The transcriptional networks underlying mammalian cell development and function are largely unknown. The recently described use of flow cell sequencing devices in combination with chromatin immunoprecipitation (ChIP-seq) stands to revolutionize the identification of DNA-protein interactions. As such, ChIP-seq is rapidly becoming the method of choice for the genome-wide localization of histone modifications and transcription factor binding sites. As further studies are performed, the information generated by ChIP-seq is expected to allow the development of a framework for networks describing the transcriptional regulation of cellular development and function. However, to date, this technology has been applied only to a small number of cell types, and even fewer tissues, suggesting a huge potential for novel discovery in this field.