I need good advice. I am doing a bunch of RT PCRs from mouse skin samples with Taqman. This takes all my technical capacity and I can not do any DNA methylation analyses at the moment. The question: how to characterize the overal epigenetic state of keratinocytes in the skin (after different drug and UV treatments) using RT PCR?
I realize that the answers will be incomplete and this is not a typical way of doing epigenetics, but I do want to do few relevant genes and I need help in picking them.
I am thinking about choosing between DNMTs, dicer, siRNA pathway genes, histones, possibly some histone-modifying enzymes... But I am not sure which of them are actually regulated on transcriptional level and how the level of their expression would correlate with global DNA silencing in the cell. The hypothesis is that UV and drugs are affecting the epigenetic status of keratinocytes and they become more or less prone to carcinogenic transformation (this part is covered in UV-carcinogenesis protocol which ends up with real tumors, but the early epigenetic changes leading to cancer - that is what I need to measure).