Regulation of gene expression is a highly complex process that requires the concerted action of many proteins, including sequence-specific transcription factors, cofactors, and chromatin proteins. In higher eukaryotes, the interplay between these proteins and their interactions with the genome still is poorly understood. We systematically mapped the in vivo binding sites of seven transcription factors with diverse physiological functions, five cofactors, and two heterochromatin proteins at Ϸ1-kb resolution in a 2.9 Mb region of the Drosophila melanogaster genome. Surprisingly, all tested transcription factors and cofactors show strongly overlapping localization patterns, and the genome contains many ''hotspots'' that are targeted by all of these proteins. Several control experiments show that the strong overlap is not an artifact of the techniques used. Colocalization hotspots are 1-5 kb in size, spaced on average by Ϸ50 kb, and preferentially located in regions of active transcription. We provide evidence that protein-protein interactions play a role in the hotspot association of some transcription factors. Colocalization hotspots constitute a previously uncharacterized type of feature in the genome of Drosophila, and our results provide insights into the general targeting mechanisms of transcription regulators in a higher eukaryote.chromatin profiling ͉ DamID ͉ tiling array ͉ transcriptional regulator T ranscription factors are proteins that control the expression of specific sets of genes. They act by binding to regulatory DNA elements in the vicinity of these genes. The target specificity of transcription factors is modulated by protein-protein interactions with other factors and by the local chromatin structure. Because of the complexity of these interactions, prediction of the in vivo binding sites of transcription factors based on sequence alone still is unreliable (1-3). In the past few years, experimental approaches have been developed to identify the binding sites of transcription factors in living cells, on a genomewide scale (4-6).Systematic mapping studies in yeast have indicated that each promoter is typically bound by a small set of transcription factors. The vast majority of promoters is occupied by only a few proteins, and binding of Ͼ10 proteins to a single promoter is rare (Ͻ1%) (7,8). Although transcription factors frequently act in a combinatorial fashion (9), these results suggest that the transcription regulatory network in yeast shows a substantial degree of ''division of labor,'' where each factor (or a small group of factors) binds a distinct set of genes.Genomes of higher eukaryotes are much more complex than those of yeast species, raising the question of how transcription factor-binding sites are organized in such more complex genomes. Although sequence analysis of the genomes of several higher eukaryotes has indicated that transcription factor consensus motifs tend to be clustered in the genome (10-12), it is still unclear whether these clusters are the predominant targets in vivo, ...