ChIP on Chip: surprising results are often artifacts.

ABSTRACT:

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-

SUBMITTER: Waldminghaus T 

PROVIDER: S-EPMC2996942 | biostudies-literature | 2010 Jul

REPOSITORIES: biostudies-literature