The Basic Principle of ChIP

The basic principle behind the ChIP method is relatively simple It is based on the selective enrichment of a chromatin fraction containing a specific antigen (e.g. transcription factors, DNA binding proteins, modified histones, etc.) by an immunoprecipitation step. Specific (important, see below ) antibodies that recognize a protein of interest or the modified form of a protein can be used to determine the relative abundance of it within DNA regions. 

Here we provide insight into the ChIP technique, the most important steps and some trouble-shooting guidelines. We describe the variations of ChIP and recent new developments, especially for genome-wide studies. We also focus on the data analysis, since in silico data analysis becomes more and more central for successful Chip experiments. In the last section we discuss two examples for data analysis based on recent publications. For detailed ChIP protocols we refer the reader to the excellent protocols database freely available at http //www.epigenome-noe.net/ researchtools/protocols.php. 

Formaldehyde cross-linldng of vvhoie cells (if required) 

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