Hel-N1, a human RNA-binding protein, shares significant homology with Drosophila protein ELAV, which is essential for fly neuronal development. Hel-N1 has been shown to bind in vitro to 3' untranslated regions of mRNAs encoding c-myc, c-fos, granulocyte/macrophage colony-stimulating factor, and transcriptional repressor, Id. We report that Hel-N1 and a related form, Hel-N2, are expressed in human medulloblastoma cells, but their ratio differs significantly from that in adult brain and fetal brain. Selection of RNA targets from randomized combinatorial libraries yielded (A+U)-rich consensus sequences for both Hel-N1 and Hel-N2. As a means to identify cellular RNA targets for these proteins, we devised combinatorial shape libraries representing naturally derived 3' untranslated regions and were able to select a structurally related subset of transcripts that bound to Hel-N1. Approximately 10% of the proteins encoded by these subset mRNAs were identifiable in the data bases and most are implicated in cell growth regulation. This approach provides a means to gain access to novel genes expressed in various cell types by partitioning mRNAs containing common sequence elements using RNA-binding proteins.