CLIP identifies Nova-regulated RNA networks in the brain.
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.
Ule
Jernej
J
Howard Hughes Medical Institute, Rockefeller University, New York, NY 10021, USA.
Jensen
Kirk B
KB
Ruggiu
Matteo
M
Mele
Aldo
A
Ule
Aljaz
A
Darnell
Robert B
RB
D020413:3' Untranslated Regions; D017398:Alternative Splicing; D000818:Animals; D000951:Antigens, Neoplasm; D001921:Brain / Q000378:metabolism*; D002352:Carrier Proteins / Q000235:genetics / Q000378:metabolism; D005091:Exons; D007438:Introns; D008565:Membrane Proteins / Q000235:genetics / Q000378:metabolism; D051379:Mice; D048056:Mitogen-Activated Protein Kinase 9; D020928:Mitogen-Activated Protein Kinases / Q000235:genetics / Q000378:metabolism; D009419:Nerve Tissue Proteins / Q000378:metabolism*; D009433:Neural Inhibition; D000090682:Neuro-Oncological Ventral Antigen; D009474:Neurons / Q000378:metabolism*; D011233:Precipitin Tests; D012322:RNA Precursors / Q000235:genetics / Q000378:metabolism*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000378:metabolism*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014466:Ultraviolet Rays
D020413:3' Untranslated Regions; D000951:Antigens, Neoplasm; D002352:Carrier Proteins; D008565:Membrane Proteins; D009419:Nerve Tissue Proteins; D000090682:Neuro-Oncological Ventral Antigen; D012322:RNA Precursors; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; C073441:gephyrin; C091279:neogenin; D048056:Mitogen-Activated Protein Kinase 9; D020928:Mitogen-Activated Protein Kinases