of DNA duplexes under molecular crowding conditions, which is a critical difference between the molecular environment in cells and test tubes. Thermodynamic parameters quantitatively demonstrated that the methylation effect and molecular crowding effect on DNA duplexes are independent and additive, in which the degree of the stabilization is the sum of the methylation effect and molecular crowding effect. Furthermore, the effects of methylation and molecular crowding correlate with the hydration states of DNA duplexes. The stabilization effect of methylation was due to the favorable enthalpic contribution, suggesting that direct interactions of the methyl group with adjacent bases and adjacent methyl groups play a role in determining the flexibility and thermodynamics of DNA duplexes. These results are useful to predict the properties of DNA duplexes with methylation in cell-mimicking conditions.

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Shock, Lisa S., Prashant V. Thakkar, Erica J. Peterson, Richard G. Moran, and Shirley M. Taylor. "DNA methyltransferase 1, cytosine methylation, and cytosine hydroxymethylation in mammalian mitochondria." Proceedings of the National Academy of Sciences 108, no. 9 (February 14, 2011): 3630–35. http://dx.doi.org/10.1073/pnas.1012311108.

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Boltz, Valerie F., Cristina Ceriani, Jason W. Rausch, Wei Shao, Michael J. Bale, Brandon F. Keele, Rebecca Hoh, et al. "CpG Methylation Profiles of HIV-1 Proviral DNA in Individuals on ART." Viruses 13, no. 5 (April 29, 2021): 799. http://dx.doi.org/10.3390/v13050799.

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The latent HIV-1 reservoir is comprised of stably integrated and intact proviruses with limited to no viral transcription. It has been proposed that latent infection may be maintained by methylation of pro-viral DNA. Here, for the first time, we investigate the cytosine methylation of a replication competent provirus (AMBI-1) found in a T cell clone in a donor on antiretroviral therapy (ART). Methylation profiles of the AMBI-1 provirus were compared to other proviruses in the same donor and in samples from three other individuals on ART, including proviruses isolated from lymph node mononuclear cells (LNMCs) and peripheral blood mononuclear cells (PBMCs). We also evaluated the apparent methylation of cytosines outside of CpG (i.e., CpH) motifs. We found no evidence for methylation in AMBI-1 or any other provirus tested within the 5′ LTR promoter. In contrast, CpG methylation was observed in the env-tat-rev overlapping reading frame. In addition, we found evidence for differential provirus methylation in cells isolated from LNMCs vs. PBMCs in some individuals, possibly from the expansion of infected cell clones. Finally, we determined that apparent low-level methylation of CpH cytosines is consistent with occasional bisulfite reaction failures. In conclusion, our data do not support the proposition that latent HIV infection is associated with methylation of the HIV 5′ LTR promoter.

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Othman Smail, Harem, and Dlnya Asaad Mohamad. "Molecular Approaches for the Detection of DNA Methylation." Academic Journal of Nawroz University 11, no. 4 (December 8, 2022): 452–63. http://dx.doi.org/10.25007/ajnu.v11n4a1225.

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The main goals of this review were to understand the main molecular approaches for the detection of different types of epigenetics modification such as chromatin modifications and DNA methylation .this review provide information about the most sensitive and reliable methods for the defection of epigenetics .generally there are two approaches for detection chromatin remodeling and five approaches for DNA methylation detection widely uses .the most of the useful techniques for chromatin remodeling was chromatin immunoprecipitation (ChIP) assay. Formaldehyde is used in this process to in vivo cross-link proteins to DNA, followed by chromatin extraction from cross-linked cells and tissues. Bisulfite conversion DNA methylation and Bisulfite sequencing methylation is used for DNA methylation. The bisulfite conversion mechanism is a key step in the identification and recognition of DNA methylation; the principles of bisulfite conversion rely on the presence or absence of unique cytosine methyl groups at the carbon-5 site. After treatment with sodium bisulfite, unmethylated cytosine residues are converted to uracil, while 5-methylcytosine (5mC) remains unchanged due to the block reaction of the methyl groups. However, the design of primers for converted and non-converted cytosine is necessary to avoid any errors.

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Pérez-Cañamás, Miryam, Elizabeth Hevia, and Carmen Hernández. "Epigenetic Changes in Host Ribosomal DNA Promoter Induced by an Asymptomatic Plant Virus Infection." Biology 9, no. 5 (April 28, 2020): 91. http://dx.doi.org/10.3390/biology9050091.

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DNA cytosine methylation is one of the main epigenetic mechanisms in higher eukaryotes and is considered to play a key role in transcriptional gene silencing. In plants, cytosine methylation can occur in all sequence contexts (CG, CHG, and CHH), and its levels are controlled by multiple pathways, including de novo methylation, maintenance methylation, and demethylation. Modulation of DNA methylation represents a potentially robust mechanism to adjust gene expression following exposure to different stresses. However, the potential involvement of epigenetics in plant-virus interactions has been scarcely explored, especially with regard to RNA viruses. Here, we studied the impact of a symptomless viral infection on the epigenetic status of the host genome. We focused our attention on the interaction between Nicotiana benthamiana and Pelargonium line pattern virus (PLPV, family Tombusviridae), and analyzed cytosine methylation in the repetitive genomic element corresponding to ribosomal DNA (rDNA). Through a combination of bisulfite sequencing and RT-qPCR, we obtained data showing that PLPV infection gives rise to a reduction in methylation at CG sites of the rDNA promoter. Such a reduction correlated with an increase and decrease, respectively, in the expression levels of some key demethylases and of MET1, the DNA methyltransferase responsible for the maintenance of CG methylation. Hypomethylation of rDNA promoter was associated with a five-fold augmentation of rRNA precursor levels. The PLPV protein p37, reported as a suppressor of post-transcriptional gene silencing, did not lead to the same effects when expressed alone and, thus, it is unlikely to act as suppressor of transcriptional gene silencing. Collectively, the results suggest that PLPV infection as a whole is able to modulate host transcriptional activity through changes in the cytosine methylation pattern arising from misregulation of methyltransferases/demethylases balance.

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da Silva, Marcel Fernando, Marcos Cesar Gonçalves, Michael dos Santos Brito, Cibele Nataliane Medeiros, Ricardo Harakava, Marcos Guimarães de Andrade Landell, and Luciana Rossini Pinto. "Sugarcane mosaic virus mediated changes in cytosine methylation pattern and differentially transcribed fragments in resistance-contrasting sugarcane genotypes." PLOS ONE 15, no. 11 (November 9, 2020): e0241493. http://dx.doi.org/10.1371/journal.pone.0241493.

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Sugarcane mosaic virus (SCMV) is the causal agent of sugarcane mosaic disease (SMD) in Brazil; it is mainly controlled by using resistant cultivars. Studies on the changes in sugarcane transcriptome provided the first insights about the molecular basis underlying the genetic resistance to SMD; nonetheless, epigenetic modifications such as cytosine methylation is also informative, considering its roles in gene expression regulation. In our previous study, differentially transcribed fragments (DTFs) were obtained using cDNA-amplified fragment length polymorphism by comparing mock- and SCMV-inoculated plants from two sugarcane cultivars with contrasting responses to SMD. In this study, the identification of unexplored DTFs was continued while the same leaf samples were used to evaluate SCMV-mediated changes in the cytosine methylation pattern by using methylation-sensitive amplification polymorphism. This analysis revealed minor changes in cytosine methylation in response to SCMV infection, but distinct changes between the cultivars with contrasting responses to SMD, with higher hypomethylation events 24 and 72 h post-inoculation in the resistant cultivar. The differentially methylated fragments (DMFs) aligned with transcripts, putative promoters, and genomic regions, with a preponderant distribution within CpG islands. The transcripts found were associated with plant immunity and other stress responses, epigenetic changes, and transposable elements. The DTFs aligned with transcripts assigned to stress responses, epigenetic changes, photosynthesis, lipid transport, and oxidoreductases, in which the transcriptional start site is located in proximity with CpG islands and tandem repeats. Real-time quantitative polymerase chain reaction results revealed significant upregulation in the resistant cultivar of aspartyl protease and VQ protein, respectively, selected from DMF and DTF alignments, suggesting their roles in genetic resistance to SMD and supporting the influence of cytosine methylation in gene expression. Thus, we identified new candidate genes for further validation and showed that the changes in cytosine methylation may regulate important mechanisms underlying the genetic resistance to SMD.

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Journal articles on the topic 'Cytosine methylation'

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