Many biological phenomena, including numerous human diseases, can be traced to the proper or improper expression of a gene or set of genes. Hence, the understanding of the mechanisms of gene regulation is essential for the successful analysis of a wide range of problems in the biological and biomedical sciences. In our lab, we study the regulation of transcription by RNA polymerase II. A surprising number of fundamental aspects of this critically important process have yet to be discovered and characterized. Fortunately, we are now in a new and exciting era in the analysis of gene regulation, as recent and emerging technologies are enabling the illumination of previously unattainable insights into key unanswered questions. We are also interested in the biological functions of chromatin, the natural state of DNA in the eukaryotic nucleus. Chromatin is complex, multidimensional, and intellectually fascinating. Ultimately, DNA-directed processes in the nucleus must be understood in the context of chromatin.