I mean, if I transfect a cell line with hypo/hyper-methylated promoter luciferase construct, how stable the methylation status will be after transfection? I read some papers suggesting the cells will automatically methylate CpGs of the transgene, if that's the case, then the luciferase assay probably won't work?
Equally people told me the same might be true for CRISPR based targeted epigenetic editing approach...
It may depend on the type of gene promoter. I have used an in vitro-methylated promoter of a drug metabolising inducible gene (CYP1) without noticeable change in methylation status after transfection. In my experience, complete in vitro methylation (with M.sss1) of the construct results in lower luciferase values (as expected), but I have not seen this kind of effect after transfecting a hypomethylated plasmid.
We have done this type of experiment many times and have seen no evidence for luciferase construct methylation in a transient transfection assay. If your controls show expected activity levels, it should not be a concern. This will be much more a concern with any stable transfection approach, including modification of an endogenous locus by CRISPR, etc. In this case, the methylation status of the endogenous locus can be directly measured. In the transient transfection approach, methylation analysis will be much more difficult.
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