Barbosa‐Morais,, N. L., Irimia,, M., Pan,, Q., Xiong,, H. Y., Gueroussov,, S., Lee,, L. J., … Blencowe,, B. J. (2012). The evolutionary landscape of alternative splicing in vertebrate species. Science, 338(6114), 1587–1593.
Barnes,, A. P., & Polleux,, F. (2009). Establishment of axon‐dendrite polarity in developing neurons. Annual Review of Neuroscience, 32, 347–381.
Black,, D. L. (2003). Mechanisms of alternative pre‐messenger RNA splicing. Annual Review of Biochemistry, 72, 291–336.
Blencowe,, B. J. (2017). The relationship between alternative splicing and proteomic complexity. Trends in Biochemical Sciences, 42(6), 407–408.
Bray,, N. L., Pimentel,, H., Melsted,, P., & Pachter,, L. (2016). Near‐optimal probabilistic RNA‐seq quantification. Nature Biotechnology, 34(5), 525–527.
Buckanovich,, R. J., & Darnell,, R. B. (1997). The neuronal RNA binding protein Nova‐1 recognizes specific RNA targets in vitro and in vivo. Molecular and Cellular Biology, 17(6), 3194–3201.
Cáceres,, A., Ye,, B., & Dotti,, C. G. (2012). Neuronal polarity: Demarcation, growth and commitment. Current Opinion in Cell Biology, 24(4), 547–553.
Chédotal,, A. (2019). Roles of axon guidance molecules in neuronal wiring in the developing spinal cord. Nature Reviews. Neuroscience, 20(7), 380–396.
Chen,, L., Liu,, Z., Zhou,, B., Wei,, C., Zhou,, Y., Rosenfeld,, M. G., … Jin,, Y. (2016). CELF RNA binding proteins promote axon regeneration in C. elegans and mammals through alternative splicing of Syntaxins. eLife, 5, e16072. https://doi.org/10.7554/eLife16072
Chen,, L., & Zheng,, S. (2009). Studying alternative splicing regulatory networks through partial correlation analysis. Genome Biology, 10(1), R3.
Cheng,, P.‐L., & Poo,, M.‐M. (2012). Early events in axon/dendrite polarization. Annual Review of Neuroscience, 35, 181–201.
Cirulli,, V., & Yebra,, M. (2007). Netrins: Beyond the brain. Nature Reviews. Molecular Cell Biology, 8(4), 296–306.
Colak,, D., Ji,, S.‐J., Porse,, B. T., & Jaffrey,, S. R. (2013). Regulation of axon guidance by compartmentalized nonsense‐mediated mRNA decay. Cell, 153(6), 1252–1265.
Curcio,, M., & Bradke,, F. (2018). Axon regeneration in the central nervous system: Facing the challenges from the inside. Annual Review of Cell and Developmental Biology, 34, 495–521.
Damianov,, A., Ying,, Y., Lin,, C.‐H., Lee,, J.‐A., Tran,, D., Vashisht,, A. A., … Black,, D. L. (2016). Rbfox proteins regulate splicing as part of a large multiprotein complex LASR. Cell, 165(3), 606–619.
Dasgupta,, T., & Ladd,, A. N. (2012). The importance of CELF control: Molecular and biological roles of the CUG‐BP, Elav‐like family of RNA‐binding proteins. Wiley Interdisciplinary Reviews. RNA, 3(1), 104–121.
Dominguez,, D., Freese,, P., Alexis,, M. S., Su,, A., Hochman,, M., Palden,, T., … Burge,, C. B. (2018). Sequence, structure, and context preferences of human RNA binding proteins. Molecular Cell, 70(5), 854–867.e9.
Fazeli,, A., Dickinson,, S. L., Hermiston,, M. L., Tighe,, R. V., Steen,, R. G., Small,, C. G., … Weinberg,, R. A. (1997). Phenotype of mice lacking functional deleted in colorectal cancer (Dec) gene. Nature, 386(6627), 796–804.
Feng,, H., Bao,, S., Rahman,, M. A., Weyn‐Vanhentenryck,, S. M., Khan,, A., Wong,, J., … Zhang,, C. (2019). Modeling RNA‐binding protein specificity in vivo by precisely registering protein‐RNA crosslink sites. Molecular Cell, 74(6), 1189–1204.e6.
Fu,, X.‐D., & Ares,, M., Jr. (2014). Context‐dependent control of alternative splicing by RNA‐binding proteins. Nature Reviews. Genetics, 15(10), 689–701.
Gehman,, L. T., Meera,, P., Stoilov,, P., Shiue,, L., O`Brien,, J. E., Meisler,, M. H., … Black,, D. L. (2012). The splicing regulator Rbfox2 is required for both cerebellar development and mature motor function. Genes %26 Development, 26(5), 445–460.
Goslin,, K., & Banker,, G. (1989). Experimental observations on the development of polarity by hippocampal neurons in culture. The Journal of Cell Biology, 108(4), 1507–1516.
Hammock,, E. A. D., & Levitt,, P. (2011). Developmental expression mapping of a gene implicated in multiple neurodevelopmental disorders, A2bp1 (Fox1). Developmental Neuroscience, 33(1), 64–74.
Hatanaka,, Y., & Yamauchi,, K. (2013). Excitatory cortical neurons with multipolar shape establish neuronal polarity by forming a tangentially oriented axon in the intermediate zone. Cerebral Cortex, 23(1), 105–113.
Hattori,, D., Chen,, Y., Matthews,, B. J., Salwinski,, L., Sabatti,, C., Grueber,, W. B., & Zipursky,, S. L. (2009). Robust discrimination between self and non‐self neurites requires thousands of Dscam1 isoforms. Nature, 461(7264), 644–648.
Holmberg,, J., Clarke,, D. L., & Frisén,, J. (2000). Regulation of repulsion versus adhesion by different splice forms of an Eph receptor. Nature, 408(6809), 203–206.
Huang,, C. S., Shi,, S.‐H., Ule,, J., Ruggiu,, M., Barker,, L. A., Darnell,, R. B., … Jan,, L. Y. (2005). Common molecular pathways mediate long‐term potentiation of synaptic excitation and slow synaptic inhibition. Cell, 123(1), 105–118.
Jacko,, M., Weyn‐Vanhentenryck,, S. M., Smerdon,, J. W., Yan,, R., Feng,, H., Williams,, D. J., … Zhang,, C. (2018). Rbfox splicing factors promote neuronal maturation and axon initial segment assembly. Neuron, 97(4), 853–868.e6.
Johnson,, V., Junge,, H. J., & Chen,, Z. (2019). Temporal regulation of axonal repulsion by alternative splicing of a conserved microexon in mammalian Robo1 and Robo2. eLife, 8, e46042. https://doi.org/10.7554/eLife46042
Kapitein,, L. C., & Hoogenraad,, C. C. (2015). Building the neuronal microtubule cytoskeleton. Neuron, 87(3), 492–506.
Keeling,, S. L., Gad,, J. M., & Cooper,, H. M. (1997). Mouse Neogenin, a DCC‐like molecule, has four splice variants and is expressed widely in the adult mouse and during embryogenesis. Oncogene, 15, 691–700. https://doi.org/10.1038/sj.onc.1201225
Kevenaar,, J. T., & Hoogenraad,, C. C. (2015). The axonal cytoskeleton: From organization to function. Frontiers in Molecular Neuroscience, 8, 44.
Kim,, K. K., Adelstein,, R. S., & Kawamoto,, S. (2009). Identification of neuronal nuclei (NeuN) as Fox‐3, a new member of the Fox‐1 gene family of splicing factors. The Journal of Biological Chemistry, 284(45), 31052–31061.
Kubo,, Y., Baba,, K., Toriyama,, M., Minegishi,, T., Sugiura,, T., Kozawa,, S., … Inagaki,, N. (2015). Shootin1‐cortactin interaction mediates signal‐force transduction for axon outgrowth. The Journal of Cell Biology, 210(4), 663–676.
Kuroyanagi,, H., Watanabe,, Y., & Hagiwara,, M. (2013). CELF family RNA‐binding protein UNC‐75 regulates two sets of mutually exclusive exons of the unc‐32 gene in neuron‐specific manners in Caenorhabditis elegans. PLoS Genetics, 9(2), e1003337.
Lee,, F. C. Y., & Ule,, J. (2018). Advances in CLIP technologies for studies of protein‐RNA interactions. Molecular Cell, 69(3), 354–369.
Lee,, Y., & Rio,, D. C. (2015). Mechanisms and regulation of alternative pre‐mRNA splicing. Annual Review of Biochemistry, 84, 291–323.
Leggere,, J. C., Saito,, Y., Darnell,, R. B., Tessier‐Lavigne,, M., Junge,, H. J., & Chen,, Z. (2016). NOVA regulates dcc alternative splicing during neuronal migration and axon guidance in the spinal cord. eLife, 5, e14264. https://doi.org/10.7554/eLife14264
Li,, B., & Dewey,, C. N. (2011). RSEM: Accurate transcript quantification from RNA‐Seq data with or without a reference genome. BMC Bioinformatics, 12, 323.
Little,, M., Rumballe,, B., Georgas,, K., Yamada,, T., & Teasdale,, R. D. (2002). Conserved modularity and potential for alternate splicing in mouse and human slit genes. The International Journal of Developmental Biology, 46(4), 385–391.
Louie,, A. L., Aigner,, S., Bergalet,, J., Zhou,, B., & Su,, A. (2018). A large‐scale binding and functional map of human RNA binding proteins. bioRxiv. Retrieved from https://www.biorxiv.org/content/10.1101/179648v2.abstract
Mahar,, M., & Cavalli,, V. (2018). Intrinsic mechanisms of neuronal axon regeneration. Nature Reviews. Neuroscience, 19(6), 323–337.
Mar,, F. M., Bonni,, A., & Sousa,, M. M. (2014). Cell intrinsic control of axon regeneration. EMBO Reports, 15(3), 254–263.
Markovtsov,, V., Nikolic,, J. M., Goldman,, J. A., Turck,, C. W., Chou,, M. Y., & Black,, D. L. (2000). Cooperative assembly of an hnRNP complex induced by a tissue‐specific homolog of polypyrimidine tract binding protein. Molecular and Cellular Biology, 20(20), 7463–7479.
Melamud,, E., & Moult,, J. (2009). Stochastic noise in splicing machinery. Nucleic Acids Research, 37(14), 4873–4886.
Merkin,, J., Russell,, C., Chen,, P., & Burge,, C. B. (2012). Evolutionary dynamics of gene and isoform regulation in mammalian tissues. Science, 338(6114), 1593–1599.
Miura,, S. K., Martins,, A., Zhang,, K. X., Graveley,, B. R., & Zipursky,, S. L. (2013). Probabilistic splicing of Dscam1 establishes identity at the level of single neurons. Cell, 155(5), 1166–1177.
Namba,, T., Funahashi,, Y., Nakamuta,, S., Xu,, C., Takano,, T., & Kaibuchi,, K. (2015). Extracellular and intracellular signaling for neuronal polarity. Physiological Reviews, 95(3), 995–1024.
Nelson,, A. D., & Jenkins,, P. M. (2017). Axonal membranes and their domains: Assembly and function of the axon initial segment and node of Ranvier. Frontiers in Cellular Neuroscience, 11, 136.
Norris,, A. D., Gao,, S., Norris,, M. L., Ray,, D., Ramani,, A. K., Fraser,, A. G., … Calarco,, J. A. (2014). A pair of RNA‐binding proteins controls networks of splicing events contributing to specialization of neural cell types. Molecular Cell, 54(6), 946–959.
Otsuka,, N., Tsuritani,, K., Sakurai,, T., Kato,, K., Matoba,, R., Itoh,, J., … Yoneda,, Y. (2009). Transcriptional induction and translational inhibition of Arc and Cugbp2 in mice hippocampus after transient global ischemia under normothermic condition. Brain Research, 1287, 136–145.
Pan,, Q., Shai,, O., Lee,, L. J., Frey,, B. J., & Blencowe,, B. J. (2008). Deep surveying of alternative splicing complexity in the human transcriptome by high‐throughput sequencing. Nature Genetics, 40(12), 1413–1415.
Patro,, R., Duggal,, G., Love,, M. I., Irizarry,, R. A., & Kingsford,, C. (2017). Salmon provides fast and bias‐aware quantification of transcript expression. Nature Methods, 14(4), 417–419.
Pickrell,, J. K., Pai,, A. A., Gilad,, Y., & Pritchard,, J. K. (2010). Noisy splicing drives mRNA isoform diversity in human cells. PLoS Genetics, 6(12), e1001236.
Pierceall,, W. E., Reale,, M. A., Candia,, A. F., Wright,, C. V. E., Cho,, K. R., & Fearon,, E. R. (1994). Expression of a homologue of the deleted in colorectal cancer (DCC) gene in the nervous system of developing Xenopus embryos. Developmental Biology, 166, 654–665. https://doi.org/10.1006/dbio.1994.1345
Polydorides,, A. D., Okano,, H. J., Yang,, Y. Y., Stefani,, G., & Darnell,, R. B. (2000). A brain‐enriched polypyrimidine tract‐binding protein antagonizes the ability of Nova to regulate neuron‐specific alternative splicing. Proceedings of the National Academy of Sciences of the United States of America, 97(12), 6350–6355.
Raj,, B., & Blencowe,, B. J. (2015). Alternative splicing in the mammalian nervous system: Recent insights into mechanisms and functional roles. Neuron, 87(1), 14–27.
Ruggiu,, M., Herbst,, R., Kim,, N., Jevsek,, M., Fak,, J. J., Mann,, M. A., … Darnell,, R. B. (2009). Rescuing Z agrin splicing in Nova mice restores synapse formation and unmasks a physiologic defect in motor neuron firing. Proceedings of the National Academy of Sciences, 106, 3513–3518. https://doi.org/10.1073/pnas.0813112106
Russell,, S. A., & Bashaw,, G. J. (2018). Axon guidance pathways and the control of gene expression. Developmental Dynamics: An Official Publication of the American Association of Anatomists, 247(4), 571–580.
Saito,, Y., Miranda‐Rottmann,, S., Ruggiu,, M., Park,, C. Y., Fak,, J. J., Zhong,, R., … Darnell,, R. B. (2016). NOVA2‐mediated RNA regulation is required for axonal pathfinding during development. eLife, 5, e14371. https://doi.org/10.7554/eLife14371
Schmucker,, D., Clemens,, J. C., Shu,, H., Worby,, C. A., Xiao,, J., Muda,, M., … Zipursky,, S. L. (2000). Drosophila Dscam is an axon guidance receptor exhibiting extraordinary molecular diversity. Cell, 101(6), 671–684.
Seiradake,, E., Jones,, E. Y., & Klein,, R. (2016). Structural perspectives on axon guidance. Annual Review of Cell and Developmental Biology, 32, 577–608.
Shalem,, O., Sanjana,, N. E., & Zhang,, F. (2015). High‐throughput functional genomics using CRISPR‐Cas9. Nature Reviews. Genetics, 16(5), 299–311.
Sorek,, R., Shamir,, R., & Ast,, G. (2004). How prevalent is functional alternative splicing in the human genome? Trends in Genetics: TIG, 20(2), 68–71.
Szu‐Yu Ho,, T., & Rasband,, M. N. (2011). Maintenance of neuronal polarity. Developmental Neurobiology, 71(6), 474–482.
Tamagnone,, L., Artigiani,, S., Chen,, H., He,, Z., Ming,, G. I., Song,, H., … Comoglio,, P. M. (1999). Plexins are a large family of receptors for transmembrane, secreted, and GPI‐anchored semaphorins in vertebrates. Cell, 99(1), 71–80.
Tissir,, F., & Goffinet,, A. M. (2013). Shaping the nervous system: Role of the core planar cell polarity genes. Nature Reviews. Neuroscience, 14(8), 525–535.
Toriyama,, M., Shimada,, T., Kim,, K. B., Mitsuba,, M., Nomura,, E., Katsuta,, K., … Inagaki,, N. (2006). Shootin1: A protein involved in the organization of an asymmetric signal for neuronal polarization. The Journal of Cell Biology, 175(1), 147–157.
Trapnell,, C., Roberts,, A., Goff,, L., Pertea,, G., Kim,, D., Kelley,, D. R., … Pachter,, L. (2012). Differential gene and transcript expression analysis of RNA‐seq experiments with TopHat and cufflinks. Nature Protocols, 7(3), 562–578.
Tress,, M. L., Abascal,, F., & Valencia,, A. (2017). Alternative splicing may not be the key to proteome complexity. Trends in Biochemical Sciences, 42(2), 98–110.
Ule,, J., Hwang,, H.‐W., & Darnell,, R. B. (2018). The future of cross‐linking and immunoprecipitation (CLIP). Cold Spring Harbor Perspectives in Biology, 10(8). https://doi.org/10.1101/cshperspect.a032243
Vuong,, C. K., Black,, D. L., & Zheng,, S. (2016). The neurogenetics of alternative splicing. Nature Reviews. Neuroscience, 17(5), 265–281.
Vuong,, J. K., Lin,, C.‐H., Zhang,, M., Chen,, L., Black,, D. L., & Zheng,, S. (2016). PTBP1 and PTBP2 serve both specific and redundant functions in neuronal pre‐mRNA splicing. Cell Reports, 17(10), 2766–2775.
Wang,, E. T., Sandberg,, R., Luo,, S., Khrebtukova,, I., Zhang,, L., Mayr,, C., … Burge,, C. B. (2008). Alternative isoform regulation in human tissue transcriptomes. Nature, 456(7221), 470–476.
Weyn‐Vanhentenryck,, S. M., Feng,, H., Ustianenko,, D., Duffié,, R., Yan,, Q., Jacko,, M., … Zhang,, C. (2018). Precise temporal regulation of alternative splicing during neural development. Nature Communications, 9(1), 2189.
Weyn‐Vanhentenryck,, S. M., Mele,, A., Yan,, Q., Sun,, S., Farny,, N., Zhang,, Z., … Zhang,, C. (2014). HITS‐CLIP and integrative modeling define the Rbfox splicing‐regulatory network linked to brain development and autism. Cell Reports, 6(6), 1139–1152.
Wheeler,, E. C., Van Nostrand,, E. L., & Yeo,, G. W. (2018). Advances and challenges in the detection of transcriptome‐wide protein‐RNA interactions. Wiley Interdisciplinary Reviews. RNA, 9(1), e1436. https://doi.org/10.1002/wrna.1436
Wojtowicz,, W. M., Flanagan,, J. J., Millard,, S. S., Zipursky,, S. L., & Clemens,, J. C. (2004). Alternative splicing of drosophila Dscam generates axon guidance receptors that exhibit isoform‐specific homophilic binding. Cell, 118(5), 619–633.
Xiong,, X., Chen,, M., Lim,, W. A., Zhao,, D., & Qi,, L. S. (2016). CRISPR/Cas9 for human genome engineering and disease research. Annual Review of Genomics and Human Genetics, 17, 131–154.
Xu,, K., Wu,, Z., Renier,, N., Antipenko,, A., Tzvetkova‐Robev,, D., Xu,, Y., … Nikolov,, D. B. (2014). Neural migration. Structures of netrin‐1 bound to two receptors provide insight into its axon guidance mechanism. Science, 344(6189), 1275–1279.
Xu,, K., Zhong,, G., & Zhuang,, X. (2013). Actin, spectrin, and associated proteins form a periodic cytoskeletal structure in axons. Science, 339(6118), 452–456.
Yano,, M., Hayakawa‐Yano,, Y., Mele,, A., & Darnell,, R. B. (2010). Nova2 regulates neuronal migration through an RNA switch in disabled‐1 signaling. Neuron, 66(6), 848–858.
Yap,, K., Xiao,, Y., Friedman,, B. A., Je,, H. S., & Makeyev,, E. V. (2016). Polarizing the neuron through sustained co‐expression of alternatively spliced isoforms. Cell Reports, 15(6), 1316–1328.
Yazdani,, U., & Terman,, J. R. (2006). The semaphorins. Genome Biology, 7(3), 211.
Ypsilanti,, A. R., Zagar,, Y., & Chédotal,, A. (2010). Moving away from the midline: New developments for slit and Robo. Development, 137(12), 1939–1952.
Zhang,, J., Kuo,, C.‐C. J., & Chen,, L. (2015). WemIQ: An accurate and robust isoform quantification method for RNA‐seq data. Bioinformatics, 31(6), 878–885.
Zhang,, M., Ergin,, V., Lin,, L., Stork,, C., Chen,, L., & Zheng,, S. (2019). Axonogenesis is coordinated by neuron‐specific alternative splicing programming and splicing regulator PTBP2. Neuron, 101(4), 690–706.e10.
Zheng,, S. (2016a). Alternative splicing and nonsense‐mediated mRNA decay enforce neural specific gene expression. International Journal of Developmental Neuroscience, 55, 102–108. https://doi.org/10.1016/j.ijdevneu.2016.03.003
Zheng,, S. (2016b). IRAS: High‐throughput identification of novel alternative splicing regulators. Methods in Enzymology, 572, 269–289.
Zheng,, S., & Black,, D. L. (2013). Alternative pre‐mRNA splicing in neurons: Growing up and extending its reach. Trends in Genetics: TIG, 29(8), 442–448.
Zheng,, S., & Chen,, L. (2009). A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level. Nucleic Acids Research, 37(10), e75.
Zheng,, S., Gray,, E. E., Chawla,, G., Porse,, B. T., O`Dell,, T. J., & Black,, D. L. (2012). PSD‐95 is post‐transcriptionally repressed during early neural development by PTBP1 and PTBP2. Nature Neuroscience, 15(3), 381–388.
Zollinger,, D. R., Baalman,, K. L., & Rasband,, M. N. (2015). The ins and outs of polarized axonal domains. Annual Review of Cell and Developmental Biology, 31, 647–667.