UV-Laser induced protein/DNA crosslinking reveals sequence variations of DNA elements bound by c-Jun in vivo

Many proteins involved in the modulation of gene expression exert their function through direct interaction with DNA. The sequence specificity of these interactions provides the basis for many regulatory mechanisms. The sites that are utilized by a transcription factor are usually analyzed using in vitro binding studies. To detect true in vivo binding sites we developed a method, presented here, that allows construction of recognition element DNA (reDNA) libraries which represent in vivo binding sites plus flanking sequences. reDNA libraries can be constructed for any well-characterized transcription factor. Here we used this method for an in vivo study of genomic DNA elements that interact with the transcription factor c-Jun in rat cerebellum.