A complex network of factors with overlapping affinities represses splicing through intronic elements (original) (raw)
References
Wang, Z. & Burge, C.B. Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. RNA14, 802–813 (2008). ArticleCAS Google Scholar
Matlin, A.J., Clark, F. & Smith, C.W. Understanding alternative splicing: towards a cellular code. Nat. Rev. Mol. Cell Biol.6, 386–398 (2005). ArticleCAS Google Scholar
Blencowe, B.J. Alternative splicing: new insights from global analyses. Cell126, 37–47 (2006). ArticleCAS Google Scholar
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). ArticleCAS Google Scholar
Fairbrother, W.G., Yeh, R.F., Sharp, P.A. & Burge, C.B. Predictive identification of exonic splicing enhancers in human genes. Science297, 1007–1013 (2002). ArticleCAS Google Scholar
Wang, Z. et al. Systematic identification and analysis of exonic splicing silencers. Cell119, 831–845 (2004). ArticleCAS Google Scholar
Goren, A. et al. Comparative analysis identifies exonic splicing regulatory sequences–the complex definition of enhancers and silencers. Mol. Cell22, 769–781 (2006). ArticleCAS Google Scholar
Yu, Y. et al. Dynamic regulation of alternative splicing by silencers that modulate 5′ splice site competition. Cell135, 1224–1236 (2008). ArticleCAS Google Scholar
Culler, S.J., Hoff, K.G., Voelker, R.B., Berglund, J.A. & Smolke, C.D. Functional selection and systematic analysis of intronic splicing elements identifies active sequence motifs and associated splicing factors. Nucleic Acids Res.38, 5152–5165 (2010). ArticleCAS Google Scholar
Sharma, S., Kohlstaedt, L.A., Damianov, A., Rio, D.C. & Black, D.L. Polypyrimidine tract binding protein controls the transition from exon definition to an intron defined spliceosome. Nat. Struct. Mol. Biol.15, 183–191 (2008). ArticleCAS Google Scholar
Kashima, T., Rao, N. & Manley, J.L. An intronic element contributes to splicing repression in spinal muscular atrophy. Proc. Natl. Acad. Sci. USA104, 3426–3431 (2007). ArticleCAS Google Scholar
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). ArticleCAS Google Scholar
Blanchette, M. & Chabot, B. Modulation of exon skipping by high-affinity hnRNP A1-binding sites and by intron elements that repress splice site utilization. EMBO J.18, 1939–1952 (1999). ArticleCAS Google Scholar
Kanopka, A., Muhlemann, O. & Akusjarvi, G. Inhibition by SR proteins of splicing of a regulated adenovirus pre-mRNA. Nature381, 535–538 (1996). ArticleCAS Google Scholar
Ibrahim, E.C., Schaal, T.D., Hertel, K.J., Reed, R. & Maniatis, T. Serine/arginine-rich protein-dependent suppression of exon skipping by exonic splicing enhancers. Proc. Natl. Acad. Sci. USA102, 5002–5007 (2005). ArticleCAS Google Scholar
Shen, M. & Mattox, W. Activation and repression functions of an SR splicing regulator depend on exonic versus intronic-binding position. Nucleic Acids Res.40, 428–437 (2012). ArticleCAS Google Scholar
McNally, L.M. & McNally, M.T. SR protein splicing factors interact with the Rous sarcoma virus negative regulator of splicing element. J. Virol.70, 1163–1172 (1996). CASPubMedPubMed Central Google Scholar
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). ArticleCAS Google Scholar
Hua, Y., Vickers, T.A., Okunola, H.L., Bennett, C.F. & Krainer, A.R. Antisense masking of an hnRNP A1/A2 intronic splicing silencer corrects SMN2 splicing in transgenic mice. Am. J. Hum. Genet.82, 834–848 (2008). ArticleCAS Google Scholar
Tange, T.O., Damgaard, C.K., Guth, S., Valcarcel, J. & Kjems, J. The hnRNP A1 protein regulates HIV-1 tat splicing via a novel intron silencer element. EMBO J.20, 5748–5758 (2001). ArticleCAS Google Scholar
Wang, Y., Ma, M., Xiao, X. & Wang, Z. Intronic splicing enhancers, cognate splicing factors and context-dependent regulation rules. Nat. Struct. Mol. Biol.19, 1044–1052 (2012). ArticleCAS Google Scholar
Wang, Z., Xiao, X., Van Nostrand, E. & Burge, C.B. General and specific functions of exonic splicing silencers in splicing control. Mol. Cell23, 61–70 (2006). ArticleCAS Google Scholar
Lim, K.H., Ferraris, L., Filloux, M.E., Raphael, B.J. & Fairbrother, W.G. Using positional distribution to identify splicing elements and predict pre-mRNA processing defects in human genes. Proc. Natl. Acad. Sci. USA108, 11093–11098 (2011). ArticleCAS Google Scholar
Huang, C. et al. A structured RNA in HBV PRE represses alternative splicing in a sequence-independent and position-dependent manner. FEBS J.278, 1533–1546 (2011). ArticleCAS Google Scholar
Pervouchine, D.D. et al. Evidence for widespread association of mammalian splicing and conserved long-range RNA structures. RNA18, 1–15 (2012). ArticleCAS Google Scholar
Dominski, Z., Yang, X.C., Kaygun, H., Dadlez, M. & Marzluff, W.F. A 3′ exonuclease that specifically interacts with the 3′ end of histone mRNA. Mol. Cell12, 295–305 (2003). ArticleCAS Google Scholar
Rothrock, C.R., House, A.E. & Lynch, K.W. HnRNP L represses exon splicing via a regulated exonic splicing silencer. EMBO J.24, 2792–2802 (2005). ArticleCAS Google Scholar
Nielsen, F.C., Nielsen, J. & Christiansen, J. A family of IGF-II mRNA binding proteins (IMP) involved in RNA trafficking. Scand. J. Clin. Lab. Invest. Suppl.234, 93–99 (2001). ArticleCAS Google Scholar
Allemand, E., Hastings, M.L., Murray, M.V., Myers, M.P. & Krainer, A.R. Alternative splicing regulation by interaction of phosphatase PP2Cgamma with nucleic acid-binding protein YB-1. Nat. Struct. Mol. Biol.14, 630–638 (2007). ArticleCAS Google Scholar
Krainer, A.R., Conway, G.C. & Kozak, D. Purification and characterization of pre-mRNA splicing factor SF2 from HeLa cells. Genes Dev.4, 1158–1171 (1990). ArticleCAS Google Scholar
Muta, T., Kang, D., Kitajima, S., Fujiwara, T. & Hamasaki, N. p32 protein, a splicing factor 2-associated protein, is localized in mitochondrial matrix and is functionally important in maintaining oxidative phosphorylation. J. Biol. Chem.272, 24363–24370 (1997). ArticleCAS Google Scholar
Oberstrass, F.C. et al. Structure of PTB bound to RNA: specific binding and implications for splicing regulation. Science309, 2054–2057 (2005). ArticleCAS Google Scholar
Spellman, R., Llorian, M. & Smith, C.W. Crossregulation and functional redundancy between the splicing regulator PTB and its paralogs nPTB and ROD1. Mol. Cell27, 420–434 (2007). ArticleCAS Google Scholar
Jin, W., Bruno, I.G., Xie, T.X., Sanger, L.J. & Cote, G.J. Polypyrimidine tract-binding protein down-regulates fibroblast growth factor receptor 1 α-exon inclusion. Cancer Res.63, 6154–6157 (2003). CASPubMed Google Scholar
Côté, J., Dupuis, S. & Wu, J.Y. Polypyrimidine track-binding protein binding downstream of caspase-2 alternative exon 9 represses its inclusion. J. Biol. Chem.276, 8535–8543 (2001). Article Google Scholar
Das, R. et al. SR proteins function in coupling RNAP II transcription to pre-mRNA splicing. Mol. Cell26, 867–881 (2007). ArticleCAS Google Scholar
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). ArticleCAS Google Scholar
Kashima, T., Rao, N., David, C.J. & Manley, J.L. hnRNP A1 functions with specificity in repression of SMN2 exon 7 splicing. Hum. Mol. Genet.16, 3149–3159 (2007). ArticleCAS Google Scholar
Hui, J., Stangl, K., Lane, W.S. & Bindereif, A. HnRNP L stimulates splicing of the eNOS gene by binding to variable-length CA repeats. Nat. Struct. Biol.10, 33–37 (2003). ArticleCAS Google Scholar
Chen, M. & Manley, J.L. Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nat. Rev. Mol. Cell Biol.10, 741–754 (2009). ArticleCAS Google Scholar
Graveley, B.R. & Maniatis, T. Arginine/serine-rich domains of SR proteins can function as activators of pre-mRNA splicing. Mol. Cell1, 765–771 (1998). ArticleCAS Google Scholar
Shen, H., Kan, J.L. & Green, M.R. Arginine-serine-rich domains bound at splicing enhancers contact the branchpoint to promote prespliceosome assembly. Mol. Cell13, 367–376 (2004). ArticleCAS Google Scholar
Graveley, B.R., Hertel, K.J. & Maniatis, T. A systematic analysis of the factors that determine the strength of pre-mRNA splicing enhancers. EMBO J.17, 6747–6756 (1998). ArticleCAS Google Scholar
Wang, Y., Cheong, C.G., Hall, T.M. & Wang, Z. Engineering splicing factors with designed specificities. Nat. Methods6, 825–830 (2009). ArticleCAS Google Scholar
Cheong, C.G. & Hall, T.M. Engineering RNA sequence specificity of Pumilio repeats. Proc. Natl. Acad. Sci. USA103, 13635–13639 (2006). ArticleCAS Google Scholar
Tourrière, H. et al. The RasGAP-associated endoribonuclease G3BP assembles stress granules. J. Cell Biol.160, 823–831 (2003). Article Google Scholar
Ufer, C. et al. Translational regulation of glutathione peroxidase 4 expression through guanine-rich sequence-binding factor 1 is essential for embryonic brain development. Genes Dev.22, 1838–1850 (2008). ArticleCAS Google Scholar
Guil, S., Long, J.C. & Caceres, J.F. hnRNP A1 relocalization to the stress granules reflects a role in the stress response. Mol. Cell Biol.26, 5744–5758 (2006). ArticleCAS Google Scholar
Boutz, P.L. et al. A post-transcriptional regulatory switch in polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons. Genes Dev.21, 1636–1652 (2007). ArticleCAS Google Scholar
Caputi, M. & Zahler, A.M. Determination of the RNA binding specificity of the heterogeneous nuclear ribonucleoprotein (hnRNP) H/H'/F/2H9 family. J. Biol. Chem.276, 43850–43859 (2001). ArticleCAS Google Scholar
Schaub, M.C., Lopez, S.R. & Caputi, M. Members of the heterogeneous nuclear ribonucleoprotein H family activate splicing of an HIV-1 splicing substrate by promoting formation of ATP-dependent spliceosomal complexes. J. Biol. Chem.282, 13617–13626 (2007). ArticleCAS Google Scholar
Chen, C.D., Kobayashi, R. & Helfman, D.M. Binding of hnRNP H to an exonic splicing silencer is involved in the regulation of alternative splicing of the rat beta-tropomyosin gene. Genes Dev.13, 593–606 (1999). ArticleCAS Google Scholar
Xiao, X., Wang, Z., Jang, M. & Burge, C.B. Coevolutionary networks of splicing cis-regulatory elements. Proc. Natl. Acad. Sci. USA104, 18583–18588 (2007). ArticleCAS Google Scholar
Xiao, X. et al. Splice site strength-dependent activity and genetic buffering by poly-G runs. Nat. Struct. Mol. Biol.16, 1094–1100 (2009). ArticleCAS Google Scholar
Katz, Y., Wang, E.T., Airoldi, E.M. & Burge, C.B. Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat. Methods7, 1009–1015 (2010). ArticleCAS Google Scholar