Signaling pathways, for all their elegance, serve but one purpose: to convert extracellular signals into intracellular changes. Whether it's insulin or isoleucine, antigen or adrenaline, the end result is most always the same: changes in transcriptional activity.
Such effects are caused by changes in transcription factor-binding patterns at gene regulatory regions like promoters, enhancers, and silencers. Classically, the electrophoretic mobility shift assay (gel shift), has been the assay of choice for demonstrating that a particular protein can bind to a specific short sequence. Yet gel shifts are slow, low-throughput, nonquantitative, and radioactive. And when they're done, you still don't know what proteins, or groups of proteins, are ultimately responsible for directing transcriptional changes in vivo, or even that the sequence in vivo is actually accessible and able to bind potential regulators.
To do that, to determine precisely what protein is binding to a site, rather than what proteins could be ...
