Measuring Changes in Chromatin Using Micrococcal Nuclease

This chapter documents a simple protocol to identify the nucleosome positioning of any given genes. The procedure includes partitioning 200-bp DNA fragments constituting the nucleosomal core region by micrococcal nuclease digestion and semiquantitative polymerase chain reaction amplification using multiple sets of primers covering arbitrary regions of approximately 150 bp in the gene. If the nuclease-digested 200-bp DNA is efficiently amplified, the region is inside the core. If the amplification is poor, the region spans the linker region. By a combination of this method with direct methylation mapping, the core region of a maize gene, ZmMI1, was shown to be less methylated than the linker region. The potential usefulness of the technique is discussed.