Abstract: The present disclosure provides methods for profiling, in a global manner, the activity of gene regulatory elements in cells, preferably eukaryotic and prokaryotic cells. The methods include use of Fluorescence Polarization and other homogeneous assays, regulatory element activity profiling (REAP), and electrophoretic mobility shift assays. Cells may be in any state of metabolism, whether resting, growing, normal, mutant, diseased or differentiating.