Ordered distribution of modified bases in the DNA of a dinoflagellate

In DNA of the dinoflagellate Crypthecodinium cohnii, 38% of the thymine is replaced by the modified base 5-hydroxymethyluracil, and approximately 3% of the cytosine is replaced by 5-methylcytosine. Both of the modified bases are non-randomly distributed in the DNA. Determinations of 3' nearest neighbors show that HOMeU is preferentially located in the dinucleotides HOMeUpA and HOMeUpC. Pyrimidine tract analysis shows that HOMeU is also greatly enriched in the trinucleotide purine-HOMeU-purine. As in other eukaryotes, methylcytosine in C. cohnii DNA occurs predominantly in the dinucleotide MeCpG. By analysis of restriction endonuclease digestion patterns of C. cohnii total DNA and ribosomal DNA, we have found that the central CpG dinucleotides in the sites for the enzymes Hpa II (CCGG) and Hha I (GCGC) are extensively methylated in both total DNA and ribosomal DNA. Results of digestion with Ava I, however, indicated that not all CpG dinucleotides in the sequence CCTCGGAG are methylated in C. cohnii DNA.