Effects of Normalization

Unexpectedly, mock-immunoprecipitations (lacking antibody) produce similar profiles of enrichment (below, left). If histone-specific immunoprecipitates are normlized to such controls, the difference between intergenic and ORF regions largely disappears (below, right).

We also find that comparisons of nucleosome modifications must take into consideration the genomic distribution of nucleosomes. The results of hybridizations of material immunoprecipitated with anti-H3K14ac vs. genomic input (whole cell extract) are shown below in red. Results of hybridizations of material immunoprecipitated with anti-H3K14ac are shown in blue. Correlation with transcriptional rates for both ORFs and intergenic regions is dependent on using the latter experimental scheme.