The nature of the interaction of nucleosomes with a eukaryotic RNA polymerase II

The integrity and stability of nucleosomes under transcription assay conditions has been found to depend on concentration and ionic environment. Rifamycin AF/013, a commonly used inhibitor of initiation, is particularly effective in destabilisation of nucleosomes. Intact nucleosomes are refractory to transcription by wheat RNA polymerase II, the histone core preventing initiation. Template titration suggests that the polymerase can, however, bind to nucleosomes, and a 15--16S complex has been observed on sucrose gradients. DNase I digestion of polymerase-nucleosome incubations indicates that whilst histone is still present in the complex, the nucleosome conformation is altered resulting in enhanced nucleolysis at sites near the DNA centre but reduced overall kinetics of digestion.