Accessibility of transcriptionally inactive genes is specifically reduced at homeoprotein-DNA binding sites in Drosophila

We showed previously that homeoproteins bind to multiple DNA sites throughout the length of most genes in Drosophila embryos. Based on a comparison of in vivo and in vitro DNA binding specificities, we suggested that homeoprotein binding sites on actively transcribed genes are largely accessible, whereas the binding of homeoproteins to inactive and poorly transcribed genes may be significantly inhibited at most sites, perhaps by chromatin structure. To test this model, we have measured the accessibility of restriction enzyme sites in a number of genes in isolated nuclei. Surprisingly, our data indicate that there is no difference in the overall accessibility of sites for several restriction enzymes on active versus inactive genes. However, consistent with our model, restriction enzyme recognition sequences that overlap with homeoprotein binding sites are less accessible on inactive genes than they are on active genes. We propose that transcriptional activation in all animals may involve a localized increase in accessibility at the AT-rich regions bound by homeoproteins and perhaps at a few other regions, rather than a generalized effect on all sites throughout a gene.