Fine mapping of chromatin structure in Drosophila melanogaster embryos using micrococcal nuclease

The structure of chromatin in eukaryotes exerts significant influences on many DNA related processes, including transcription, replication, recombination and repair. A useful tool for mapping chromatin structure is micrococcal nuclease (MNase), which induces double-strand breaks within nucleosome linker regions, and with more extensive digestion, single-strand nicks within the nucleosome itself. Many studies, carried out largely with microbes and cell cultures, have used MNase to determine the positions of nucleosomes within a region of DNA to identify dynamic changes induced during gene regulation. To measure similar processes in a developmental context, we turned to a tractable model system, the Drosophila embryo. Here we describe a protocol that enables MNase mapping of the enhancer chromatin structure in the embryo, and show how it can be used to identify structural changes on a cis-regulatory element targeted by the Knirps repressor.