The goal of this book is to provide a detailed description of the approaches to be employed and issues to be considered when undertaking a molecular analysis of the transcriptional regulatory mechanisms for a newly isolated gene, or a biochemical analysis of a new transcription factor. Our emphasis is on mammalian transcription, which is complicated by the combinatorial nature of regulation and the lack of facile genetics.We refer periodically to studies in yeast, Drosophila, and other organisms where more tractable genetic approaches have led to a detailed understanding of particular mechanistic issues. The topics covered in the book extend from the determination of whether a gene is in fact regulated at the level of transcription initiation to advanced strategies for characterizing the biochemical mechanism underlying its combinatorial regulation by activators. Although numerous specialized and detailed techniques are included, the unique characteristics of this book are its strategic and conceptual emphasis on analysis of individual genes and the
transcription factors that regulate them.