To localize protein binding sites in the DNA. For example sites where transcription factors (proteins, products of other genes) bind. This is important in understanding gene regulation, gene regulation networks.
Understanding which genes (the ones that code for transcription factors) affect the expression of certain genes of interest (like for example genes with an important role in cancer cells) is for example important to develop medication to try and block these gene networks.
Knowledge of protein binding sites in DNA is useful for numerous other reasons. Mapping and quantifying gene regulatory networks (the networks of genes affecting the expression of other genes) is also important in metabolic engineering, bio-engineering, to manipulate the gene regulatory network so that it overproduces a certain compound of interest. To do that knowledge of regulatory proteins and sequences is needed.