One of the defining characteristics of ciliates is nuclear dimorphism: two types of nuclei with distinct genome architectures exist within one cell. In Oxytricha trifallax, one nucleus contains a fragmented and scrambled germline copy of the somatic genome. During mating, a haploid germline nucleus transfers between cells. After fertilization, a zygotic germline nucleus matures into a new somatic nucleus by undergoing a process of DNA elimination and rearrangement. In addition to fragments of coding sequences that are retained in the somatic genome and noncoding sequences that are eliminated, 810 recently discovered germline-restricted genes also reside in the germline genome and are eliminated during development. These genes are only transcribed during the process of DNA elimination and rearrangement, and their elimination during development of the somatic genome may constitute a mechanism of developmental gene regulation. I have shown that microinjection of RNA matching the sequences of germline-restricted genes reprograms the cell to retain these genes in a heritable manner. Furthermore, it appears that retained germline genes are transcribed outside of their normal developmental window. These data support a model in which germline-restricted genes are relegated to the germline nucleus to ensure that they are only expressed during the sexual cycle.