Is it possible to use ChIP-chip for identifying CpG island methylation? - (Mar/20/2006 )

Hi,

I am interested in epigenetics, especially the methylation status of CpG island. I am wondering why no lab used ChIP-chip to identify CpG island methylation?

actually if you have a look at this link http://nar.oxfordjournals.org/cgi/content/abstract/33/9/2952 you will find that such an array is available and you can rest assured that people are performing ChIP on this Chip with anti 5mC IP.

it's only a matter of time.

nick

Many thanks!

also this paper http://www.ncbi.nlm.nih.gov/entrez/query.f...t_uids=16444255

And this paper too,
http://www.ncbi.nlm.nih.gov/entrez/query.f...t_uids=16007088

I am so confused. Looks like you could amplify your DNA using Klenow fragment to random priming. Then Why LM-PCR? Is it more sensitive?

LM-PCR is more representative reportedly,

as for sensitivity, I think it's the same as random priming, although as the name suggests it is random, there could be some inherant biases towards particular regions of the genome and thus it becomes non-representative.

LM-PCR is more representative if you assume the primers ligate with equal efficency to all fragments within the genome.

Nick

This makes sense. Thanks a lot!

Hi, Methylink:

Could you please take a look at this protocol from AVIVA. I found people using different IP buffer. Not sure if this one would work. The elution buffer I used is 1xTE ,1%SDS

Thanks a lot!

different salt and detergent conditions affect the binding of the antibody to it's antigen.

As for elution it is also the same thing so depending on your antibody/antigen you need to adjust the salt and detergent and invariably the pH of your buffer. It's a shame you don't know what "elution buffer" is made of, but your DNA should elute with your buffer.

you can test this with a IP-PCR on a known hypermethylated CpG island prior to arraying if that is what you intend to do.

nick