CpG island identification - (Jan/11/2005 )
I looked for CpG islands within the promoter of my gene. MethPrimer and CpG plot analysis revealed that in this genes promoter region there were two big CpG islands at locations 280-603 and 693-859. In primer design I got two very different primer sets at different locations of the bigger island. What would be optimal parameters when I´m choosing the proper primer? How can I know which one work or do I have to just try and hope for the best?
You can focus on the region surrounding the transcriptional start site or the core promoter, but better to map at first a larger area to decide the methylation of which region(s) matters to transcription.
If someone else has established the methylation-transcription relationship, just see which region is important.
You may also focus on spots where major transcriptional factors bind or cis-acting elements reside.
No matter what strategy you will use, the purpose is to find out the place whose methylation has an impact on transcription because not every CpG methylation has such an impact.