Method to look for novel methylated gene - (Aug/09/2004 )

Hi. I am a new member of this forum. Currently I am trying to look for some novel methylated gene in NPC cell line. What method should I start with? Pls help. Thank you.

there are many approaches to this goal.

1. CpG island microarray
2. Gene expression microarry approach: treat your cells with demethylation agents such as azo-cytidine, find genes whos expression is upregulated by treatment as your candidate gene for methylation mapping
3. RLGS-M.
4. If you can find existing expression data such as EST, SAGE, microarray in NCBI's database for NPC, genes that are expressed lower in cancer may be good candidates.
5. If you have some candidate genes in mind such as 10-20, just screen them one by one.

Thanks you your reply. actually my ultimate goal is to look for aberrantly methylated CpG islands in npc and spot those target onto a chip for highthroughput screening.

In your reply, you mentioned about CpG islands microarray. is the microarray commercially available or i have to constrcut myself? what genes are spotted on the microarray? is it cancer specific CpG islands?
thank you.

Now I understand what you want to do. In that case I think the strategy would be different. I would suggest that you select some known methylated genes (genes that are frequently methylated in NPC), amplify their CpG island and spot them on a chip which can then be used to screen large number of samples.

Yes there are commercial (not really) cpg microarray available at
http://www.microarrays.ca/products/types.html

Look for "Human CpG 12K Arrays"