Rapid in vivo footprinting method for the detection of DNA-protein interactions in isolated nuclei

Here we report a simple method of in vivo footprinting for the detection of DNA-protein interactions in the liver of a small teleost fish, Fundulus heteroclitus. This method allows the determination of these interactions in nuclei isolated from intact liver, obviating the need for cell culture. Cells in culture often do not respond to environmental cues in the same way as do tissues within the intact organism and therefore may be inappropriate for the study of certain adaptive responses. Furthermore, cell lines are available for only a small number of marine organisms. This technique may therefore be of general utility for the study of gene regulation in a wide variety of marine organisms.