Hi, I’ve just started looking at promoter methylation as a possible mechanism for regulation of several genes I have been studying in T-cell lymphoma. I have many many questions and wondered if people here could help clarify matters.

I understand the logic behind the definition of a CpG island and have found that map viewer in entrez can show me the location of islands alongside transcript details. For my first gene, Fas the information is fairly clear, there is an island which covers the 5’UTR and transcriptional start site, this is what I shall investigate.

The second gene I looked at, SHP-1 is more ambiguous. Firstly, there are two promoters. Some reading informed me that the upstream one, confusingly named promoter 2,is responsible for the transcript found in haematopoeitic cells so I will focus on this. But the relavent island has been found using less stringent criteria as indicated by the light blue colour. Further upstream is another island, identified with the more stringent set of criteria. Could this one affect transcription of SHP-1, I guessed it could cover the binding site for a factor involved in the initiation complex but am not sure how spread out such factors are.

Basically my questions are,
1. How far back from the transcriptional start site are the regulatory sequences for that gene expected to extend?
2. Does a CpG island have to cover the transcriptional start site to regulate transcription from that gene?

I would love to hear anyone’s opinion on the matter.