Figure 5

Analysis of chromatin immunoprecipitation. (a) DP1 complex with DHFR and GAPDH promoters. NIH 3T3 cells were transiently transfected with pBBHN.DP1 vector and subjected to the chromatin immunoprecipitation procedure. Shown is the ratio between amounts of DFHR (lanes 1 and 2) and GAPDH DNA (lanes 3 and 4) pulled down from the DP1 transfected sample (lanes 2 and 4) and GFP transfected sample (lanes 1 and 3), considered as a nonspecific background (mean of 2 experiments). 500 μ g of chromatin were used for the ChIP. 5% of the input chromatin for each sample was decrosslinked, processed and analyzed in the same way by q-PCR. For each sample the value of the signal is presented as a percent of input. (b) MDA without any religation. Immunoprecipitate from the same experiment as in fig. 5a was diluted 100 fold and subjected to MDA before q-PCR analysis. (c) MDA with religation. Immunoprecipitate from the same experiment as in fig. 5a was diluted 100 fold and then subjected to religation, MDA and q-PCR as above. (d) MDA with religation in the presence of stuffer DNA. Immunoprecipitate from the same experiment as in fig. 5a was diluted 100 fold and then subjected to religation in the presence of 100 ng of HaeIII digested pUC19 and then MDA and q-PCR as above.