why do I see enrichment in ChIP inner control? - (Oct/29/2007 )

I'm doing ChIP using protein X antibody, to try to find the target gene of protein X. The experimental group and control group cells are the same except the experimental group has the protein X, while the control group cells don't.
After ChIP, I see enrichment for some gene promoters, which is good. But I see enrichment of my inner control, such as Gapdh, Actin, Hsp90 et al in the experimental group compared to control group also. And the GAPDH and Actin enrichment is pretty big (16 fold). Can anybody tell me why I got high enrichment of GAPDH and Actin inner control? (I tried multiple inner controls, they all show significant enrichment).
Thanks a lot!!
--sure

Hello?? Anybody can help???

Without more detail it's hard to say,

assuming that your experimental cells contain an expression construct of your protein of interest, could it be an artefact of overexpressing your protein of interest?