A comparison of in vivo and in vitro DNA-binding specificities suggests a new model for homeoprotein DNA binding in Drosophila embryos

Little is known about the range of DNA sequences bound by transcription factors in vivo. Using a sensitive UV cross-linking technique, we show that three classes of homeoprotein bind at significant levels to the majority of genes in Drosophila embryos. The three classes bind with specificities different from each other; however, their levels of binding on any single DNA fragment differ by no more than 5- to 10-fold. On actively transcribed genes, there is a good correlation between the in vitro DNA-binding specificity of each class and its in vitro DNA-binding specificity, In contrast, no such correlation is seen on inactive or weakly transcribed genes. These genes are bound pearly in vivo, even though they contain many high affinity homeoprotein-binding sites. Based on these results, we suggest how the in vivo pattern of homeoprotein DNA binding is determined.