Genomic analysis of protein–DNA interactions in bacteria: insights into transcription and chromosome organization

Chromatin immunoprecipitation (ChIP) is a powerful method to measure protein-DNA interactions in vivo, and it can be applied on a genomic scale with microarray technology (ChIP-chip). ChIP-chip has been used extensively to map DNA-protein interactions across eukaryotic chromosomes. Here we review recent applications of ChIP-chip to the study of bacteria, which provide important and unexpected insights into transcription and chromosome organization.