primer design for MSP and BSP - primers must be in promoter region? (Jun/25/2007 )
I want to study methylation of a gene, and attempted to design primers for it through the methprimer website. This came up with some options for primers, all of which were 3,000bp or more downstream of the start site. I was under the impression that methylation had to be analysed in the promoter region? However, since this I have found a paper which looks at methylation in the same gene and the primers they use are also in this region, far away from the promoter. Can I use these primers in my study even though they are not in the promoter region?
CpG islands are normally believed to be related to the promoter or the exon 1 region, but can also be in the promoter regions of alternative exons 1 (for example rat GR has seven different promoters for tissue specific alternative splicing, allmost each has a CpG island.) If you experience problems with your primers, try Methylprimer Express, you can download it free at ABI's website. Or check out the primer notes by methylnick in the pinned section of this forum.