Genome-wide methylation analysis - (Jul/10/2006 )

I am trying to determine if methylation is in fact playing a role in the virus I am studying. To do this, I was thinking to do a methylation-sensitive restriction enzyme analysis of the entire genome, using HpaII/MspI. (The genome is much smaller than human or mouse, so it's not as daunting)
Are there any other ways to determine if methylation does play a part in regulating these genes? I understand the value of assays previously described in this forum in comparative studies, as in normal vs. tumor tissues. But since I don't have a "normal" to compare to, would the restriction digest be the fastest way to determine if methylation could potentially be involved? I've read a little bit about Restriction Landmark Genome Scanning- is this something similar? It seems to involve 2-D gels- yikes.

I'm thankful for any help

AIMS (amplification of intermethylated sites) and AMP are two other methods of genome-wide methylation studies. RGLS looks at more sites that an traditional restriction and southern blot analysis.

I wonder if CpG islands exist within a viral genome? hmmmm
Nick

Hi ,
I thinks in market if microarray chips available then you can check its on these chips by compairing with normal Vs sample.
In this way you able to detect its at expression level if chips are available in the market.

Thanks for your answer- you're very reliable. According to the default parameters set by Methprimer for CpG island prediction, there are more than 50 CpG islands in the virus I am studying, most of them clustered near gene promoters. I've done some bisulfite sequencing for a couple genes for which regulation by methylation might be expected, but the results have been unfruitful, and now I'm looking in novel areas.
As far as your protocol suggestions, is this article a good representation of the technique?

Methylome profiling of cancer cells by amplification of inter-methylated sites (AIMS)
Frigola J, Ribas M, Risques RA, Peinado MA. (2002) Nucleic Acids Res. 30: e28

What is AMP, and how is it different?

Thanks for your help-

very interesting to hear the viruses have cpg islands!!!

Indeed the frigola paper is the one describing AIMS

as for AMP, it is a variation of the AIMS technique and can be found in this citation:

Webster KE, O'Bryan MK, Fletcher S, Crewther PE, Aapola U, Craig J, Harrison DK, Aung H, Phutikanit N, Lyle R, Meachem SJ, Antonarakis SE, de Kretser DM, Hedger MP, Peterson P, Carroll BJ, Scott HS. Related Articles, Links
Meiotic and epigenetic defects in Dnmt3L-knockout mouse spermatogenesis.
Proc Natl Acad Sci U S A. 2005 Mar 15;102(11):4068-73. Epub 2005 Mar 7.

Nick