I want to carry out MSP for a gene that is located on the reverse strand. And thats what finally got me thinking:
- Methylation occurs at CpGs, so does it occur for each strand separately? A CpG in the forward strand would be a GpC in the reverse, meaning the C would not be methylatable. On the other hand, forward-strand GpCs would be CpGs in the reverse strand, making them potential methylation targets.
- If the strands methylation differs, which strand's methylation is relevant (or both)? In the past I have always looked at forward strand methylation, but now I have a gene on the reverse strand. How should I design my primers? To include forward-strand CpGs or reverse-strand CpGs?
- Is there any literature on this? I haven't found anything! This must have been investigated at some point!
I'm pretty sure I'm just missing something but I haven't been able to find it by myself... so someone please enlighten me