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Science 302 (5648): 1212-1215

Copyright © 2003 by the American Association for the Advancement of Science

CLIP Identifies Nova-Regulated RNA Networks in the Brain

Jernej Ule,1,2* Kirk B. Jensen,1,2* Matteo Ruggiu,1,2 Aldo Mele,1,2 Aljaz Ule,3 Robert B. Darnell1,2{dagger}

Abstract: Nova proteins are neuron-specific antigens targeted in paraneoplastic opsoclonus myoclonus ataxia (POMA), an autoimmune neurologic disease characterized by abnormal motor inhibition.Nova proteins regulate neuronal pre-messenger RNA splicing by directly binding to RNA.To identify Nova RNA targets, we developed a method to purify protein-RNA complexes from mouse brain with the use of ultraviolet cross-linking and immunoprecipitation (CLIP).Thirty-four transcripts were identified multiple times by Nova CLIP.Three-quarters of these encode proteins that function at the neuronal synapse, and one-third are involved in neuronal inhibition.Splicing targets confirmed in Nova–/– mice include c-Jun N-terminal kinase 2, neogenin, and gephyrin; the latter encodes a protein that clusters inhibitory {gamma}-aminobutyric acid and glycine receptors, two previously identified Nova splicing targets.Thus, CLIP reveals that Nova coordinately regulates a biologically coherent set of RNAs encoding multiple components of the inhibitory synapse, an observation that may relate to the cause of abnormal motor inhibition in POMA.

1 Howard Hughes Medical Institute, Rockefeller University, New York, NY 10021, USA.
2 Laboratory of Molecular Neuro-Oncology, Rockefeller University, New York, NY 10021, USA.
3 Center for Research in Experimental Economics and Political Decision-Making, University of Amsterdam, 1018 WB Amsterdam, Netherlands.

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* These authors contributed equally to this work.

{dagger} To whom correspondence should be addressed. E-mail: darnelr{at}

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