I am working on non-viral vector DNA and trying to figure out why the transgene is silenced in our vectors. To that end, I'm trying to come up with a cell culture model.
I was wondering if anyone's had a stab at doing ChIP on non-integrated, episomal forms of plasmid DNA?
Do you start with the Hirt method to isolate your extrachromosomal DNA first and then proceed to ChIP as 'standard' (haven't picked a particular protocol yet)?
Would this pDNA be much more susceptible to sonication? (I've read the fab article on here by Dukey about sonication vs MNase digestion- too bad MNase digestion still requires sonication though).
Many thanks in advance for your help!
Edited by cathyolive, 08 December 2011 - 04:00 AM.