Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators.
Alternative splicing (AS) dramatically expands the complexity of the mammalian brain transcriptome, but its atlas remains incomplete. Here we performed deep mRNA sequencing of mouse cortex to discover and characterize alternative exons with potential functional significance. Our analysis expands the list of AS events over 10-fold compared with previous annotations, demonstrating that 72% of multiexon genes express multiple splice variants in this single tissue. To evaluate functionality of the newly discovered AS events, we conducted comprehensive analyses on central nervous system (CNS) cell type-specific splicing, targets of tissue- or cell type-specific RNA binding proteins (RBPs), evolutionary selection pressure, and coupling of AS with nonsense-mediated decay (AS-NMD). We show that newly discovered events account for 23-42% of all cassette exons under tissue- or cell type-specific regulation. Furthermore, over 7,000 cassette exons are under evolutionary selection for regulated AS in mammals, 70% of which are new. Among these are 3,058 highly conserved cassette exons, including 1,014 NMD exons that may function directly to control gene expression levels. These NMD exons are particularly enriched in RBPs including splicing factors and interestingly also regulators for other steps of RNA metabolism. Unexpectedly, a second group of NMD exons reside in genes encoding chromatin regulators. Although the conservation of NMD exons in RBPs frequently extends into lower vertebrates, NMD exons in chromatin regulators are introduced later into the mammalian lineage, implying the emergence of a novel mechanism coupling AS and epigenetics. Our results highlight previously uncharacterized complexity and evolution in the mammalian brain transcriptome.
Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032;
Qinghong
Q
Yan
Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032;
Sebastien M
SM
Weyn-Vanhentenryck
Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032;
Jie
J
Wu
Department of Neurobiology, Stanford University School of Medicine, Stanford, CA 94305;
Steven A
SA
Sloan
Department of Neurobiology, Stanford University School of Medicine, Stanford, CA 94305;
Ye
Y
Zhang
The Vivian L. Smith Department of Neurosurgery, University of Texas Medical School at Houston, Houston, TX 77057; and Center for Stem Cell and Regenerative Medicine, University of Texas Brown Institute of Molecular Medicine, Houston, TX 77057.
Kenian
K
Chen
The Vivian L. Smith Department of Neurosurgery, University of Texas Medical School at Houston, Houston, TX 77057; and Center for Stem Cell and Regenerative Medicine, University of Texas Brown Institute of Molecular Medicine, Houston, TX 77057.
Jia Qian
JQ
Wu
Department of Neurobiology, Stanford University School of Medicine, Stanford, CA 94305; cz2294@columbia.edu barres@stanford.edu.
Ben A
BA
Barres
Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032; cz2294@columbia.edu barres@stanford.edu.
Chaolin
C
Zhang
D017398:Alternative Splicing / Q000235:genetics*; D000818:Animals; D001483:Base Sequence; D001921:Brain / Q000378:metabolism*; D002540:Cerebral Cortex / Q000378:metabolism; D002843:Chromatin / Q000378:metabolism*; D017124:Conserved Sequence / Q000235:genetics*; D019143:Evolution, Molecular; D005091:Exons / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D008322:Mammals / Q000235:genetics*; D008810:Mice, Inbred C57BL; D008969:Molecular Sequence Data; D059365:Nonsense Mediated mRNA Decay / Q000235:genetics*; D016366:Open Reading Frames / Q000235:genetics; D009928:Organ Specificity / Q000235:genetics; D012641:Selection, Genetic; D059467:Transcriptome / Q000235:genetics
D002843:Chromatin
RNA-Seq; brain transcriptome; chromatin regulator; new alternative exon; nonsense-mediated decay