Detection and analysis of “CpG-rich” islands in the genome of Physarum polycephalum

Summary A small fraction (Physarum polycephalum contains a high-density of cleavage sites for the restriction endonuclease HpaII. This component can be distinguished from the bulk of the DNA by ³²P-end-labelling followed by size-fractionation using agarose-gel or polyacrylamide-gel electrophoresis. In contrast to the situation in mammalian-cell DNA, where the majority of such small HpaII DNA fragments are derived from CpG-rich islands within diverse single-copy sequences located in the proximity of housekeeping genes, most of the Physarum small HpaII DNA fragments form an array of distinct bands when analysed on polyacrylamide gels, indicating that they are repetitive DNA sequences. Direct sequence analysis shows that the majority of these sequences are derived from the Physarum rDNA minichromosome.