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Updated: Jun 11, 2026
High-Throughput Total Internal Reflection Fluorescence and Direct Stochastic Optical Reconstruction Microscopy Using a Photonic Chip
Published on: November 16, 2019
ChIP on Chip: surprising results are often artifacts
Torsten Waldminghaus1, Kirsten Skarstad
1Department of Cell Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital and University of Oslo, 0310 Oslo, Norway.
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.
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