The molecular mechanisms that regulate patterns of gene expression have been studied intensively over the past 20 years and many of the critical interactions have been characterized in detail (Bulger et al., 2002; Butler and Kadonaga, 2002; Emerson, 2002; Jenuwein and Allis, 2001; Maniatis and Reed, 2002; Orphanides and Reinberg, 2002). The process is inevitably complex and recent reviews focus on the complex interplay of networks that somehow integrate different types of information that influence levels and patterns of gene expression. Indeed, the control of this process is so sophisticated that for the sake of understanding it is helpful to consider specific features that impact on the behaviour of these regulatory networks. For simplicity, five broad areas will be considered here:
1. Transcriptions factors-function as adaptors to decode the genetic information within DNA and then recruit the transcription machinery to gene promoters to engage gene expression. Transcription factors bind within the promoter and at more distal upstream activator elements and sequences such as enhancers that stimulate levels of gene expression. The behaviour of transcription factors, their concentrations in the nucleus and the structure and stability of the promoter-associated complexes are likely to play a critical role in determining levels of mRNA synthesis. Note that the concentration of transcription factors within nuclei and their affinity for different promoters can vary enormously.