DNA Methylation — Overview

Notes on DNA methylation (甲基化): the addition of a methyl group to cytosine, its role in epigenetic regulation, and how we measure it.

Topics to cover

• 5-methylcytosine (5mC) and the CpG dinucleotide context
• CpG islands, promoters, and gene silencing
• DNA methyltransferases (DNMT1, DNMT3A/3B) and demethylation (TET enzymes)
• Profiling: bisulfite sequencing (WGBS, RRBS), methylation arrays, nanopore

Quantifying methylation

The methylation level ($\beta$ value) at a CpG site is commonly defined from methylated ($M$) and unmethylated ($U$) signal intensities:

$$\beta = \frac{M}{M + U + \alpha}$$

where $\alpha$ is a small offset (often $100$) to stabilize the ratio at low intensities. The $\beta$ value lies in $[0, 1]$, where $0$ is fully unmethylated and $1$ is fully methylated.

An alternative, more statistically well-behaved measure is the M-value:

$$M\text{-value} = \log_2\!\left( \frac{\beta}{1 - \beta} \right).$$

Next steps

Add pages such as bisulfite-sequencing.md or tet-enzymes.md to this folder.