title: Accessibility of transcriptionally inactive genes is specifically reduced at homeoprotein-DNA binding sites in Drosophila.
abstract: 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 homeo-proteins and perhaps at a few other regions, rather than a generalized effect on all sites throughout a gene.
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, PO Box 208114, 260 Whitney Avenue, New Haven, CT 06520-8114, USA.
authors.forename: A
authors.initials: A
authors.lastname: Carr
authors.forename: M D
authors.initials: MD
authors.lastname: Biggin
mesh_terms: D000818:Animals; D001426:Bacterial Proteins; D001665:Binding Sites; D002467:Cell Nucleus / Q000235:genetics / Q000378:metabolism; D004247:DNA / Q000235:genetics / Q000378:metabolism*; D004249:DNA Damage; D004262:DNA Restriction Enzymes / Q000378:metabolism; D004330:Drosophila / Q000196:embryology / Q000235:genetics*; D029721:Drosophila Proteins; D004625:Embryo, Nonmammalian / Q000378:metabolism / Q000528:radiation effects; D051717:Fushi Tarazu Transcription Factors; D017344:Genes, Insect / Q000235:genetics*; D018398:Homeodomain Proteins / Q000235:genetics / Q000378:metabolism* / Q000528:radiation effects; D011485:Protein Binding; D014157:Transcription Factors; D014158:Transcription, Genetic; D014466:Ultraviolet Rays
chemical_list: D001426:Bacterial Proteins; D029721:Drosophila Proteins; D051717:Fushi Tarazu Transcription Factors; D018398:Homeodomain Proteins; D014157:Transcription Factors; C052837:eve protein, Drosophila; C497169:ftz protein, Drosophila; D004247:DNA; D004262:DNA Restriction Enzymes