The characterization of ribosomal RNA gene chromatin from Physarum polycephalum

We have isolated ribosomal RNA gene (rDNA) chromatin from Physarum polycephalum using a nucleolar isolation procedure that minimizes protein loss from chromatin and, subsequently, either agarose gel electrophoresis or metrizamide gradient centrifugation to purify this chromatin fraction (Amero, S. A., Ogle, R. C., Keating, J. L., Montoya, V. L., Murdoch, W. L., and Grainger, R. M. (1988) J. Biol. Chem. 263, 10725-10733). Metrizamide-purified rDNA chromatin obtained from nucleoli isolated according to the new procedure has a core histone/DNA ratio of 0.77:1. The major core histone classes comigrate electrophoretically with their nuclear counterparts on Triton-acid-urea/sodium dodecyl sulfate two-dimensional gels, although they may not possess the extent of secondary modification evident with the nuclear histones. This purified rDNA chromatin also possesses RNA polymerase I activity, and many other nonhistone proteins, including two very abundant proteins (26 and 38 kDa) that may be either ribonucleoproteins or nucleolar matrix proteins. Micrococcal nuclease digestion of the metrizamide-purified rDNA chromatin produces particles containing 145-base pair DNA fragments identical in length to those in total chromatin and which contain both transcribed and nontranscribed rDNA sequences. Some smaller fragments (30, 70, and 110 base pairs) are also seen, but their sequence content is not known. These particles sediment uniformly at 11 S in sucrose gradients containing 15 mM NaCl, and at 4-11 S in gradients containing 0.35 M NaCl. Particles enriched in gene or nontranscribed spacer sequences are not resolved in these sucrose gradients or in metrizamide gradients. Our findings suggest that the rDNA chromatin fraction we have identified contains transcriptionally active genes and that an organized, particle-containing structure exists in active rDNA chromatin.