GENOMIC FOOTPRINTING OF DROSOPHILA EMBRYO NUCLEI BY LINKER TAG SELECTION LM-PCR

The unmatched power of Drosophila genetics revealed the complex regula tory network of gene activities that governs the development of higher eukaryotes. An understanding of gene control at the level of transcri ption requires insight into the protein/DNA interactions that regulate transcription in the developing embryo. Genomic footprinting allows t he direct visualization of these protein/DNA interactions within intac t nuclei or cells. In combination with other in vivo assays such as pr otein/DNA crosslinking and classical biochemistry, genomic footprintin g can give valuable insight into the architecture of promoters in vari ous states of activity. In this article we summarize our experience in analyzing Drosophila embryos by genomic footprinting and describe mod ifications of the ligation-mediated PCR procedure that have improved t his analysis. Applications of genomic footprinting to embryos are curr ently limited by the fact that all target nuclei must be uniform with respect to the protein/DNA interactions at the chosen site. We discuss strategies that should allow the analysis of small numbers of cells d erived from heterogeneous populations and tissues. (C) 1997 Academic P ress.