In vivo footprinting of protein-DNA interactions

This chapter focuses on in vivo footprinting of protein–DNA interactions. In vitro DNA binding studies by DNase I footprinting or band-shift is the most popular method for searching for protein–DNA interactions. These methods have been used to great advantage in many systems. The value of in vivo dimethyl sulfate (DMS) footprinting is based on the ability of DMS to interact with the genome in its natural state to reveal points of protein–DNA interactions of the native chromatin within living cells. These interactions precisely define cis elements as areas of protein contacts and provide a characteristic set of nucleotide interactions that serve as a unique signature of any given protein–DNA interaction. Thus DMS footprinting offers the ability to define cis elements, the ability to determine whether the elements are occupied by transacting factors during any given stress response, and the ability to distinguish even subtle differences in the binding signature that might indicate the occupancy of an element by a different factor. © 1995, Academic Press Inc.