How to find promoter regulation region CpG islands - (Jun/25/2005 )
I am intended to find the CpG islands in promoter regulation region of a gene, could someone suggest me how to do it?
In my idea,
First, I must find the promoter region of gene,this can be scanned by PromoterInspector;
Second, I must find the promoter regulation region of gene, how can I do that?
Third, I must find if the promoter regulation region is located in CpG island ,this can be done by CpG island searcher, I think;
Fourth, I must find if we can design primer to amplicate the found promoter regulation region CpG island through MSP or BS-MSP? Is it right? Can it be done by Methprimer?
Is my idea right? I hope anyone gives me some advise! Thanks!
Please read these two posts
I seldomly use promoter prediction software to find a promoter because the result is unreliable. For the purpose of methylation study, to find a promoter, the best way is to find a CpG island in the sequence upstream a gene because over 60% of genes have CpG island in their promoter and usually only CpG island methylation is of biological significance.
Yes, you can focus on important regulatory regions or some cis-acting elements. Get the promoter sequence from GenBank to see if there such features annotated on the sequence or search Pubmed to see if there are papers characterizing the promoter. You can also query transcriptional factor database with a sequence to find TF binding sites.
MethPrimer can help you find CpG islands and subsequently design primers on them.
Thank your advice,PCRMAN!