DNA methylation adds methyl groups to cytosine or adenine.
We are gonna focus on cytosine methylation today!
So... What is gonna happen when cytosine is methylated?
The methylation of Cytosine is mostly observed in the promoter region.
They are related to gene silencing!
To make it easier you can just remember it with that..
Methylation of Cytosine --> promoter region = gene silencing
You can also think about the other nucleotide base following cytosine.
There are three major patterns you should know.
1) CG
2) CHG (where H can be A, C, or T)
3) CHH (where H can be A, C, or T)
The reason why we should consider the nucleotide after Cytosine is that the ratio of methylation is different by three patterns.
When we are looking at all the promoter regions in the genomic sequence, methylation of CG is higher than other patterns. (CG: 3 -13%, CHG: 3 - 4%, CHH: 1 - 2 %).
However, you can find CG methylation in genes in plants! (CHG and CHH contexts are little)
CG methylation in gene regions in plants is called gene body methylation.
We don't know exactly why CG methylation exists in the gene body yet. One of the clues is that higher methylation in gene bodies is related to higher gene expression.
We are studying what is gene body methylation effect is and why it has happened.
The interesting thing is that Eutrema(a genus of flowering plant) have little gene body methylation!
The reason is that Eutrema doesn't have CMT3.
We can talk about Eutema more later!
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