What is the meaning of methylation level of C in DNA Sequenced data?

Question

[bioinfo816]

Hi bioinfo guys,

I am new in the field of DNA methylation. I read one paper where they have described about the methylation level of Cytosine in DNA. I am working on bench and for me either the C is methylation or not but how it could be 80% methylation or 50% methylation. I know the procedure that this methylation level came from the aligned reads which are methylation / total alinged read. But I really would like to know What does this actually meant for? Is it related with the probability of occurance of methylation at that C?

I would appreciate if somebody could explain this to me in detail.

Thanks in advance.

[bioinfo816]

Thanks for the quick reply.

So, what would we say biologically when we have 50% of methylation?

[Devon Ryan]

It depends on what context you're asking that in. If you're looking at a transcription factor binding site that you think is important in your tissue of interest then you'd say that the binding site may be only partially occluded (assuming the TF binding has some known methylation sensitivity, otherwise it's a question of overall chromatin compactness).

If the percentage were 80, then it'd be less likely that a transcription factor could bind, simply because of the raised probability that that area was is inaccessible (due to being compacted). However, there's no perfect correspondence here and that should always be kept in mind.

In general, regions with lower methylation are likely to be more accessible and regions with higher methylation less, though this isn't always the case. Welcome to epigenetics, where there are no great rules yet :)

Answer 1

[Devon Ryan]

The percentage refers to the likelihood of finding it methylated in the dataset. Obviously an individual C on a strand of DNA is either methylated or not, but we don't do much single-cell sequencing yet (and even if we did, given that most species people look at are diploid that would still only limit things to 0, 50, or 100%). Consequently, one pools a large number of cells and looks at the methylation level averaged across them. That will often not be 0 or 100%, since there's typically a bit of heterogeneity.

[t2g4free]

Bravo answer! How to deal with heterogeneous in practice? Thx