The myoplasm is a localized cytoplasmic region that is involved in axis determination, gastrulation, muscle cell specification, and the pattern of cell divisions during ascidian development. The noncoding yellow crescent (YC) RNA is localized in the myoplasm, but the function of this transcript is unknown. Probes containing the 3' region of YC RNA hybridize to other RNAs in ascidian eggs. A cDNA library from the ascidian Styela clava was screened with a YC probe to identify maternal YC-related RNAs. This screen resulted in isolation of ScYC26b, a cDNA clone encoding the ascidian proliferating cell nuclear antigen (PCNA). The PCNA mRNA has a long 3' untranslated region containing a 521-nucleotide sequence with antisense complementarity to part of the 3' region of YC RNA. The PCNA and YC genes appear to be single copy and may overlap in their 3' regions on opposite DNA strands. The ascidian PCNA protein has 61, 69, and 71% amino acid identity to the Drosophila, Xenopus, and human PCNAs, respectively. S. clava embryos contain maternal and zygotic PCNA mRNAs. Maternal PCNA mRNA is localized in the ectoplasm, a cytoplasmic region that is segregated to cell lineages that proliferate extensively during embryogenesis, and is depleted in the myoplasm, which is segregated to cell lineages that undergo fewer divisions. Zygotic PCNA mRNA is confined to the developing nervous system and is still abundant after the neural cells have ceased to proliferate. PCNA protein, detected with PC10 monoclonal antibody, is also excluded from the myoplasm. These results show that the 3' UTR of PCNA mRNA is antisense and complementary to YC RNA and suggest that differential cell proliferation in the embryo may be limited by localization of maternal PCNA mRNA and protein. Furthermore, zygotic PCNA may have a novel role in neural development in the tadpole larva.