Genomic Footprinting Using Nucleases

Gene expression is regulated by complex mechanisms involving dynamic interactions between cis-acting elements and trans-acting factors in a highly structured chromatin environment. Investigations of protein/DNA interactions in vitro may not have relevance to a living cell system. To analyze events occurring at the DNA level in a living cell, Church et al. introduced the genomic footprinting procedure (1 ). The procedure was developed further (2 ) but ligation-mediated PCR (LM-PCR) was the breakthrough that rendered the technique accessible to many laboratories (3 ).