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“Omics”
Published in Kirk A. Phillips, Dirk P. Yamamoto, LeeAnn Racz, Total Exposure Health, 2020
Sun et al. (2015) and Dirks et al. (2016) have reviewed the status of genome-wide epigenetic profiling technologies. To probe the methylation status genome wide, methylated DNA is treated with sodium bisulfite which converts methylated cytosine to uracil (read as thymine when sequenced or probed by a methylation microarray such as the Illumina Methylation Epic BeadChip assay). For known human genes, the Illumina Methylation Epic BeadChip assay reports methylation status at ~853,307 CpG sites with coverage of >90% of ~26,000 CpG islands (regions of >200 bp with %GC >50%), North and South Shores of islands (2,000 bp regions upstream and downstream of CpG islands) and 80% coverage of North and South Shelves (regions between 2,000–4,000 bp upstream and downstream of CpG islands). A limitation of array-based technology is that it is difficult to incorporate single nucleotide polymorphism-type data that might be uncovered by bisulfite sequencing approaches. Whole-genome bisulfite sequencing offers the ability to probe all 28 million known CpG and correlate genotype and methylation patterns. Reduced representation bisulfite sequencing and variants offer coverage of 1.5–4 million unique CpG by using methylation-sensitive restriction digestion to enrich CpG-rich regions and sequence only these. The impact of histone modifications is frequently assayed by immunoprecipitation of chromatin using affinity tags directed against specific histone modifications followed by sequencing.
Classification of Lung Diseases Using Machine Learning Techniques
Published in Ranjeet Kumar Rout, Saiyed Umer, Sabha Sheikh, Amrit Lal Sangal, Artificial Intelligence Technologies for Computational Biology, 2023
Sudipto Bhattacharjee, Banani Saha, Sudipto Saha
Patient data can be of three kinds–clinical, radiological and genomic. Clinical data consists of demographic information, history, medication and investigations. Demographic information relevant to ML applications mainly include age, sex, ethnicity and occupation. Patient history includes smoking profile, comorbidities and allergies. Some examples of investigations include basic examinations (such as blood pressure, SaO2 and body temperature), blood tests, pulmonary function tests (PFT) and echocardiography. Radiological data include lung imagery such as chest X-ray (CXR) and computed tomography (CT) scans. Popular genomic investigations include single nucleotide polymorphism (SNP), gene expression and DNA methylation. SNP refers to the substitution of a single nucleotide with another at any position in the DNA sequence. Gene expression investigations are performed using methods such as microarray analysis [23] and RNA-seq [67]. DNA methylation refers to the addition of methyl groups (CH3) at cytosine (C) nucleotides of DNA in CpG sites - the “5′−C−phosphate−G−3′ ” sequence of nucleotides. Techniques such as Bisulfite Sequencing (BS-seq) [15] and BeadChip Array analysis [3] are used for DNA methylation investigations.
The deamination mechanism of the 5,6-dihydro-6-hydro-6-hydroxylcytosine and 5,6-dihydro-5-methyl-6-hydroxylcytosine under typical bisulfite conditions
Published in Molecular Physics, 2019
Lingxia Jin, Gongwei Qin, Caibin Zhao, Xiaohu Yu, Jiufu Lu, Hao Meng
Although bisulfite sequencing can be used for the genome-wide detection of 5-MeCyt, it possesses some drawbacks. Cyt treated with bisulfite were either converted to uracil, or failed to be converted and remained as Cyt, and the 5-MeCyt either did not undergo conversion, or were inappropriately converted to thymine. Both types of conversion would lead to the erroneous estimates of methylation densities [18]. There are many reasons for this phenomenon, such as bisulfite concentration, pH value, temperature and so on. One possible reason is the difference of activation free energy barrier between Cyt and 5-MeCyt under bisulfite conditions, which is only 0.49 kJ·mol-1 based on the previous theoretical data [19,20].
The interplay between DNA methylation and cardiac autonomic system functioning: a systematic review
Published in International Journal of Environmental Health Research, 2023
Nayara Cristina Dos Santos Oliveira, Fernanda Serpeloni, Simone Gonçalves de Assis
Studies in humans measured DNAm from the blood (N = 11), saliva (N = 3), buccal epithelial cells (N = 2), placental tissue (N = 1), and umbilical cord tissue (N = 1). Nonhuman animal studies used more invasive methods to extracted DNA samples from brain tissue, mesenteric endothelial cells, and bisected placenta. Sixteen studies focused on candidate genes and six on genome-wide DNAm. The candidate gene studies assessed DNAm using bisulfite pyrosequencing (N = 11), bisulfite sequencing (N = 3), methylation-sensitive restriction enzymes, and quantitative PCR (N = 2). One of them also used the Illumina HumanMethylation450 array to measure methylation at a candidate site.
Effects of tobacco compound 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) on the expression of epigenetically regulated genes in lung carcinogenesis
Published in Journal of Toxicology and Environmental Health, Part A, 2021
Sun Woo Jin, Jong Seung Im, Jae Hyeon Park, Hyung Gyun Kim, Gi Ho Lee, Se Jong Kim, Seung Jun Kwack, Kyu-Bong Kim, Kyu Hyuck Chung, Byung Mu Lee, Sam Kacew, Hye Gwang Jeong, Hyung Sik Kim
DNA promoter methylation patterns were examined using bisulfite sequencing of CpG sites at single-base pair resolution across 4 genes from DNA collected via laser capture microdissection (LCM). The mean % of differentially hypermethylated or hypomethylated values corresponding to the CpG site sequenced are illustrated in Figure 2, with data organized according to experimental groups. Unsupervised bi-directional hierarchical clustering was performed using mean methylation data for each comparison group to identify differences in methylation profiles according to NNK exposure in lung tissues (Supplementary Figure 1).