Figure 1

Comparison of actual methods for TFBS analysis with the site-specific ChIP. Principles of commonly applied techniques for TFBS analysis in comparison to the concept of the site-specific ChIP. (A) The Electrophoretic Mobility Shift Assay (EMSA) provides a specific identification of nucleotides sequences involved in TF binding, but does not work under in vivo conditions. (B) The in vivo footprinting allows the specification of which nucleotides are bound by TFs, but it is not capable to identify the protein(s) involved in binding. (C) Concept of the site-specific ChIP in comparison to the standard ChIP method. By replacing the traditionally used random fragmentation step with a site-specific enzyme digestion, this site-specific ChIP enables the immunoprecipitation and enrichment of single TFBSs, thus allowing a differentiation between adjacent occupied and non- occupied binding sequences in vivo.