Nova regulates brain-specific splicing to shape the synapse.
Alternative RNA splicing greatly increases proteome diversity and may thereby contribute to tissue-specific functions. We carried out genome-wide quantitative analysis of alternative splicing using a custom Affymetrix microarray to assess the role of the neuronal splicing factor Nova in the brain. We used a stringent algorithm to identify 591 exons that were differentially spliced in the brain relative to immune tissues, and 6.6% of these showed major splicing defects in the neocortex of Nova2-/- mice. We tested 49 exons with the largest predicted Nova-dependent splicing changes and validated all 49 by RT-PCR. We analyzed the encoded proteins and found that all those with defined brain functions acted in the synapse (34 of 40, including neurotransmitter receptors, cation channels, adhesion and scaffold proteins) or in axon guidance (8 of 40). Moreover, of the 35 proteins with known interaction partners, 74% (26) interact with each other. Validating a large set of Nova RNA targets has led us to identify a multi-tiered network in which Nova regulates the exon content of RNAs encoding proteins that interact in the synapse.
Ule
Jernej
J
Howard Hughes Medical Institute and Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York, USA.
Ule
Aljaz
A
Spencer
Joanna
J
Williams
Alan
A
Hu
Jing-Shan
JS
Cline
Melissa
M
Wang
Hui
H
Clark
Tyson
T
Fraser
Claire
C
Ruggiu
Matteo
M
Zeeberg
Barry R
BR
Kane
David
D
Weinstein
John N
JN
Blume
John
J
Darnell
Robert B
RB
D017398:Alternative Splicing / Q000502:physiology*; D000818:Animals; D000951:Antigens, Neoplasm / Q000502:physiology*; D051379:Mice; D018345:Mice, Knockout; D019579:Neocortex / Q000378:metabolism; D009419:Nerve Tissue Proteins / Q000502:physiology*; D000090682:Neuro-Oncological Ventral Antigen; D020411:Oligonucleotide Array Sequence Analysis; D016601:RNA-Binding Proteins / Q000502:physiology*; D013569:Synapses / Q000378:metabolism*
D000951:Antigens, Neoplasm; D009419:Nerve Tissue Proteins; D000090682:Neuro-Oncological Ventral Antigen; D016601:RNA-Binding Proteins