Nova-1, an autoantigen in paraneoplastic opsoclonus myoclonus ataxia (POMA), a disorder associated with breast cancer and motor dysfunction, is a neuron-specific nuclear RNA binding protein. We elements were identified in two neuronal pre-mRNAs, one encoding the inhibitory glycine receptor ␣2 (GlyR ␣2) and a second encoding Nova-1 itself. Nova-1 protein binds these RNAs with high affinity and specificity in vitro, and this binding can be blocked by POMA antisera. Moreover, both Nova-1 and GlyR ␣2 pre-mRNAs specifically coimmunoprecipitated with Nova-1 protein from brain extracts. Thus, Nova-1 functions as a sequence-specific nuclear RNA binding protein in vivo; disruption of the specific interaction between Nova-1 and GlyR ␣2 pre-mRNA may underlie the motor dysfunction seen in POMA.RNA-protein interactions are important in the posttranscriptional regulation of RNA metabolism and expression. Nascent RNA transcripts associate with large multiprotein complexes that include hnRNP proteins and snRNP particles (19). RNA protein complexes subsequently participate in polyadenylation, RNA splicing, RNA transport, and translational control. Defining target RNAs with which RNA binding proteins (RBPs) interact has been critical in defining their function. In Drosophila melanogaster, the identification of sequence-specific targets for the sex-lethal (sxl) (5, 30) and transformer-2 (28) RBPs has led to a precise understanding of their role in regulating RNA splicing. In mammals, the ability of U2AF(65) to bind to polypyrimidine tracts is believed to recruit U2 snRNP to the branch site (48, 69). Identification of specific RNA ligands for the human immunodeficiency virus Rev and Tat proteins has clarified their role in regulating viral RNA transcription, processing, and transport (14,27,34,40,70). There remain, however, many RBPs for which specific RNA targets have not been identified.RNA selection has been used as an in vitro approach to identify RNA ligands for RBPs (61,65). This approach was originally used to confirm the specificity of rRNA binding sites recognized by T4 DNA polymerase (65) and has subsequently been used to confirm and extend known binding sites for the U1-snRNP-A protein (64), sxl (55), and the viral Rev (3, 31) and Tat (66) proteins. RNA selection experiments have also been used in efforts to identify RNA ligands for RBPs that do not have known sequence-specific binding sites, including hnRNP proteins (12), SR proteins (29, 62), and the neuronal RBP (n-RBP) Hel-N1 (36), although in general these studies have yielded short in vitro consensus RNA ligands whose in vivo significance is currently being explored.Nova-1 is a nuclear n-RBP identified as a target antigen in paraneoplastic opsoclonus myoclonus ataxia (POMA) (9, 10,