Measurement of in vivo DNA binding by sequence-specific transcription factors using UV cross-linking

This paper describes an in vivo UV cross-linking protocol that is sensitive enough to detect DNA binding by sequence-specific transcription factors in Drosophila embryos and tissue culture cells. The strength of this approach is that it provides a quantitative measure of DNA binding in vivo with unambiguous identification of the factor involved in the binding. This assay often detects DNA binding properties of proteins that were not predicted from previous experiments, and it can be used to directly test diverse models of gene regulation in the context of a living organism.