Genomic studies of transcription factor-DNA interactions

A central issue in the regulation of gene expression is the physical association of transcription factors with relevant promoter sequences. Recently, technological advances have allowed researchers to analyze these processes on a genomic scale. In particular, the combination of the chromatin immunoprecipitation (ChIP) technique with microarray analysis (the 'ChIP to chip' experiment) is providing a wealth of new and surprising data on transcription factor-chromatin interactions. These advances are reviewed here. We also discuss future challenges in the area.