The ciliates, named for the intricate array of swimming organelles on the cell surface, all share a second remarkable feature. These single-celled organisms have two different kinds of nuclei, the germ line micronucleus and the transcriptionally active, somatic macronucleus. Tetrahymena have proved to be a particularly good system for the study of this nuclear dimorphism. Here we will focus on the developmentally programmed DNA rearrangement and DNA methylation which produce radical differences in the micro- and macronuclear genomes.