So, with my new found sucess in the world of bisulfite sequencing.....I now have a list of genes that I am interested in investigating. I have found genomic sequence and have found a number of CpG islands upstream of the putative transcription start sites and CpG islands that encompass the putative start sites. Given that I am working with bovine DNA sequences there isn't so much in the literature yet about methylation.

Does anyone have a gut feeling (I'm sure that there isn't a hard and fast rule-although if there is I would love to hear it) about choosing which CpG islands are more likley to be involved in the regulation of those genes? Do CpG islands right next to the start site more often regulate the gene than those further away.

Ideally I would like to analyse all of them, but due to money and manpower constraints that isn't possible, and I'm sure with the wealth of experience on this site that some people have views on this subject.

THanks

ultragirl,

congratulations on the grappling of bisulfite sequencing, it's a beast but once mastered, a powerful one at that.

As a general rule (and there will be exceptions) the promoter region of genes are within 2kbp upstream of the transcription start site to about 500bp downstream of the transcription start site. And within these promoters you may find a CpG island that could be responsible for regulating the transcription of that gene.

Within a CpG island there is more likely to be transcription factor binding sites for which their methylation status will govern the affinity of the transcription factor to that site. This is not always the case as it could well be that the chromatin surrounding the transcription start site maybe such that transcription is permissible regardless of DNA methylation status. Nevertheless looking at DNA methylation of your genes of interest is a good starting point.

good luck with it!!