How to measure the methylation level of a gene?

Question

[yinzl2007]

If I known the methylation information of every site of genome, how to measure the methylation level of a gene?

Answer 1

[Sean Davis]

Genes do not have methylation levels, but you can certainly summarize the methylation around a gene (average, median, min, max; 2kb upstream, gene body, first intron). You will need to determine how best to summarize your own data, though (or if summarizing even makes sense for your questions).

[yinzl2007]

Thanks for your answer.

Answer 2

[Devon Ryan]

There's are a couple ways to do this, none of which are exactly perfect.

1. Average (or take the median of) all of the methylation percentages in the gene.
   1. You'll likely want to filter out low-coverage Cs.
2. Use the methylation counts (i.e., the number of fragments supporting methylated/unmethylated Cs at a position), where you just sum everything and take the percentage.
   1. Again, you probably want to filter out low-coverage Cs.
   2. This only makes sense if you have even coverage or similarly biased coverage between samples.
3. Forget trying to come up with a single number and just compare sites with some minimum coverage.

I actually prefer (3), but it seems that most other people prefer to average methylation percentages. To each their own.

[yinzl2007]

Thanks for your answer!

Maybe it's impossible to measure the methylation of a gene by a single number, but the second method is a nice way for my questions.

Answer 3

[bmartinez]

Hi,

As Yinzl2007, I would like to summarize the methylation level in each gene in order to correlate these values with gene expression levels in different tissues of a non-model species. I have WGBS data for four individuals of the same population, three of them at 6-7x and the fourth at a lower coverage. The gene expression profiles (obtained in a different study) comes from a different individual in the same population.

One of my doubts is whether to pool the methylomes of all the individuals to get the methylation values for each gene. I will filter out low-coverage Cs as well as for too high-coverage Cs. Do you think that this approach is adequate?

I planned of averaging the methylation percentage in each gene (approach 1), although I understand that this is a rough approach and would imply that every methylated C “weights” the same. I was considering to summarize the methylation just in the promoter region, but I wonder whether using all the methylated c's in promoter+gene body, or promoter+first intron would be a better option. Or even other alternative. I do not find any consensus on that.

Should I consider only genes containing a mínimum number of methylated C’s and discard the rest of genes? I was thinking of putting a mínimum limit of 20 Cs with a methylation level over 30%.

Any suggestion is more than welcome.

Thanks a lot in advance,

Begoña