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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
Alja Ule,3
Robert B. Darnell1,2
Abstract:
Nova proteins are neuron-specific antigens targeted in paraneoplasticopsoclonus myoclonus ataxia (POMA), an autoimmune neurologicdisease characterized by abnormal motor inhibition.Nova proteinsregulate neuronal pre-messenger RNA splicing by directly bindingto RNA.To identify Nova RNA targets, we developed a method topurify protein-RNA complexes from mouse brain with the use ofultraviolet cross-linking and immunoprecipitation (CLIP).Thirty-fourtranscripts were identified multiple times by Nova CLIP.Three-quartersof these encode proteins that function at the neuronal synapse,and one-third are involved in neuronal inhibition.Splicing targetsconfirmed in Nova/ mice include c-Jun N-terminalkinase 2, neogenin, and gephyrin; the latter encodes a proteinthat clusters inhibitory -aminobutyric acid and glycine receptors,two previously identified Nova splicing targets.Thus, CLIP revealsthat Nova coordinately regulates a biologically coherent setof RNAs encoding multiple components of the inhibitory synapse,an observation that may relate to the cause of abnormal motorinhibition 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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