CHIP assay shows same fold enrichments over IgG in both my gene promoter and bet - CHIP negative control (Apr/15/2007 )

I did CHIP on Mouse ES cells with an antibody against a gene X and PCR amplified both my gene of interest (gene Y) and control beta-actin gene promoter in wild type ES, but not in ES knocked out of X gene. The fold enrichments with my antibody over IgG on gene Y and beta-actin promoter are the same, 8-fold, and RNA Poly II antibody IP also showed the same fold enrichments (30-fold) on both Y gene promoter and beta-actin promoter. There are no PCR amplification with my gene X antibody from chromatin isolated from Gene X knocked-out ES on both promoters. There were same levels of PCR products with RNA poly II antibody from both WT and mutant ES in both promoters.

What is the problem ? Would it suggest that my gene X was non-specifically associated with beta-actin gene promoter as well as gene Y promoter ? Since there were no PCR bands on both Gene Y and beta-actin promoters in Gene X null ES with Gene X antibody, it would suggest the specificity of gene X antibody against gene X. Apparantly, CHIP worked because RNA poly II antibody worked on both promoters (Gene Y and beta-actin) in both wt and mutant ES cells.

Is there any chanse that your protein X is bound to the promoter of the beta-actin gene. Is it a transcription factor? Then you'd have perfect results. Maybe design primers for some other promoter and test if you have a signal for your protein X.