Deoxyribonucleic acid (DNA) of the transcriptionally active macronucleus of Tetrahymena thermophila is methylated at the N6 position of adenine to produce methyladenine (MeAde); approximately 1 in every 125 adenine residues (0.8 mol%) is methylated. Transcriptionally inert micronuclear DNA is not methylated (s0.01 mol% MeAde; M. A. Gorovsky, S. Hattman, and G. L. Pleger, J. Cell Biol. 56:697-701, 1973). There is no detectable cytosine methylation in macronuclei in Tetrahymena DNA (s0.01 mol% 5-methylcytosine). MeAde-containing DNA sequences in macronuclei are preferentially digested by both staphylococcal nuclease and pancreatic deoxyribonuclease I. In contrast, there is no preferential release of MeAde during digestion of purified DNA. These results indicate that MeAde residues are predominantly located in "linker DNA" and perhaps have a function in transcription. Pulse-chase studies showed that labeled MeAde remains preferentially in linker DNA during subsequent rounds of DNA replication; i.e., there is little, if any, movement of nucleosomes during chromatin replication. This implies that nucleosomes may be phased with respect to DNA sequence.Deoxyribonucleic acid (DNA) methylation specifies genetic infornation in that specific sequences are methylated and the amount of methylation is both species and tissue specific (5,15,19,42,56,64,74,78,83,84). In nuclear DNA of multicellular eucaryotes, the amount of 5-methylcytosine (MeCyt) varies from as little as 0.17 mol% in insects (3) to as much as 50 mol% in certain plants (72). DNA of unicellular eucaryotes generally contains either MeCyt or methyladenine (MeAde), or both (19,31,36,54,56). Recent evidence suggests that site-specific methylation of cytosine in eucaryotes may be related to the control of transcription; e.g., transcriptionally competent genes are not methylated at sites which are methylated in cells not transcribing those genes (11,14,16,17,20,21,24,45,48,50,61,70,73,75,78