Genome-wide mapping of in vivo targets of the Drosophila transcription factor Kruppel

Kruppel (Kr), a member of the gap class of Drosophila segmentation genes, encodes a DNA binding zinc finger-type transcription factor. In addition to its segmentation function at the blastoderm stage, Kruppel also plays a critical role in organ formation during later stages of embryogenesis. To systematically identify in vivo target genes of Kruppel, we isolated DNA fragments from the Kruppel-associated portion of chromatin and used them to find and map Kruppel-dependent cis-acting regulatory sites in the Drosophila genome. We show that Kruppel binding sites are not enriched in Kruppel-associated chromatin and that the clustering of Kruppel binding sites, as found in the cis-acting elements of Kruppel-dependent segmentation genes used for in silico searches of Kruppel target genes, is not a prerequisite for the in vivo binding of Kruppel to its regulatory elements. Results obtained with the newly identified target gene ken and barbie (ken) indicate that Kruppel represses transcription and thereby restricts the spatial expression pattern of ken during blastoderm and gastrulation.