An RNA map predicting Nova-dependent splicing regulation

Hallikas, O. et al. Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity. Cell 124, 47–59 (2006)

Wasserman, W. W. & Sandelin, A. Applied bioinformatics for the identification of regulatory elements. Nature Rev. Genet. 5, 276–287 (2004)

Fairbrother, W. G., Yeh, R. F., Sharp, P. A. & Burge, C. B. Predictive identification of exonic splicing enhancers in human genes. Science 297, 1007–1013 (2002)

Hui, J. et al. Intronic CA-repeat and CA-rich elements: a new class of regulators of mammalian alternative splicing. EMBO J. 24, 1988–1998 (2005)

Liu, H. X., Zhang, M. & Krainer, A. R. Identification of functional exonic splicing enhancer motifs recognized by individual SR proteins. Genes Dev. 12, 1998–2012 (1998)

Wang, Z. et al. Systematic identification and analysis of exonic splicing silencers. Cell 119, 831–845 (2004)

Yeo, G. W., Van Nostrand, E., Holste, D., Poggio, T. & Burge, C. B. Identification and analysis of alternative splicing events conserved in human and mouse. Proc. Natl Acad. Sci. USA 102, 2850–2855 (2005)

Goren, A. et al. Comparative analysis identifies exonic splicing regulatory sequences—The complex definition of enhancers and silencers. Mol. Cell 22, 769–781 (2006)

Ryder, S. P., Frater, L. A., Abramovitz, D. L., Goodwin, E. B. & Williamson, J. R. RNA target specificity of the STAR/GSG domain post-transcriptional regulatory protein GLD-1. Nature Struct. Mol. Biol. 11, 20–28 (2004)

Han, K., Yeo, G., An, P., Burge, C. B. & Grabowski, P. J. A combinatorial code for splicing silencing: UAGG and GGGG motifs. PLoS Biol. 3, e158 (2005)

Ule, J. & Darnell, R. B. RNA binding proteins and the regulation of neuronal synaptic plasticity. Curr. Opin. Neurobiol. 16, 102–110 (2006)

Licatalosi, D. D. & Darnell, R. B. Splicing regulation in neurologic disease. Neuron 52, (1)93–101 (2006)

Buckanovich, R. J., Yang, Y. Y. & Darnell, R. B. The onconeural antigen Nova-1 is a neuron-specific RNA-binding protein, the activity of which is inhibited by paraneoplastic antibodies. J. Neurosci. 16, 1114–1122 (1996)

Jensen, K. B. et al. Nova-1 regulates neuron-specific alternative splicing and is essential for neuronal viability. Neuron 25, 359–371 (2000)

Yang, Y. Y., Yin, G. L. & Darnell, R. B. The neuronal RNA-binding protein Nova-2 is implicated as the autoantigen targeted in POMA patients with dementia. Proc. Natl Acad. Sci. USA 95, 13254–13259 (1998)

Buckanovich, R. J. & Darnell, R. B. The neuronal RNA binding protein Nova-1 recognizes specific RNA targets in vitro and in vivo.. Mol. Cell. Biol. 17, 3194–3201 (1997)

Jensen, K. B., Musunuru, K., Lewis, H. A., Burley, S. K. & Darnell, R. B. The tetranucleotide UCAY directs the specific recognition of RNA by the Nova K-homology 3 domain. Proc. Natl Acad. Sci. USA 97, 5740–5745 (2000)

Lewis, H. A. et al. Sequence-specific RNA binding by a Nova KH domain: implications for paraneoplastic disease and the fragile X syndrome. Cell 100, 323–332 (2000)

Dredge, B. K. & Darnell, R. B. Nova regulates GABAA receptor γ2 alternative splicing via a distal downstream UCAU-rich intronic splicing enhancer. Mol. Cell. Biol. 23, 4687–4700 (2003)

Dredge, B. K., Stefani, G., Engelhard, C. C. & Darnell, R. B. Nova autoregulation reveals dual functions in neuronal splicing. EMBO J. 24, 1608–1620 (2005)

Ule, J. et al. CLIP identifies Nova-regulated RNA networks in the brain. Science 302, 1212–1215 (2003)

Ule, J. et al. Nova regulates brain-specific splicing to shape the synapse. Nature Genet. 37, 844–852 (2005)

Michaud, S. & Reed, R. An ATP-independent complex commits pre-mRNA to the mammalian spliceosome assembly pathway. Genes Dev. 5, 2534–2546 (1991)

Bennett, M., Michaud, S., Kingston, J. & Reed, R. Protein components specifically associated with prespliceosome and spliceosome complexes. Genes Dev. 6, 1986–2000 (1992)

Sharma, S., Falick, A. M. & Black, D. L. Polypyrimidine tract binding protein blocks the 5′ splice site-dependent assembly of U2AF and the prespliceosomal E complex. Mol. Cell 19, 485–496 (2005)

Tarn, W. Y. & Steitz, J. A. proteins can compensate for the loss of U1 snRNP functions in vitro.. Genes Dev. 8, 2704–2717 (1994)

Barabino, S. M., Blencowe, B. J., Ryder, U., Sproat, B. S. & Lamond, A. I. Targeted snRNP depletion reveals an additional role for mammalian U1 snRNP in spliceosome assembly. Cell 63, 293–302 (1990)

Query, C. C., McCaw, P. S. & Sharp, P. A. A minimal spliceosomal complex A recognizes the branch site and polypyrimidine tract. Mol. Cell. Biol. 17, 2944–2953 (1997)

Buratti, E. & Baralle, F. E. Influence of RNA secondary structure on the pre-mRNA splicing process. Mol. Cell. Biol. 24, 10505–10514 (2004)

Xing, Y. & Lee, C. Alternative splicing and RNA selection pressure—evolutionary consequences for eukaryotic genomes. Nature Rev. Genet. 7, 499–509 (2006)

Coulter, L. R., Landree, M. A. & Cooper, T. A. Identification of a new class of exonic splicing enhancers by in vivo selection. Mol. Cell. Biol. 17, 2143–2150 (1997)

Gersappe, A. & Pintel, D. J. CA- and purine-rich elements form a novel bipartite exon enhancer which governs inclusion of the minute virus of mice NS2-specific exon in both singly and doubly spliced mRNAs. Mol. Cell. Biol. 19, 364–375 (1999)

Polydorides, A. D., Okano, H. J., Yang, Y. Y., Stefani, G. & Darnell, R. B. A brain-enriched polypyrimidine tract-binding protein antagonizes the ability of Nova to regulate neuron-specific alternative splicing. Proc. Natl Acad. Sci. USA 97, 6350–6355 (2000)

Valcarcel, J., Singh, R., Zamore, P. D. & Green, M. R. The protein Sex-lethal antagonizes the splicing factor U2AF to regulate alternative splicing of transformer pre-mRNA. Nature 362, 171–175 (1993)

Del Gatto-Konczak, F., Olive, M., Gesnel, M. C. & Breathnach, R. hnRNP A1 recruited to an exon in vivo can function as an exon splicing silencer. Mol. Cell. Biol. 19, 251–260 (1999)

Zhu, J., Mayeda, A. & Krainer, A. R. Exon identity established through differential antagonism between exonic splicing silencer-bound hnRNP A1 and enhancer-bound SR proteins. Mol. Cell 8, 1351–1361 (2001)

Izquierdo, J. M. et al. Regulation of Fas alternative splicing by antagonistic effects of TIA-1 and PTB on exon definition. Mol. Cell 19, 475–484 (2005)

Chou, M. Y., Rooke, N., Turck, C. W. & Black, D. L. hnRNP H is a component of a splicing enhancer complex that activates a c-Src alternative exon in neuronal cells. Mol. Cell. Biol. 19, 69–77 (1999)

Underwood, J. G., Boutz, P. L., Dougherty, J. D., Stoilov, P. & Black, D. L. Homologues of the Caenorhabditis elegans Fox-1 protein are neuronal splicing regulators in mammals. Mol. Cell. Biol. 25, 10005–10016 (2005)

Carlo, T., Sterner, D. A. & Berget, S. M. An intron splicing enhancer containing a G-rich repeat facilitates inclusion of a vertebrate micro-exon. RNA 2, 342–353 (1996)

Lewis, H. A. et al. Crystal structures of Nova-1 and Nova-2 K-homology RNA-binding domains. Struct. Fold. Des. 7, 191–203 (1999)

Chou, M. Y., Underwood, J. G., Nikolic, J., Luu, M. H. & Black, D. L. Multisite RNA binding and release of polypyrimidine tract binding protein during the regulation of c-Src neural-specific splicing. Mol. Cell 5, 949–957 (2000)

Martinez-Contreras, R. et al. Intronic binding sites for hnRNP A/B and hnRNP F/H proteins stimulate pre-mRNA splicing. PLoS Biol. 4, e21 (2006)

Gee, S. L. et al. Alternative splicing of protein 4.1R exon 16: ordered excision of flanking introns ensures proper splice site choice. Blood 95, 692–699 (2000)

Kessler, O., Jiang, Y. & Chasin, L. A. Order of intron removal during splicing of endogenous adenine phosphoribosyltransferase and dihydrofolate reductase pre-mRNA. Mol. Cell. Biol. 13, 6211–6222 (1993)

Lang, K. M. & Spritz, R. A. In vitro splicing pathways of pre-mRNAs containing multiple intervening sequences?. Mol. Cell. Biol. 7, 3428–3437 (1987)

Tsai, M. J., Ting, A. C., Nordstrom, J. L., Zimmer, W. & O’Malley, B. W. Processing of high molecular weight ovalbumin and ovomucoid precursor RNAs to messenger RNA. Cell 22, 219–230 (1980)

Cook, H. L. et al. Small nuclear RNAs encoded by Herpesvirus saimiri upregulate the expression of genes linked to T cell activation in virally transformed T cells. Curr. Biol. 15, 974–979 (2005)

Beffert, U. et al. Modulation of synaptic plasticity and memory by Reelin involves differential splicing of the lipoprotein receptor Apoer2. Neuron 47, 567–579 (2005)

Huang, C. S. et al. Common molecular pathways mediate long-term potentiation of synaptic excitation and slow synaptic inhibition. Cell 123, 105–118 (2005)