ChIP on Chip: surprising results are often artifacts

Background: The method of chromatin immunoprecipitation combined with microarrays (ChIP-Chip) is a powerful tool for genome-wide analysis of protein binding. However, a high background signal is a common phenomenon. Results: Reinvestigation of the chromatin immunoprecipitation procedure led us to discover four causes of high background: i) non-unique sequences, ii) incomplete reversion of crosslinks, iii) retention of protein in spin-columns and iv) insufficient RNase treatment. The chromatin immunoprecipitation method was modified and applied to analyze genome-wide binding of SeqA and sigma(32) in Escherichia coli. Conclusions: False positive findings originating from these shortcomings of the method could explain surprising and contradictory findings in published ChIP-Chip studies. We present a modified chromatin immunoprecipitation method greatly reducing the background signal.