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Nova regulates brain-specific splicing to shape the synapse
Abstract
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.
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“These data reveal the largest program of neural-regulated AS events defined to date, and that this program is associated with a broader range of functional processes and pathways linked to nervous system biology than previously detected (Boutz et al., 2007; Fagnani et al., 2007; Ule et al., 2005).”
From A Highly Conserved Program of Neuronal Microexons Is Misregulated in Autistic Brains (2014) · cites this paper as Ule et al., 2005
Citations
Cites
Finishing the euchromatic sequence of the human genome
International Human Genome Sequencing Consortium (2004) · Nature · doi:10.1038/nature03001 · Cited by 4,971
From molecular to modular cell biology.
Hartwell, L. H., Hopfield, J. J., Leibler, S., & Murray, A. W. (1999) · Nature · doi:10.1038/35011540 · Cited by 3,632
Light-Directed, Spatially Addressable Parallel Chemical Synthesis
Fodor, S. P. A., Read, J., Pirrung, M. C., Stryer, L., Lu, A. T., & Solas, D. W. (1991) · Science · doi:10.1126/science.1990438 · Cited by 2,697
Transcriptional regulatory code of a eukaryotic genome
Harbison, C. T., Gordon, D. B., Lee, T. I., Rinaldi, N. J., MacIsaac, K. D., Danford, T., Hannett, N. M., Tagne, J., Reynolds, D. B., Yoo, J. Y., et al. (2004) · Nature · doi:10.1038/nature02800 · Cited by 2,135
Metaplasticity: the plasticity of synaptic plasticity
Abraham, W. C., & Bear, M. F. (1996) · Trends in Neurosciences · doi:10.1016/s0166-2236(96)80018-x · Cited by 1,833
Genome-Wide Survey of Human Alternative Pre-mRNA Splicing with Exon Junction Microarrays
Johnson, J. M., Castle, J. C., Garrett-Engele, P. W., Kan, Z., Loerch, P., Armour, C. D., Santos, R., Schadt, E. E., Stoughton, R. B., & Shoemaker, D. D. (2003) · Science · doi:10.1126/science.1090100 · Cited by 1,418
Hentze, M. W., & Kühn, L. C. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.16.8175 · Cited by 1,292
GoMiner: a resource for biological interpretation of genomic and proteomic data
Zeebèrg, B. R., Feng, W., Wang, G., Wang, M. D., Fojo, A. T., Sunshine, M., Narasimhan, S., Kane, D. W., Reinhold, W. C., Lababidi, S., et al. (2003) · Genome biology · doi:10.1186/gb-2003-4-4-r28 · Cited by 1,198
Self-citationCLIP Identifies Nova-Regulated RNA Networks in the Brain
Ule, J., Jensen, K. B., Ruggiu, M., Mele, A., Ule, A., & Darnell, R. B. (2003) · Science · doi:10.1126/science.1090095 · Cited by 1,120
Self-citationBrown, V., Jin, P., Ceman, S., Darnell, J. C., O'Donnell, W. T., Tenenbaum, S. A., Jin, X., Feng, Y., Wilkinson, K. D., Keene, J. D., et al. (2001) · Cell · doi:10.1016/s0092-8674(01)00568-2 · Cited by 1,109
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Research works printed but not linked: 1
- Huang, C.S. et al. Long-term potentiation of slow synaptic inhibition induced by coincidence detection of excitation in the CA1 pyramidal neuron requires Nova-2 function. Cell (in the press).
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“For example, YCAY-rich HITS-CLIP clusters were present downstream of the known Nova2 target Grin1 exon 19 (E19; Fig 1b-c(ii))20, in a position previously predicted by the Nova bioinformatic map18 (Supplemental Fig.”
Self-citationMechanisms of alternative splicing regulation: insights from molecular and genomics approaches
Chen, M., & Manley, J. L. (2009) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2777 · Cited by 1,284
MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery
Wang, K., Singh, D., Zeng, Z., Coleman, S. J., Huang, Y., Savich, G. L., He, X., Mieczkowski, P., Grimm, S. A., Perou, C. M., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq622 · Cited by 1,193
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König, J., Zarnack, K., Rot, G., Curk, T., Kayikci, M., Zupan, B., Turner, D. J., Luscombe, N. M., & Ule, J. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1838 · Cited by 1,126
Self-citationThe SR protein family of splicing factors: master regulators of gene expression
Long, J. C., & Cáceres, J. F. (2008) · Biochemical Journal · doi:10.1042/bj20081501 · Cited by 1,125
Alternative Splicing: New Insights from Global Analyses
Blencowe, B. J. (2006) · Cell · doi:10.1016/j.cell.2006.06.023 · Cited by 1,122
Splicing in disease: disruption of the splicing code and the decoding machinery
Wang, G., & Cooper, T. A. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2164 · Cited by 1,077
Context-dependent control of alternative splicing by RNA-binding proteins
Fu, X.-D., & Ares, M. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3778 · Cited by 1,044
Epigenetics in Alternative Pre-mRNA Splicing
Luco, R. F., Alló, M., Schor, I. E., Kornblihtt, A. R., & Misteli, T. (2011) · Cell · doi:10.1016/j.cell.2010.11.056 · Cited by 827
Lim, J., Hao, T., Shaw, C., Patel, A. J., Szabó, G., Rual, J.-F., Fisk, C. J., Li, N., Smolyar, A., Hill, D. E., et al. (2006) · Cell · doi:10.1016/j.cell.2006.03.032 · Cited by 789
A Highly Conserved Program of Neuronal Microexons Is Misregulated in Autistic Brains
Irimia, M., Weatheritt, R. J., Ellis, J. D., Parikshak, N. N., Gonatopoulos-Pournatzis, T., Babor, M., Quesnel-Vallières, M., Tapial, J., Raj, B., O’Hanlon, D., et al. (2014) · Cell · doi:10.1016/j.cell.2014.11.035 · Cited by 693
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Kalsotra, A., & Cooper, T. A. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3052 · Cited by 729
Zhang, Z., Lotti, F., Dittmar, K. A., Younis, I., Wan, L., Kasim, M., & Dreyfuss, G. (2008) · Cell · doi:10.1016/j.cell.2008.03.031 · Cited by 610
Hogan, D. J., Riordan, D. P., Gerber, A. P., Herschlag, D., & Brown, P. O. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060255 · Cited by 609
Repeatability of published microarray gene expression analyses
Ioannidis, J. P. A., Allison, D. B., Ball, C. A., Coulibaly, I., Cui, X., Culhane, A. C., Falchi, M., Furlanello, C., Game, L., Jurman, G., et al. (2009) · Nature Genetics · doi:10.1038/ng.295 · Cited by 551
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Warzecha, C. C., Sato, T. K., Nabet, B., Hogenesch, J. B., & Carstens, R. P. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.01.025 · Cited by 580
Boutz, P. L., Stoilov, P., Li, Q., Lin, C.-H., Chawla, G., Ostrow, K., Shiue, L., Ares, M., & Black, D. L. (2007) · Genes & Development · doi:10.1101/gad.1558107 · Cited by 577
Millan, M. J. (2006) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2005.11.006 · Cited by 569
Ni, J. Z., Grate, L. R., Donohue, J. P., Preston, C. G., Nobida, N., O’Brien, G. S., Shiue, L., Clark, T. A., Blume, J. E., & Ares, M. (2007) · Genes & Development · doi:10.1101/gad.1525507 · Cited by 551
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Ule, J., Stefani, G., Mele, A., Ruggiu, M., Wang, X., Taneri, B., Gaasterland, T., Blencowe, B. J., & Darnell, R. B. (2006) · Nature · doi:10.1038/nature05304 · Cited by 528
Self-citationA postnatal switch of CELF and MBNL proteins reprograms alternative splicing in the developing heart
Kalsotra, A., Xiao, X., Ward, A. J., Castle, J. C., Johnson, J. M., Burge, C. B., & Cooper, T. A. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0809045105 · Cited by 508
Raj, B., & Blencowe, B. J. (2015) · Neuron · doi:10.1016/j.neuron.2015.05.004 · Cited by 475
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Ellis, J. D., Barrios-Rodiles, M., Çolak, R., Irimia, M., Kim, T., Calarco, J. A., Wang, X., Pan, Q., O'Hanlon, D., Kim, P. M., et al. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.05.037 · Cited by 431
Tapial, J., Ha, K., Sterne-Weiler, T., Gohr, A., Braunschweig, U., Hermoso, A., Quesnel-Vallières, M., Permanyer, J., Sodaei, R., Márquez, Y., et al. (2017) · Genome Research · doi:10.1101/gr.220962.117 · Cited by 441
Ward, A. J., & Cooper, T. A. (2009) · The Journal of Pathology · doi:10.1002/path.2649 · Cited by 436
Elia, J., Glessner, J. T., Wang, K., Takahashi, N., Shtir, C. J., Hadley, D., Sleiman, P. M. A., Zhang, H., Kim, C. E., Robison, R., et al. (2012) · Nature Genetics · doi:10.1038/ng.1013 · Cited by 406
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Weyn-Vanhentenryck, S. M., Mele, A., Yan, Q., Sun, S., Farny, N., Zhang, Z., Xue, C., Herre, M., Silver, P. A., Zhang, M. Q., et al. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.02.005 · Cited by 333
Self-citationBechara, E., Sebestyén, E., Bernardis, I., Eyras, E., & Valcárcel, J. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.11.010 · Cited by 374
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Gardina, P. J., Clark, T. A., Shimada, B., Staples, M. K., Yang, Q., Veitch, J. M., Schweitzer, A. C., Awad, T. A., Sugnet, C. W., Dee, S., et al. (2006) · BMC Genomics · doi:10.1186/1471-2164-7-325 · Cited by 352
Self-citationPradeepa, M. M., Sutherland, H. G. E., Ule, J., Grimes, G. R., & Bickmore, W. A. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002717 · Cited by 365
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Ameur, A., Zaghlool, A., Halvardson, J., Wetterbom, A., Gyllensten, U., Cavelier, L., & Feuk, L. (2011) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2143 · Cited by 323
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Spellman, R., Llorian, M., & Smith, C. W. J. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.06.016 · Cited by 313
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Self-citationUnderstanding splicing regulation through RNA splicing maps
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Xu, J., Li, C., Li, Y.-S., Lv, J., Ma, Y., Shao, T.-T., Xu, L., Wang, Y.-Y., Du, L., Zhang, Y. P., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq832 · Cited by 280
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Llorian, M., Schwartz, S., Clark, T. A., Hollander, D., Tan, L.-Y., Spellman, R., Gordon, A., Schweitzer, A. C., de la Grange, P., Ast, G., et al. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1881 · Cited by 263
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Venables, J. P., Koh, C., Froehlich, U., Lapointe, E., Couture, S., Inkel, L., Bramard, A., Paquet, É. R., Watier, V., Durand, M., et al. (2008) · Molecular and Cellular Biology · doi:10.1128/mcb.00726-08 · Cited by 158
Huang, C. S., Shi, S.-H., Ule, J., Ruggiu, M., Barker, L. A., Darnell, R. B., Jan, Y. N., & Jan, L. Y. (2005) · Cell · doi:10.1016/j.cell.2005.07.033 · Cited by 157
Self-citationSystems biology of innate immunity
Zak, D. E., & Aderem, A. A. (2008) · Immunological Reviews · doi:10.1111/j.1600-065x.2008.00721.x · Cited by 157
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Ben-Dov, C., Hartmann, B., Lundgren, J., & Valcárcel, J. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.r700033200 · Cited by 151
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Danan-Gotthold, M., Golan‐Gerstl, R., Eisenberg, E., Meir, K., Karni, R., & Levanon, E. Y. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv210 · Cited by 154
Kishore, S., Gruber, A. R., Jedlinski, D., Syed, A. P., Jorjani, H., & Zavolan, M. (2013) · Genome biology · doi:10.1186/gb-2013-14-5-r45 · Cited by 150
Control of neuronal synapse specification by a highly dedicated alternative splicing program
Traunmüller, L., Gomez, A. M., Nguyen, T.-M., & Scheiffele, P. (2016) · Science · doi:10.1126/science.aaf2397 · Cited by 144
Alternative splicing: global insights
Hallegger, M., Llorian, M., & Smith, C. W. J. (2010) · FEBS Journal · doi:10.1111/j.1742-4658.2009.07521.x · Cited by 147
Vanharanta, S., Marney, C. B., Shu, W., Valiente, M., Zou, Y., Mele, A., Darnell, R. B., & Massagué, J. (2014) · eLife · doi:10.7554/elife.02734 · Cited by 146
Self-citationReintroduction of the archaic variant of NOVA1 in cortical organoids alters neurodevelopment
Trujillo, C. A., Rice, E. S., Schaefer, N. K., Chaim, I. A., Wheeler, E. C., Madrigal, A. A., Buchanan, J., Preißl, S., Wang, A., Negraes, P. D., et al. (2021) · Science · doi:10.1126/science.aax2537 · Cited by 148
OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds
Wu, J., Anczuków, O., Krainer, A. R., Zhang, M. Q., & Zhang, C. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt216 · Cited by 123
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Jangi, M., & Sharp, P. A. (2014) · Cell · doi:10.1016/j.cell.2014.09.054 · Cited by 141
Anvar, S. Y., Allard, G., Tseng, E., Sheynkman, G. M., de Klerk, E., Vermaat, M., Yin, R. H., Johansson, H. E., Ariyurek, Y., den Dunnen, J. T., et al. (2018) · Genome Biology · doi:10.1186/s13059-018-1418-0 · Cited by 118
Warzecha, C. C., & Carstens, R. P. (2012) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2012.04.003 · Cited by 144
Metadata
- Authors
- Ule, J., Ule, A., Spencer, J., Williams, A., Hu, J.-S., Cline, M., Wang, H., Clark, T., Fraser, C., Ruggiu, M., Zeeberg, B. R., Kane, D., Weinstein, J. N., Blume, J., & Darnell, R. B.
- Affiliations
- Howard Hughes Medical Institute (US)
- University of Amsterdam (NL)
- Affymetrix (United States) (US)
- SRA International (United States) (US)
- National Institutes of Health (US)
- Corresponding author
- Darnell, Robert B
- ORCID
- Venue
- Nature Genetics
- Published
- 2005-07-24
- Volume
- 37
- Issue
- 8
- Pages
- 844-852
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- OpenAlex
- W2118823143
- Cited by
- 509
- References
- 49
- Citations by year
- 2026: 7 · 2025: 16 · 2024: 16 · 2023: 9 · 2022: 12 · 2021: 14 · 2020: 20 · 2019: 13 · 2018: 17 · 2017: 18 · 2016: 19 · 2015: 22 · 2014: 30 · 2013: 25 · 2012: 38
- FWCI
- 17.19
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Neuroscience and Neuropharmacology Research
- Keywords
- alternative splicing, synapses, neocortex, exon skipping, protein-protein interaction network, axon guidance, neurotransmitter receptors, cation channels, adhesion proteins, scaffold proteins, tissue-specific splicing
- MeSH terms
- Neuro-Oncological Ventral Antigen, Animals, Antigens, Neoplasm, Nerve Tissue Proteins, Synapses, RNA-Binding Proteins, Alternative Splicing, Mice, Knockout, Neocortex, Oligonucleotide Array Sequence Analysis, Mice
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