Probing the nature of chromosomal DNA-protein contacts by in vivo footprinting

Abstract

Of the various approaches employed to unravel the mechanisms of gene regulation, the method of in vivo footprinting seems likely to be increasingly perceived as indispensable. A clear knowledge of the actual pattern of DNA-protein interactions occurring at a given gene within a cell, gained from data obtained with a minimum of external perturbation, can provide a benchmark against which attempts at in vitro reconstruction of the relevant interactions can be judged. This appears particularly important given our current awareness of the degeneracy displayed by certain DNA sequences in terms of their in vitro ability to separately bind to more than one (sometimes several) species of protein factor present in a nuclear extract. The mutual pursuit of both in vivo and in vitro approaches will likely provide the best route to a detailed molecular description of regulatory interactions. Following the introduction of both improved and novel technical approaches, the possibility of probing chromosomal DNA-protein associations at nucleotide resolution is now well within the capacity of most laboratories. In this article the techniques of, probing reagents used for, and some important results obtained by in vivo footprinting are critically discussed.