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DNA Methylation Analysis
Methylation analysis is quantifying and mapping the addition of methyl groups to DNA. The addition of methyl groups is involved in regulating gene expression and is epigenetic, meaning it is a DNA modification that does not affect gene sequence but can be passed on through generations. Methylation analysis technologies are based on: 1) the ability of restriction enzymes to cleave sequences based on methylation state, 2) affinity enrichment through immunoprecipitation of methylated DNA, or 3) the use of bisulfite to convert unmethylated cytosines to uracils. Restriction enzyme-based approaches involve methylation detection through in-gel analysis, blotting with methylation sensitive probes, microarrays, and sequencing. Affinity enrichment is commonly chromatin immunoprecipitation (ChIP) followed by a microarray (ChIP-chip) or sequencing (ChIP-seq). Bisulfite treatment is usually followed by polymerase chain reaction (PCR) to amplify commonly methylated regions (CpG sites) followed by sequencing of the amplified fragments. Mass spectrometry techniques and computational predictions are used as well. Considerations for methylation analysis include the desired coverage and resolution, accuracy and reproducibility, and sensitivity. Methylation analysis is important for the study of epigenetics, cell differentiation, gene regulation, and disease. DNA methylation has been implicated in several diseases including cancer, heart disease, MS, and schizophrenia. (Credit: Brooke Anderson-White)
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