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DNA methylation appears absolutely required in differentiated cells, as knockout of any of the three competent DNA methyltransferase results in embryonic or post-partum lethality. By contrast, DNA methylation is dispensable in undifferentiated cell types, such as the inner cell mass of the blastocyst, primordial germ cells or embryonic stem cells.
Differentially methylated regions (DMRs) are genomic regions with different DNA methylation status across different biological samples and regarded as possible functional regions involved in gene transcriptional regulation. The biological samples can be different cells/tissues within the same individual, the same cell/tissue at different times ...
The whole genome sequencing technique was first applied to the DNA methylation mapping at single nucleotide resolution to Arabidopsis thaliana in 2008, and shortly after in 2009, the first single-base-resolution DNA methylation map of the entire human genome was created using whole genome bisulfite sequencing.
Bisulfite [1] sequencing (also known as bisulphite sequencing) is the use of bisulfite treatment of DNA before routine sequencing to determine the pattern of methylation. DNA methylation was the first discovered epigenetic mark, and remains the most studied.
DNA methylation patterns: CpG methylation has been closely linked with transcriptional silencing. This methylation causes a rearrangement of the chromatin, condensing and inactivating it transcriptionally. Methylated CpG falling within DHSs impedes the association of transcription factor to DNA, inhibiting the accessibility of chromatin.
DNA methylation is typically quantified on a scale of 0–1, as the methylation array measures the proportion of DNA molecules that are methylated at a particular CpG site. The initial analyses performed are univariate tests of association to identify sites where DNA methylation varies with exposure and/or phenotype.
In mammals, DNA methylation occurs almost exclusively at a cytosine that is followed by a guanine. DNA methylation is a widespread mechanism for epigenetic influence on gene expression and is seen in bacteria and eukaryotes and has roles in heritable transcription silencing and transcription regulation. Methylation most often occurs on a ...
MGMT (O-6-methylguanine-DNA methyltransferase) is an important cancer biomarker because it is involved in the repair of DNA damage and is often silenced or inactivated in cancer cells. The loss of MGMT function leads to a higher rate of mutations, promoting the formation and progression of tumors.