Micrococcal nuclease as a probe of DNA sequence organization and chromatin structure

We have investigated micrococcal nuclease digestion of chromatin and purified DNA at the heat-shock locus 67B in Drosophila melanogaster. At early stages of the reaction a distinct set of fragments is generated, indicating the presence of preferential cleavage sites. These sites are also observed when purified recombinant plasmid DNA is used as the substrate, demonstrating that the sites are specified by the DNA sequence. At Drosophila locus 67B, prominent sites occur frequently, spaced approximately 200 bp apart, within the nontranscribed portions of the locus, but are generally not observed within the regions that are transcribed. In contrast, such sites are randomly distributed along the procaryotic plasmid pBR322. The results indicate that specific patterns of digestion of eucaryotic chromatin by micrococcal nuclease cannot be simply interpreted as the consequence of the nucleosome array. However, it is possible that the organization of eucaryotic DNA sequences detected by micrococcal nuclease bears a functional relationship to the organization of DNA by nucleosomes and, in fact, was so selected through evolution.