An RNA map predicting Nova-dependent splicing regulation
10.1038/nature05304
Crossref journal-article
Springer Science and Business Media LLC
Nature (297)
Bibliography

Ule, J., Stefani, G., Mele, A., Ruggiu, M., Wang, X., Taneri, B., Gaasterland, T., Blencowe, B. J., & Darnell, R. B. (2006). An RNA map predicting Nova-dependent splicing regulation. Nature, 444(7119), 580–586.

Authors 9
  1. Jernej Ule (first)
  2. Giovanni Stefani (additional)
  3. Aldo Mele (additional)
  4. Matteo Ruggiu (additional)
  5. Xuning Wang (additional)
  6. Bahar Taneri (additional)
  7. Terry Gaasterland (additional)
  8. Benjamin J. Blencowe (additional)
  9. Robert B. Darnell (additional)
References 50 Referenced 454
  1. Hallikas, O. et al. Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity. Cell 124, 47–59 (2006) (10.1016/j.cell.2005.10.042) / Cell by O Hallikas (2006)
  2. Wasserman, W. W. & Sandelin, A. Applied bioinformatics for the identification of regulatory elements. Nature Rev. Genet. 5, 276–287 (2004) (10.1038/nrg1315) / Nature Rev. Genet. by WW Wasserman (2004)
  3. 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) (10.1126/science.1073774) / Science by WG Fairbrother (2002)
  4. 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) (10.1038/sj.emboj.7600677) / EMBO J. by J Hui (2005)
  5. 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) (10.1101/gad.12.13.1998) / Genes Dev. by HX Liu (1998)
  6. Wang, Z. et al. Systematic identification and analysis of exonic splicing silencers. Cell 119, 831–845 (2004) (10.1016/j.cell.2004.11.010) / Cell by Z Wang (2004)
  7. 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) (10.1073/pnas.0409742102) / Proc. Natl Acad. Sci. USA by GW Yeo (2005)
  8. Goren, A. et al. Comparative analysis identifies exonic splicing regulatory sequences—The complex definition of enhancers and silencers. Mol. Cell 22, 769–781 (2006) (10.1016/j.molcel.2006.05.008) / Mol. Cell by A Goren (2006)
  9. 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) (10.1038/nsmb706) / Nature Struct. Mol. Biol. by SP Ryder (2004)
  10. 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) (10.1371/journal.pbio.0030158) / PLoS Biol. by K Han (2005)
  11. Ule, J. & Darnell, R. B. RNA binding proteins and the regulation of neuronal synaptic plasticity. Curr. Opin. Neurobiol. 16, 102–110 (2006) (10.1016/j.conb.2006.01.003) / Curr. Opin. Neurobiol. by J Ule (2006)
  12. Licatalosi, D. D. & Darnell, R. B. Splicing regulation in neurologic disease. Neuron 52, (1)93–101 (2006) (10.1016/j.neuron.2006.09.017) / Neuron by DD Licatalosi (2006)
  13. 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) (10.1523/JNEUROSCI.16-03-01114.1996) / J. Neurosci. by RJ Buckanovich (1996)
  14. Jensen, K. B. et al. Nova-1 regulates neuron-specific alternative splicing and is essential for neuronal viability. Neuron 25, 359–371 (2000) (10.1016/S0896-6273(00)80900-9) / Neuron by KB Jensen (2000)
  15. 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) (10.1073/pnas.95.22.13254) / Proc. Natl Acad. Sci. USA by YY Yang (1998)
  16. 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) (10.1128/MCB.17.6.3194) / Mol. Cell. Biol. by RJ Buckanovich (1997)
  17. 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) (10.1073/pnas.090553997) / Proc. Natl Acad. Sci. USA by KB Jensen (2000)
  18. 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) (10.1016/S0092-8674(00)80668-6) / Cell by HA Lewis (2000)
  19. 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) (10.1128/MCB.23.13.4687-4700.2003) / Mol. Cell. Biol. by BK Dredge (2003)
  20. 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) (10.1038/sj.emboj.7600630) / EMBO J. by BK Dredge (2005)
  21. Ule, J. et al. CLIP identifies Nova-regulated RNA networks in the brain. Science 302, 1212–1215 (2003) (10.1126/science.1090095) / Science by J Ule (2003)
  22. Ule, J. et al. Nova regulates brain-specific splicing to shape the synapse. Nature Genet. 37, 844–852 (2005) (10.1038/ng1610) / Nature Genet. by J Ule (2005)
  23. Michaud, S. & Reed, R. An ATP-independent complex commits pre-mRNA to the mammalian spliceosome assembly pathway. Genes Dev. 5, 2534–2546 (1991) (10.1101/gad.5.12b.2534) / Genes Dev. by S Michaud (1991)
  24. Bennett, M., Michaud, S., Kingston, J. & Reed, R. Protein components specifically associated with prespliceosome and spliceosome complexes. Genes Dev. 6, 1986–2000 (1992) (10.1101/gad.6.10.1986) / Genes Dev. by M Bennett (1992)
  25. 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) (10.1016/j.molcel.2005.07.014) / Mol. Cell by S Sharma (2005)
  26. Tarn, W. Y. & Steitz, J. A. proteins can compensate for the loss of U1 snRNP functions in vitro.. Genes Dev. 8, 2704–2717 (1994) (10.1101/gad.8.22.2704) / Genes Dev. by WY Tarn (1994)
  27. 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) (10.1016/0092-8674(90)90162-8) / Cell by SM Barabino (1990)
  28. 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) (10.1128/MCB.17.5.2944) / Mol. Cell. Biol. by CC Query (1997)
  29. Buratti, E. & Baralle, F. E. Influence of RNA secondary structure on the pre-mRNA splicing process. Mol. Cell. Biol. 24, 10505–10514 (2004) (10.1128/MCB.24.24.10505-10514.2004) / Mol. Cell. Biol. by E Buratti (2004)
  30. Xing, Y. & Lee, C. Alternative splicing and RNA selection pressure—evolutionary consequences for eukaryotic genomes. Nature Rev. Genet. 7, 499–509 (2006) (10.1038/nrg1896) / Nature Rev. Genet. by Y Xing (2006)
  31. 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) (10.1128/MCB.17.4.2143) / Mol. Cell. Biol. by LR Coulter (1997)
  32. 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) (10.1128/MCB.19.1.364) / Mol. Cell. Biol. by A Gersappe (1999)
  33. 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) (10.1073/pnas.110128397) / Proc. Natl Acad. Sci. USA by AD Polydorides (2000)
  34. 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) (10.1038/362171a0) / Nature by J Valcarcel (1993)
  35. 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) (10.1128/MCB.19.1.251) / Mol. Cell. Biol. by F Del Gatto-Konczak (1999)
  36. 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) (10.1016/S1097-2765(01)00409-9) / Mol. Cell by J Zhu (2001)
  37. 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) (10.1016/j.molcel.2005.06.015) / Mol. Cell by JM Izquierdo (2005)
  38. 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) (10.1128/MCB.19.1.69) / Mol. Cell. Biol. by MY Chou (1999)
  39. 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) (10.1128/MCB.25.22.10005-10016.2005) / Mol. Cell. Biol. by JG Underwood (2005)
  40. 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) / RNA by T Carlo (1996)
  41. 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) (10.1016/S0969-2126(99)80025-2) / Struct. Fold. Des. by HA Lewis (1999)
  42. 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) (10.1016/S1097-2765(00)80260-9) / Mol. Cell by MY Chou (2000)
  43. 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) (10.1371/journal.pbio.0040021) / PLoS Biol. by R Martinez-Contreras (2006)
  44. 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) (10.1182/blood.V95.2.692) / Blood by SL Gee (2000)
  45. 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) (10.1128/MCB.13.10.6211) / Mol. Cell. Biol. by O Kessler (1993)
  46. Lang, K. M. & Spritz, R. A. In vitro splicing pathways of pre-mRNAs containing multiple intervening sequences?. Mol. Cell. Biol. 7, 3428–3437 (1987) (10.1128/MCB.7.10.3428) / Mol. Cell. Biol. by KM Lang (1987)
  47. 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) (10.1016/0092-8674(80)90170-1) / Cell by MJ Tsai (1980)
  48. 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) (10.1016/j.cub.2005.04.034) / Curr. Biol. by HL Cook (2005)
  49. 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) (10.1016/j.neuron.2005.07.007) / Neuron by U Beffert (2005)
  50. Huang, C. S. et al. Common molecular pathways mediate long-term potentiation of synaptic excitation and slow synaptic inhibition. Cell 123, 105–118 (2005) (10.1016/j.cell.2005.07.033) / Cell by CS Huang (2005)
Dates
Type When
Created 18 years, 10 months ago (Oct. 25, 2006, 2:24 p.m.)
Deposited 2 years, 3 months ago (May 18, 2023, 2 p.m.)
Indexed 4 hours, 15 minutes ago (Sept. 3, 2025, 6:44 a.m.)
Issued 18 years, 10 months ago (Nov. 1, 2006)
Published 18 years, 10 months ago (Nov. 1, 2006)
Published Online 18 years, 10 months ago (Nov. 1, 2006)
Published Print 18 years, 10 months ago (Nov. 1, 2006)
Funders 0

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@article{Ule_2006, title={An RNA map predicting Nova-dependent splicing regulation}, volume={444}, ISSN={1476-4687}, url={http://dx.doi.org/10.1038/nature05304}, DOI={10.1038/nature05304}, number={7119}, journal={Nature}, publisher={Springer Science and Business Media LLC}, author={Ule, Jernej and Stefani, Giovanni and Mele, Aldo and Ruggiu, Matteo and Wang, Xuning and Taneri, Bahar and Gaasterland, Terry and Blencowe, Benjamin J. and Darnell, Robert B.}, year={2006}, month=nov, pages={580–586} }