Methylation patterns through Methyl-Seq

[adrian]

Dear group:
Hello! I am interested in learning the possibilities about identifying DNA methylation patterns at CpG islands. Since many CpG repeats located in repetitive areas of genome, I would like to know how a targetted methy-seq is done using either MeDIP-Seq or Methyl-Seq (as described by Brunner AL et al. in GR june-2009).
What would be the options for selecting only those important CpGs and not sequencing entire genome.
I appreciate your help and input. thanks Adrian.

[andrewdsusc]

We used a combination of bisulfite sequencing and hybrid capture ("Bisulfite Capture"), which allows you to select regions where you are interested in the methylation status. Check out this paper, which may be a useful method for what you want to do:

http://genome.cshlp.org/content/19/9/1593

[franyl]

We used a combination of bisulfite sequencing and hybrid capture ("Bisulfite Capture"), which allows you to select regions where you are interested in the methylation status. Check out this paper, which may be a useful method for what you want to do:

http://genome.cshlp.org/content/19/9/1593

If I would attach so called MID tags together with the methylated illumina adaptors. Do you think it would be possible to capture fragments from several samples with the same array and be able to seperate them after sequencing?
Regards Frank.

[hanjaylee]

We used a combination of bisulfite sequencing and hybrid capture ("Bisulfite Capture"), which allows you to select regions where you are interested in the methylation status. Check out this paper, which may be a useful method for what you want to do:

http://genome.cshlp.org/content/19/9/1593

hi. i am wondering if we are able to deep-sequence the methylation pattern of the whole genome? i mean can we get the whole genome methylation state aside from the sequence information?
thanks a lot.
hanjay

[htorres]

hi. i am wondering if we are able to deep-sequence the methylation pattern of the whole genome? i mean can we get the whole genome methylation state aside from the sequence information?
thanks a lot.
hanjay

Yes! See:

https://en.wikipedia.org/wiki/Reduced_representation_bisulfite_sequencing

https://en.wikipedia.org/wiki/Bisulfite_sequencing#Applications:_genome-wide_methylation_analysis