With the completion of the human genome-sequencing project, it is more apparent than ever before that we are only at the very beginning stages of understanding the mechanistic complexity required to regulate genomic functions. In cells, the genome exists as an assemblage of DNA and proteins called chromatin. Chromatin is the interface through which the transcription machinery gains access to the gene template. Therefore, chromatin is a critical regulator of transcription, and conversely, transcription drives changes in chromatin organization. Most conventional techniques for studying gene regulation require the disruption of cellular architecture rendering them unable to reveal how factors are temporally and spatially organized at genes during activation. Visualizing factor dynamics at individual transcription sites in single living cells, however, can provide insight into gene-specific regulatory mechanisms as well as genome organization and epigenetic inheritance because of the important role transcription plays in these processes.