CLIP identifies Nova-regulated RNA networks in the brain

Science. 2003 Nov 14;302(5648):1212-5. doi: 10.1126/science.1090095.

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • 3' Untranslated Regions
  • Alternative Splicing
  • Animals
  • Antigens, Neoplasm*
  • Brain / metabolism*
  • Carrier Proteins / genetics
  • Carrier Proteins / metabolism
  • Exons
  • Introns
  • Membrane Proteins / genetics
  • Membrane Proteins / metabolism
  • Mice
  • Mitogen-Activated Protein Kinase 9
  • Mitogen-Activated Protein Kinases / genetics
  • Mitogen-Activated Protein Kinases / metabolism
  • Nerve Tissue Proteins / metabolism*
  • Neural Inhibition
  • Neurons / metabolism*
  • Precipitin Tests
  • RNA Precursors / genetics
  • RNA Precursors / metabolism*
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism*
  • RNA-Binding Proteins / metabolism*
  • Reverse Transcriptase Polymerase Chain Reaction
  • Ultraviolet Rays

Substances

  • 3' Untranslated Regions
  • Antigens, Neoplasm
  • Carrier Proteins
  • Membrane Proteins
  • Nerve Tissue Proteins
  • Nova antigen
  • RNA Precursors
  • RNA, Messenger
  • RNA-Binding Proteins
  • gephyrin
  • neogenin
  • Mitogen-Activated Protein Kinase 9
  • Mitogen-Activated Protein Kinases