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Journal articles on the topic 'Method for DNA methylation'

Author: Grafiati

Published: 11 March 2023

Last updated: 31 July 2025

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1

Dang, Pengtao, Xiao Wang, Haiqi Zhu, et al. "Abstract 5352: Targeting DNA methylation in T cells to improve the efficacy of immunotherapy." Cancer Research 83, no. 7_Supplement (2023): 5352. http://dx.doi.org/10.1158/1538-7445.am2023-5352.

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Abstract T-cells are critical mediators of immunity and immunologic memory. Their cell fates are regulated in part through epigenetic mechanisms, including DNA methylation. Recent genome-wide methylation analyses have revealed dynamic alterations in the methylome at various stages of development and differentiation of T cells. At single cell level, it is not easy to simultaneously collect RNA-seq and RBBS methylation profiling. An important task is to understand the expression change of which genes and pathways are regulated by DNA methylations, especially for the ones that are associated with

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Majchrzak-Celińska, A., M. Naskret-Barciszewska, M. Giel-Pietraszuk, W. Nowak, P. Śron, and A. Barciszewska. "P02.08.A The relations of focal and total DNA methylation in gliomas." Neuro-Oncology 24, Supplement_2 (2022): ii31. http://dx.doi.org/10.1093/neuonc/noac174.101.

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Abstract Background The role of epigenetic events in gliomagenesis is undoubtful. However, the role of specific pathological events is not so clear. It was shown that loss in total DNA methylation correlates with higher tumor malignancy and oxidative DNA damage. But promoter methylation of many genes was reported to be significant for gliomas’ malignancy and predictive for the treatment outcome. In carcinogenesis in general global DNA hypomethylation and focal hypermethylation coexist. The aim of our project was to evaluate the correlation between total DNA methylation and promoter methylation

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Kim, Sook Ho, Hae Jun Jung, and Seok-Cheol Hong. "Z-DNA as a Tool for Nuclease-Free DNA Methyltransferase Assay." International Journal of Molecular Sciences 22, no. 21 (2021): 11990. http://dx.doi.org/10.3390/ijms222111990.

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Methylcytosines in mammalian genomes are the main epigenetic molecular codes that switch off the repertoire of genes in cell-type and cell-stage dependent manners. DNA methyltransferases (DMT) are dedicated to managing the status of cytosine methylation. DNA methylation is not only critical in normal development, but it is also implicated in cancers, degeneration, and senescence. Thus, the chemicals to control DMT have been suggested as anticancer drugs by reprogramming the gene expression profile in malignant cells. Here, we report a new optical technique to characterize the activity of DMT a

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Li, W., A. Van Soom, and L. Peelman. "Repeats as global DNA methylation marker in bovine preimplantation embryos." Czech Journal of Animal Science 62, No. 2 (2017): 43–50. http://dx.doi.org/10.17221/29/2016-cjas.

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DNA methylation undergoes dynamic changes and is a crucial part of the epigenetic regulation during mammalian early development. To determine the DNA methylation levels in bovine embryos, we applied a bisulfite sequencing based method aimed at repetitive sequences including three retrotransposons (L1_BT, BovB, and ERV1-1-I_BT) and Satellite I. A more accurate estimate of the global DNA methylation level compared to previous methods using only one repeat sequence, like Alu, could be made by calculation of the weighted arithmetic mean of multiple repetitive sequences, considering the copy number

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Kurdyukov, Sergey, and Martyn Bullock. "DNA Methylation Analysis: Choosing the Right Method." Biology 5, no. 1 (2016): 3. http://dx.doi.org/10.3390/biology5010003.

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6

IMAMURA, TAKUYA. "DNA methylation analysis with bisulfite sequencing method." Newsletter of Japan Society for Comparative Endocrinology, no. 113 (2004): 25–29. http://dx.doi.org/10.5983/nl2001jsce.2004.113_25.

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7

Hou, Peng, Meiju Ji, Song Li, Nongyue He, and Zuhong Lu. "High-throughput method for detecting DNA methylation." Journal of Biochemical and Biophysical Methods 60, no. 2 (2004): 139–50. http://dx.doi.org/10.1016/j.jbbm.2004.05.001.

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Choi, Woo Lee, Young Geun Mok, and Jin Hoe Huh. "Application of 5-Methylcytosine DNA Glycosylase to the Quantitative Analysis of DNA Methylation." International Journal of Molecular Sciences 22, no. 3 (2021): 1072. http://dx.doi.org/10.3390/ijms22031072.

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In higher eukaryotes DNA methylation is a prominent epigenetic mark important for chromatin structure and gene expression. Thus, profiling DNA methylation is important for predicting gene expressions associated with specific traits or diseases. DNA methylation is achieved by DNA methyltransferases and can be actively removed by specific enzymes in a replication-independent manner. DEMETER (DME) is a bifunctional 5-methylcytosine (5mC) DNA glycosylase responsible for active DNA demethylation that excises 5mC from DNA and cleaves a sugar-phosphate bond generating a single strand break (SSB). In

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Ridha, Inam, Chenxi Xu, Yining Zhang, et al. "Multiplexed Methylated DNA Immunoprecipitation Sequencing (Mx-MeDIP-Seq) to Study DNA Methylation Using Low Amounts of DNA." DNA 4, no. 4 (2024): 397–416. http://dx.doi.org/10.3390/dna4040028.

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Background/Objectives: DNA methylation is a key epigenetic mark involved in regulating gene expression. Aberrant DNA methylation contributes to various human diseases, including cancer, autoimmune disorders, atherosclerosis, and cardiovascular diseases. While whole-genome bisulfite sequencing and methylated DNA immunoprecipitation (MeDIP) are standard techniques for studying DNA methylation, they are typically limited to a few samples per run, making them expensive and low-throughput. Therefore, an automation-friendly method is needed to increase throughput and reduce costs without compromisin

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Khodadadi, Ehsan, Leila Fahmideh, Ehsaneh Khodadadi, et al. "Current Advances in DNA Methylation Analysis Methods." BioMed Research International 2021 (March 20, 2021): 1–9. http://dx.doi.org/10.1155/2021/8827516.

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DNA methylation is one of the epigenetic changes, which plays a major role in regulating gene expression and, thus, many biological processes and diseases. There are several methods for determining the methylation of DNA samples. However, selecting the most appropriate method for answering biological questions appears to be a challenging task. The primary methods in DNA methylation focused on identifying the state of methylation of the examined genes and determining the total amount of 5-methyl cytosine. The study of DNA methylation at a large scale of genomic levels became possible following

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Han, Pingping, and Sašo Ivanovski. "Effect of Saliva Collection Methods on the Detection of Periodontium-Related Genetic and Epigenetic Biomarkers—A Pilot Study." International Journal of Molecular Sciences 20, no. 19 (2019): 4729. http://dx.doi.org/10.3390/ijms20194729.

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Different collection methods may influence the ability to detect and quantify biomarker levels in saliva, particularly in the expression of DNA/RNA methylation regulators of several inflammations and tissue turnover markers. This pilot study recruited five participants and unstimulated saliva were collected by either spitting or drooling, and the relative preference for each method was evaluated using a visual analogue scale. Subsequently, total RNA, gDNA and proteins were isolated using the Trizol method. Thereafter, a systematic evaluation was carried out on the potential effects of differen

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Ni, Peng, Neng Huang, Zhi Zhang, et al. "DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning." Bioinformatics 35, no. 22 (2019): 4586–95. http://dx.doi.org/10.1093/bioinformatics/btz276.

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Abstract Motivation The Oxford Nanopore sequencing enables to directly detect methylation states of bases in DNA from reads without extra laboratory techniques. Novel computational methods are required to improve the accuracy and robustness of DNA methylation state prediction using Nanopore reads. Results In this study, we develop DeepSignal, a deep learning method to detect DNA methylation states from Nanopore sequencing reads. Testing on Nanopore reads of Homo sapiens (H. sapiens), Escherichia coli (E. coli) and pUC19 shows that DeepSignal can achieve higher performance at both read level an

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Hu, Wenxing, Lixin Guan, and Mengshan Li. "Prediction of DNA Methylation based on Multi-dimensional feature encoding and double convolutional fully connected convolutional neural network." PLOS Computational Biology 19, no. 8 (2023): e1011370. http://dx.doi.org/10.1371/journal.pcbi.1011370.

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DNA methylation takes on critical significance to the regulation of gene expression by affecting the stability of DNA and changing the structure of chromosomes. DNA methylation modification sites should be identified, which lays a solid basis for gaining more insights into their biological functions. Existing machine learning-based methods of predicting DNA methylation have not fully exploited the hidden multidimensional information in DNA gene sequences, such that the prediction accuracy of models is significantly limited. Besides, most models have been built in terms of a single methylation

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Martisova, Andrea, Jitka Holcakova, Nasim Izadi, Ravery Sebuyoya, Roman Hrstka, and Martin Bartosik. "DNA Methylation in Solid Tumors: Functions and Methods of Detection." International Journal of Molecular Sciences 22, no. 8 (2021): 4247. http://dx.doi.org/10.3390/ijms22084247.

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DNA methylation, i.e., addition of methyl group to 5′-carbon of cytosine residues in CpG dinucleotides, is an important epigenetic modification regulating gene expression, and thus implied in many cellular processes. Deregulation of DNA methylation is strongly associated with onset of various diseases, including cancer. Here, we review how DNA methylation affects carcinogenesis process and give examples of solid tumors where aberrant DNA methylation is often present. We explain principles of methods developed for DNA methylation analysis at both single gene and whole genome level, based on (i)

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Di Lena, Pietro, Claudia Sala, Andrea Prodi, and Christine Nardini. "Missing value estimation methods for DNA methylation data." Bioinformatics 35, no. 19 (2019): 3786–93. http://dx.doi.org/10.1093/bioinformatics/btz134.

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Abstract Motivation DNA methylation is a stable epigenetic mark with major implications in both physiological (development, aging) and pathological conditions (cancers and numerous diseases). Recent research involving methylation focuses on the development of molecular age estimation methods based on DNA methylation levels (mAge). An increasing number of studies indicate that divergences between mAge and chronological age may be associated to age-related diseases. Current advances in high-throughput technologies have allowed the characterization of DNA methylation levels throughout the human g

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Zhu, Tiansheng, Jihong Guan, Hui Liu, and Shuigeng Zhou. "RMDB: An Integrated Database of Single-cytosine-resolution DNA Methylation in Oryza Sativa." Current Bioinformatics 14, no. 6 (2019): 524–31. http://dx.doi.org/10.2174/1574893614666190211161717.

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Background: Previous studies have revealed that DNA methylation plays a crucial role in eukaryotic growth and development via involvement in the regulation of gene expression and chromosomal instability. With the advancement of biotechnology, next-generation sequencing (NGS) is emerging as a popular method to explore the functions of DNA methylation, and an increasing number of genome-scale DNA methylation datasets have been published. Several DNA methylation databases, including MethDB, NGSmethDB and MENT have been developed for storing and analyzing the DNA methylation data. However, no publ

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Altaf, Adil, and Ahmad Zada. "DNA METHYLATION IN PLANTS." Journal of Global Innovations in Agriculture Sciences 9, no. 3 (2021): 109–14. http://dx.doi.org/10.22194/jgias/9.954.

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Common DNA methylation controls gene expression and preserves genomic integrity. Mal methylation can cause developmental abnormalities in the plants. Multiple enzymes carrying out de novo methylation, methylation maintenance, and active demethylation culminate in a particular DNA methylation state. Next-generation sequencing advances and computational methods to analyze the data. The model plant Arabidopsis thaliana was used to study DNA methylation patterns, epigenetic inheritance, and plant methylation. Plant DNA methylation research reveals methylation patterns and describing variations in

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Lu, Zhiquan, Zilu Ye, Ping Li, Yike Jiang, Sanyang Han, and Lan Ma. "An MSRE-Assisted Glycerol-Enhanced RPA-CRISPR/Cas12a Method for Methylation Detection." Biosensors 14, no. 12 (2024): 608. https://doi.org/10.3390/bios14120608.

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Background: Nasopharyngeal carcinoma (NPC) is a malignant tumor with high prevalence in southern China. Aberrant DNA methylation, as a hallmark of cancer, is extensively present in NPC, the detection of which facilitates early diagnosis and prognostic improvement of NPC. Conventional methylation detection methods relying on bisulfite conversion have limitations such as time-consuming, complex processes and sample degradation; thus, a more rapid and efficient method is needed. Methods: We propose a novel DNA methylation assay based on methylation-sensitive restriction endonuclease (MSRE) HhaI d

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Gao, Hui, Jiahai Li, Qiaoli Ma, Qinghui Zhang, Man Li, and Xiaoliang Hu. "Causal Associations of DNA Methylation and Cardiovascular Disease: A Two-Sample Mendelian Randomization Study." Global Heart 19, no. 1 (2024): 48. http://dx.doi.org/10.5334/gh.1324.

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Background: There is growing evidence that concentrations of DNA methylation are associated with cardiovascular disease; however, it is unclear whether this association reflects a causal relationship. Methods: We utilized a two-sample Mendelian randomization (MR) approach to investigate whether DNA methylation can affect the risk of developing cardiovascular disease in human life. We primarily performed the inverse variance weighted (IVW) method to analyze the causal effect of DNA methylation on multiple cardiovascular diseases. Additionally, to ensure the robustness of our findings, we conduc

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Celik Uzuner, Selcen. "Mitochondrial DNA methylation misleads global DNA methylation detected by antibody-based methods." Analytical Biochemistry 601 (July 2020): 113789. http://dx.doi.org/10.1016/j.ab.2020.113789.

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Bailey, Vasudev J., Yi Zhang, Brian P. Keeley, et al. "Single-Tube Analysis of DNA Methylation with Silica Superparamagnetic Beads." Clinical Chemistry 56, no. 6 (2010): 1022–25. http://dx.doi.org/10.1373/clinchem.2009.140244.

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Abstract Background: DNA promoter methylation is a signature for the silencing of tumor suppressor genes. Most widely used methods to detect DNA methylation involve 3 separate, independent processes: DNA extraction, bisulfite conversion, and methylation detection via a PCR method, such as methylation-specific PCR (MSP). This method includes many disconnected steps with associated losses of material, potentially reducing the analytical sensitivity required for analysis of challenging clinical samples. Methods: Methylation on beads (MOB) is a new technique that integrates DNA extraction, bisulfi

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Baránková, Kateřina, Anna Nebish, Jan Tříska, Jana Raddová, and Miroslav Baránek. "Comparison of DNA methylation landscape between Czech and Armenian vineyards show their unique character and increased diversity." Czech Journal of Genetics and Plant Breeding 57, No. 2 (2021): 67–75. http://dx.doi.org/10.17221/90/2020-cjgpb.

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Grapevine is a worldwide crop and it is also subject to global trade in wine, berries and grape vine plants. Various countries, including the countries of the European Union, emphasize the role of product origin designation and suitable methods are sought, able to capture distinct origins. One of the biological matrices that can theoretically be driven by individual vineyards’ conditions represents DNA methylation. Despite this interesting hypothesis, there is a lack of respective information. The aim of this work is to examine whether DNA methylation can be used to relate a sample to a given

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Kwon, Seulgi, Sang Mi An, Go Eun Yu, et al. "A prognostic method for the litter size in Berkshire pigs based on DNA methylation of IGFBP4 gene." Canadian Journal of Animal Science 98, no. 4 (2018): 845–51. http://dx.doi.org/10.1139/cjas-2017-0160.

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Litter size is an important trait in the pig industry. Therefore, a lot of effort has been put into improving this trait. DNA methylation is an essential epigenetic modification present in unique DNA sequences. Alterations in methylation can affect transcription and phenotypic variation. The purpose of this study was to investigate the effect of DNA methylation on litter size. Methylation-specific restriction enzymes are simple and useful tools for detecting DNA methylation status. We used a pair of methylation-sensitive isoschizomers, which have the same recognition site, HpaII and MspI. Insu

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Bonanno, Cinzia, Erlet Shehi, Daniel Adlerstein, and G. Mike Makrigiorgos. "MS-FLAG, a Novel Real-Time Signal Generation Method for Methylation-Specific PCR." Clinical Chemistry 53, no. 12 (2007): 2119–27. http://dx.doi.org/10.1373/clinchem.2007.094011.

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Abstract Background: Aberrant promoter methylation is a major mechanism for silencing tumor suppressor genes in cancer. Detection of hypermethylation is used as a molecular marker for early cancer diagnosis, as a prognostic index, or to define therapeutic targets for reversion of aberrant methylation. We report on a novel signal generation technology for real-time PCR to detect gene promoter methylation. Methods: FLAG (fluorescent amplicon generation) is a homogeneous signal generation technology based on the exceptionally thermostable endonuclease PspGI. FLAG provides real-time signal generat

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Sharma, Nidhi, Chittaranjan Behera, and Sudhir K. Gupta. "DNA Methylation: An Approach to Forensic Age Prediction by Molecular Mechanism." Journal of Forensic Chemistry and Toxicology 8, no. 2 (2022): 81–88. http://dx.doi.org/10.21088/jfct.2454.9363.8222.8.

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Epigenetic processes have an important role in gene expression which is affected by living environments conditions. Occurrence of epigenetics is conciliated by two major molecular mechanisms which includes histone modification and DNA methylation. DNA methylation is an epigenetic channel action, this is a natural process where transmission of a methyl group on the C5 position of the cytosine to form 5-methylcytosine at genome. So, epigenetic change is normal and continual fact that may be influenced by many factors including age, the environment / lifestyle, and disease state. The normal proce

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Wojtczyk-Miaskowska, Anita, Malgorzata Presler, Jerzy Michajlowski, Marcin Matuszewski, Beata Schlichtholz, and Medical University of Gdansk. "Gene Expression, DNA Methylation and Prognostic Significance of DNA Repair Genes in Human Bladder Cancer." Cellular Physiology and Biochemistry 42, no. 6 (2017): 2404–17. http://dx.doi.org/10.1159/000480182.

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Background/Aims: This study investigated the gene expression and DNA methylation of selected DNA repair genes (MBD4, TDG, MLH1, MLH3) and DNMT1 in human bladder cancer in the context of pathophysiological and prognostic significance. Methods: To determine the relationship between the gene expression pattern, global methylation and promoter methylation status, we performed real-time PCR to quantify the mRNA of selected genes in 50 samples of bladder cancer and adjacent non-cancerous tissue. The methylation status was analyzed by methylation-specific polymerase chain reaction (MSP) or digestion

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Klobučar, Tajda, Elisa Kreibich, Felix Krueger, et al. "IMPLICON: an ultra-deep sequencing method to uncover DNA methylation at imprinted regions." Nucleic Acids Research 48, no. 16 (2020): e92-e92. http://dx.doi.org/10.1093/nar/gkaa567.

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Abstract Genomic imprinting is an epigenetic phenomenon leading to parental allele-specific expression. Dosage of imprinted genes is crucial for normal development and its dysregulation accounts for several human disorders. This unusual expression pattern is mostly dictated by differences in DNA methylation between parental alleles at specific regulatory elements known as imprinting control regions (ICRs). Although several approaches can be used for methylation inspection, we lack an easy and cost-effective method to simultaneously measure DNA methylation at multiple imprinted regions. Here, w

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Li, Zhandong, Wei Guo, Shijian Ding, et al. "Detecting Blood Methylation Signatures in Response to Childhood Cancer Radiotherapy via Machine Learning Methods." Biology 11, no. 4 (2022): 607. http://dx.doi.org/10.3390/biology11040607.

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Radiotherapy is a helpful treatment for cancer, but it can also potentially cause changes in many molecules, resulting in adverse effects. Among these changes, the occurrence of abnormal DNA methylation patterns has alarmed scientists. To explore the influence of region-specific radiotherapy on blood DNA methylation, we designed a computational workflow by using machine learning methods that can identify crucial methylation alterations related to treatment exposure. Irrelevant methylation features from the DNA methylation profiles of 2052 childhood cancer survivors were excluded via the Boruta

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Zuo, Tao, Benjamin Tycko, Ta-Ming Liu, Huey-Jen L. Lin, and Tim H.-M. Huang. "Methods in DNA methylation profiling." Epigenomics 1, no. 2 (2009): 331–45. http://dx.doi.org/10.2217/epi.09.31.

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Shen, Lanlan, and Robert A. Waterland. "Methods of DNA methylation analysis." Current Opinion in Clinical Nutrition and Metabolic Care 10, no. 5 (2007): 576–81. http://dx.doi.org/10.1097/mco.0b013e3282bf6f43.

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Aung, Hnin T., Dion K. Harrison, Ian Findlay, John S. Mattick, Nicholas G. Martin, and Bernard J. Carroll. "Stringent Programming of DNA Methylation in Humans." Twin Research and Human Genetics 13, no. 5 (2010): 405–11. http://dx.doi.org/10.1375/twin.13.5.405.

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We describe a PCR-based method called Amplified Methylation Polymorphism (AMP) for scanning genomes for DNA methylation changes. AMP detects tissue-specific DNA methylation signatures often representing junctions between methylated and unmethylated DNA close to intronexon junctions and/or associated with CpG islands. Identical AMP profiles are detected for healthy, young, monozygotic twins.

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Chen, Bao-An, Fan Zhang, Yan Wang, et al. "Microarray-Based Method for Quantificationally Detecting Methylation Changes of E-Cadherin Gene in Acute Leukemia." Blood 108, no. 11 (2006): 4406. http://dx.doi.org/10.1182/blood.v108.11.4406.4406.

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Abstract Aberrant DNA methylation of CpG sites is among the earliest and most frequent alterations in cancer. Several studies suggest that aberrant methylation of the CpG sites of the tumor suppressor gene is closely associated with carcinogenesis. So methylation detection is very important. The aim of this study was to describe a microarray-based method for quantificationally detecting changes of E-cadherin methylation in acute leukemia and to simply discuss the effect of microarray on detecting tumor methylation. This method used bisulfite-modified DNA as a template for PCR amplification, re

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Saheb, Amir, Stephanie Patterson, and Mira Josowicz. "Probing for DNA methylation with a voltammetric DNA detector." Analyst 139, no. 4 (2014): 786–92. http://dx.doi.org/10.1039/c3an02154h.

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Trinh, Binh N., Tiffany I. Long, and Peter W. Laird. "DNA Methylation Analysis by MethyLight Technology." Methods 25, no. 4 (2001): 456–62. http://dx.doi.org/10.1006/meth.2001.1268.

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Xu, Ximing, Jiayu Chen, and Yang Shen. "Construction of DNA methylation-based biomarkers for diagnosis of hepatocellular carcinoma." Journal of Clinical Oncology 41, no. 16_suppl (2023): 3048. http://dx.doi.org/10.1200/jco.2023.41.16_suppl.3048.

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3048 Background: Hepatocellular carcinoma is the most common malignant tumor in China. Most of the patients are found in the advanced stage, which causes its low survival rate. According to the latest epidemiological data, hepatocellular carcinoma is the second leading cause of cancer mortality. DNA methylation is closely related to tumor development. In this study, differentially expressed methylated genes related to tumorigenesis and development were screened from the database and the diagnostic model was constructed for early screening. Methods: Limma package was used to analyze the differe

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Stensrud, Colton Duran, Leonardo Gonzalez-Smith, Claire Stevens, et al. "Abstract 7028: Optimization of DNA extraction methods and DNA methylation array quality from FFPE prostate tumor tissues to identify DNA methylation biomarkers." Cancer Research 84, no. 6_Supplement (2024): 7028. http://dx.doi.org/10.1158/1538-7445.am2024-7028.

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Abstract Prostate cancer is the second leading cause of cancer related deaths among men in the United States. Health disparities in men diagnosed with prostate cancer are observed between patients of African and those of European ancestry. To elucidate molecular mechanisms behind prostate tumorigenesis and racial disparities, researchers have identified genetic alterations such as gene fusions, deletions, and mutations that occur at varying frequencies among different ethnic groups. However, results are inconsistent across studies, suggesting that racial disparities may be multifactorial. Our

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Chen, Bao-An, Bei-ming Shou, Dong-rui Zhou, et al. "Quantitate Detect of the Methylation of Three Hematopathy Patients’ P16 Gene." Blood 112, no. 11 (2008): 4499. http://dx.doi.org/10.1182/blood.v112.11.4499.4499.

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Abstract Objective: The changes of methylation of CpG Island are the frequent changes in epigenetic. Nowadays, there are many methods to detect the changes of methylation, but all these method are hard to quantitate precisely. In our experiment, we will establish a new precise method. Methods: Use hydrosulfite to handle the DNA, and then do PCR. The cytosine will change to thymine, if it hasn’t been methylation. On the other side, the cytosine will maintain its state if it has been methylation. Design a pair of probe, which contain one methylation probe and one un methylation probe. This pair

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Higgs, Alysha, Angelique Ryan, Jayanthi Ramprakash, et al. "Abstract 7030: Reference materials for analysis of DNA methylation in cell-free circulating tumor DNA." Cancer Research 84, no. 6_Supplement (2024): 7030. http://dx.doi.org/10.1158/1538-7445.am2024-7030.

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Abstract Aberrant DNA methylation is associated with many cancers including breast, liver, bone, and colon and has been identified as a biomarker for early cancer screening. Liquid biopsies are beginning to screen for DNA methylation in cancer-derived DNA, but accurate assessment of methylation is not trivial, and methods like bisulfite sequencing can result in biased data. Reference materials for establishing the analytical validity of measurements of CpG methylation are not widely available. In order to prepare such reference materials, genomic DNA (gDNA) was extracted from the well characte

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Minegishi, Ryu, Osamu Gotoh, Norio Tanaka, Reo Maruyama, Jeffrey T. Chang, and Seiichi Mori. "A method of sample-wise region-set enrichment analysis for DNA methylomics." Epigenomics 13, no. 14 (2021): 1081–93. http://dx.doi.org/10.2217/epi-2021-0065.

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Aim: Gene set analysis has commonly been used to interpret DNA methylome data. However, summarizing the DNA methylation level of a gene is challenging due to variability in the number, density and methylation levels of CpG sites, and the numerous intergenic CpGs. Instead, we propose to use region sets to annotate the DNA methylome. Methods: We developed single sample region-set enrichment analysis for DNA methylome (methyl-ssRSEA) to conduct sample-wise, region-set enrichment analysis. Results: Methyl-ssRSEA can handle both microarray- and sequencing-based platforms and reproducibly recover th

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Shi, Lijuan, Boquan Hai, Zhejun Kuang, Han Wang, and Jian Zhao. "ResnetAge: A Resnet-Based DNA Methylation Age Prediction Method." Bioengineering 11, no. 1 (2023): 34. http://dx.doi.org/10.3390/bioengineering11010034.

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Aging is a significant contributing factor to degenerative diseases such as cancer. The extent of DNA methylation in human cells indicates the aging process and screening for age-related methylation sites can be used to construct epigenetic clocks. Thereby, it can be a new aging-detecting marker for clinical diagnosis and treatments. Predicting the biological age of human individuals is conducive to the study of physical aging problems. Although many researchers have developed epigenetic clock prediction methods based on traditional machine learning and even deep learning, higher prediction ac

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Roeh, Simone, Tobias Wiechmann, Susann Sauer, Maik Ködel, Elisabeth B. Binder, and Nadine Provençal. "HAM-TBS: high-accuracy methylation measurements via targeted bisulfite sequencing." Epigenetics & Chromatin 11, no. 1 (2018): 39. https://doi.org/10.1186/s13072-018-0209-x.

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<strong>Background: </strong>The ability to accurately and efficiently measure DNA methylation is critical to advance the understanding of this epigenetic mechanism and its contribution to common diseases. Here, we present a highly accurate method to measure methylation using bisulfite sequencing (termed HAM-TBS). This novel method is able to assess DNA methylation in multiple samples with high accuracy in a cost-effective manner. We developed this assay for the <i>FKBP5</i> locus, an important gene in the regulation of the stress system and previously linked to stress-related disorders, but t

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Zhang, Yuanyuan, Shudong Wang, and Xinzeng Wang. "Data-Driven-Based Approach to Identifying Differentially Methylated Regions Using Modified 1D Ising Model." BioMed Research International 2018 (November 18, 2018): 1–8. http://dx.doi.org/10.1155/2018/1070645.

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Background. DNA methylation is essential for regulating gene expression, and the changes of DNA methylation status are commonly discovered in disease. Therefore, identification of differentially methylation patterns, especially differentially methylated regions (DMRs), in two different groups is important for understanding the mechanism of complex diseases. Few tools exist for DMR identification through considering features of methylation data, but there is no comprehensive integration of the characteristics of DNA methylation data in current methods. Results. Accounting for the characteristic

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Bruce, Sara, Katariina Hannula-Jouppi, Cecilia M. Lindgren, Marita Lipsanen-Nyman, and Juha Kere. "Restriction Site–Specific Methylation Studies of Imprinted Genes with Quantitative Real-Time PCR." Clinical Chemistry 54, no. 3 (2008): 491–99. http://dx.doi.org/10.1373/clinchem.2007.098491.

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Abstract Background: Epigenetic studies, such as the measurement of DNA methylation, are important in the investigation of syndromes influenced by imprinted genes. Quick and accurate quantification of methylation at such genes can be of appreciable diagnostic aid. Methods: We first digested genomic DNA with methylation-sensitive restriction enzymes and used DNA without digestion as a control and nonmethylated λ DNA as an internal control for digestion efficiency. We then performed quantitative real-time PCR analyses with 6 unique PCR assays to investigate 4 imprinting control regions on chromo

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Mizoguchi, Beatriz A., and Nicole Valenzuela. "A Cautionary Tale of Sexing by Methylation: Hybrid Bisulfite-Conversion Sequencing of Immunoprecipitated Methylated DNA in Chrysemys picta Turtles with Temperature-Dependent Sex Determination Reveals Contrasting Patterns of Somatic and Gonadal Methylation, but No Unobtrusive Sex Diagnostic." Animals 13, no. 1 (2022): 117. http://dx.doi.org/10.3390/ani13010117.

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Background: The gonads of Chrysemys picta, a turtle with temperature-dependent sex determination (TSD), exhibit differential DNA methylation between males and females, but whether the same is true in somatic tissues remains unknown. Such differential DNA methylation in the soma would provide a non-lethal sex diagnostic for TSD turtle hatchings who lack visually detectable sexual dimorphism when young. Methods: Here, we tested multiple approaches to study DNA methylation in tail clips of Chrysemys picta hatchlings, to identify differentially methylated candidate regions/sites that could serve a

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Farhana, Fatema Zerin, Muhammad Umer, Ayad Saeed, et al. "e-MagnetoMethyl IP: a magnetic nanoparticle-mediated immunoprecipitation and electrochemical detection method for global DNA methylation." Analyst 146, no. 11 (2021): 3654–65. http://dx.doi.org/10.1039/d1an00345c.

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e-MagnetoMethyl IP is a new method for electrochemical analysis of global DNA methylation. It avoids bisulfite treatment, PCR amplification, and enzyme-based signal generation and can detect differences as low as 5% in global DNA methylation levels.

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Koczor, Christopher A., Eva K. Lee, Rebecca A. Torres, et al. "Detection of differentially methylated gene promoters in failing and nonfailing human left ventricle myocardium using computation analysis." Physiological Genomics 45, no. 14 (2013): 597–605. http://dx.doi.org/10.1152/physiolgenomics.00013.2013.

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Human dilated cardiomyopathy (DCM) is characterized by congestive heart failure and altered myocardial gene expression. Epigenetic changes, including DNA methylation, are implicated in the development of DCM but have not been studied extensively. Clinical human DCM and nonfailing control left ventricle samples were individually analyzed for DNA methylation and expressional changes. Expression microarrays were used to identify 393 overexpressed and 349 underexpressed genes in DCM (GEO accession number: GSE43435 ). Gene promoter microarrays were utilized for DNA methylation analysis, and the res

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Viswanathan, Ramya, Elsie Cheruba, and Lih Feng Cheow. "DNA Analysis by Restriction Enzyme (DARE) enables concurrent genomic and epigenomic characterization of single cells." Nucleic Acids Research 47, no. 19 (2019): e122-e122. http://dx.doi.org/10.1093/nar/gkz717.

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Abstract Genome-wide profiling of copy number alterations and DNA methylation in single cells could enable detailed investigation into the genomic and epigenomic heterogeneity of complex cell populations. However, current methods to do this require complex sample processing and cleanup steps, lack consistency, or are biased in their genomic representation. Here, we describe a novel single-tube enzymatic method, DNA Analysis by Restriction Enzyme (DARE), to perform deterministic whole genome amplification while preserving DNA methylation information. This method was evaluated on low amounts of

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Taylor, Aaron Michael, Jody T. Lombardi, Areeba Patel, et al. "PATH-11. FEASIBILITY OF BRAIN TUMOR CLASSIFICATION BY ENZYMATIC DNA METHYLATION SEQUENCING ANALYSIS OF CELL-FREE DNA OBTAINED FROM CEREBROSPINAL FLUID." Neuro-Oncology 26, Supplement_4 (2024): 0. http://dx.doi.org/10.1093/neuonc/noae064.714.

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Abstract BACKGROUND Array-based DNA methylation profiling is the gold standard for molecular classification of brain tumors. However, it relies on significant amount of input DNA extracted from surgical tissue, thus limiting its use for tumors where biopsy is challenging or limited in quantity. Cell-free tumor DNA (cfDNA) in cerebrospinal fluid (CSF) presents alternative opportunities for brain tumor diagnosis and disease monitoring following treatment. Novel enzymatic DNA methylation sequencing (EM-seq) methods may allow us to overcome input DNA limitations and accurately quantify methylation

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Usui, Fumitake, Yoshiaki Nakamura, Yasuhiro Yamamoto, Ayako Bitoh, Tamao Ono, and Hiroshi Kagami. "Analysis of Developmental Changes in Avian DNA Methylation Using a Novel Method for Quantifying Genome-wide DNA Methylation." Journal of Poultry Science 46, no. 4 (2009): 286–90. http://dx.doi.org/10.2141/jpsa.46.286.

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Desyatova, M., A. Ponomarev, A. Korotkov, and O. Makeyev. "DNA METHYLATION IS AN EPIGENETIC BIOMARKER OF AGING." International independent scientific journal, no. 45 (December 6, 2022): 10–12. https://doi.org/10.5281/zenodo.7418287.

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<strong><em>Abstract</em></strong> <strong><em>Introduction. </em></strong><em>Recently, epigenetic markers of aging have become a necessity and their identification is a major goal of gerontology. They can be thought of as measures of ageing at the individual level that capture inter-individual differences in the timing of onset, functional decline and death over the life course.</em> <strong><em>The aim of the study</em></strong><em> is to show the role of DNA methylation in the aging process of the body.</em> <strong><em>Materials and methods. </em></strong><em>A study algorithm has been de

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