How can I identify the binding sites of my transcription factor using ChIP?
FAQ ID -2753

First of all, the actual binding site for a specific TF might be known already in the literature. If so, the primer can be designed based on that information and ChIP-qPCR can be performed to detect the enrichment of the region by TF. If binding information for the TF is not known, ChIP-tiling assay allows sensitive analysis of up to 30kb around the promoter region if the TF of interest is known to bind to a specific promoter region. If nothing is known about the TF, ChIP-chip or ChIP-seq are recommended to discover unknown binding sites. When using these techniques, ChIP-qPCR is recommended to validate your results.