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CpG ISLAND METHYLATION QUESTION
I have been working on the methylation status of the promotor of a gene involving CpG islands that contains a total of 69 CpG residues, but I only analyzed two regions, the first having 14 CpG sites and the second region with 18 CpG sites (see Figure attached). That means, the rest of the CpGs were not looked at for their methylation status. How many do I need to look at to determine the methylation status of the promotor.
I was wondering WHETHER 1) the methylation present only in certain subset of CpG spots within the CpG island is sufficient to inactivate the gene transcription (if this is true, there still is a chance that the middle region that we didn't check may be methylated leading to inhibition of gene transcription OR 2) those genes epigenetically silenced would contain methylation in, more or less, all the CpG sites cross the CpG island
Re: CpG ISLAND METHYLATION QUESTION
it varies how many CpGs must be methylated for a certain gene that the gene is silicenced, in theory one could be enough depending on how many are in the promoter in total, but it should be the case that the more are methylated less transcription takes place (since it is harder for TFs to bind).
Yes it is true that if you find no methylation in your regions and the gene is silenced it may be due to methylation in the middle region you not checked.
Normally the primers are designed that way that you amplify regions were a lot of TFs bind so you get a good chance that the methylation took place there if transcription is affected.
Once the gene is silenced, it may be the case that all CpGs get methylated over time to keep it in a silenced state, but that depends heavily on the case of cell you look at (cell growth, differentiation, how fast they divide, etc.).
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