Devising transcriptional regulatory networks operating during the cell cycle and differentiation using ChIP-on-chip

The study of global transcriptional regulatory networks in eukaryotes has advanced rapidly in the last five years with the advent of genomic microarrays that allow investigators to comprehensively scrutinize the structure and composition of transcriptomes and chromatin. Many facets of this field have benefited from an examination of the location of proteins associated with chromatin. We describe here how we have used genomic arrays to perform location analysis (or ChIP-on-chip analysis) of regulatory factors that control the complex process of cell cycle progression and differentiation, in order to identify key direct transcriptional targets. Combining this information with data obtained through expression profiling and computational analysis of transcription factor binding sites has also allowed us to devise transcriptional regulatory networks governing these processes.