nature.com

RS domain–splicing signal interactions in splicing of U12-type and U2-type introns - Nature Structural & Molecular Biology

  • ️Green, Michael R
  • ️Sun Jul 01 2007
  • Black, D.L. Mechanisms of alternative pre-messenger RNA splicing. Annu. Rev. Biochem. 72, 291–336 (2003).

    Article  CAS  Google Scholar 

  • Valcarcel, J. & Green, M.R. The SR protein family: pleiotropic functions in pre-mRNA splicing. Trends Biochem. Sci. 21, 296–301 (1996).

    Article  CAS  Google Scholar 

  • Tacke, R. & Manley, J.L. Determinants of SR protein specificity. Curr. Opin. Cell Biol. 11, 358–362 (1999).

    Article  CAS  Google Scholar 

  • Blencowe, B.J. Exonic splicing enhancers: mechanism of action, diversity and role in human genetic diseases. Trends Biochem. Sci. 25, 106–110 (2000).

    Article  CAS  Google Scholar 

  • Graveley, B.R. Sorting out the complexity of SR protein functions. RNA 6, 1197–1211 (2000).

    Article  CAS  Google Scholar 

  • Staley, J.P. & Guthrie, C. Mechanical devices of the spliceosome: motors, clocks, springs, and things. Cell 92, 315–326 (1998).

    Article  CAS  Google Scholar 

  • Will, C.L. & Luhrmann, R. Splicing of a rare class of introns by the U12-dependent spliceosome. Biol. Chem. 386, 713–724 (2005).

    Article  CAS  Google Scholar 

  • Hall, S.L. & Padgett, R.A. Conserved sequences in a class of rare eukaryotic nuclear introns with non-consensus splice sites. J. Mol. Biol. 239, 357–365 (1994).

    Article  CAS  Google Scholar 

  • Sharp, P.A. & Burge, C.B. Classification of introns: U2-type or U12-type. Cell 91, 875–879 (1997).

    Article  CAS  Google Scholar 

  • Burge, C.B., Padgett, R.A. & Sharp, P.A. Evolutionary fates and origins of U12-type introns. Mol. Cell 2, 773–785 (1998).

    Article  CAS  Google Scholar 

  • Hastings, M.L. & Krainer, A.R. Pre-mRNA splicing in the new millennium. Curr. Opin. Cell Biol. 13, 302–309 (2001).

    Article  CAS  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. Cell 13, 367–376 (2004).

    Article  CAS  Google Scholar 

  • Shen, H. & Green, M.R. A pathway of sequential arginine-serine rich domain-splicing signal interactions during mammalian spliceosome assembly. Mol. Cell 16, 363–373 (2004).

    Article  CAS  Google Scholar 

  • Hastings, M.L. & Krainer, A.R. Functions of SR proteins in the U12-dependent AT-AC pre-mRNA splicing pathway. RNA 7, 471–482 (2001).

    Article  CAS  Google Scholar 

  • Wu, Q. & Krainer, A.R. Purine-rich enhancers function in the AT-AC pre-mRNA splicing pathway and do so independently of intact U1 snRNP. RNA 4, 1664–1673 (1998).

    Article  CAS  Google Scholar 

  • Chew, S.L., Liu, H.X., Mayeda, A. & Krainer, A.R. Evidence for the function of an exonic splicing enhancer after the first catalytic step of pre-mRNA splicing. Proc. Natl. Acad. Sci. USA 96, 10655–10660 (1999).

    Article  CAS  Google Scholar 

  • Zamore, P.D., Patton, J.G. & Green, M.R. Cloning and domain structure of the mammalian splicing factor U2AF. Nature 355, 609–614 (1992).

    Article  CAS  Google Scholar 

  • Valcarcel, J., Gaur, R.K., Singh, R. & Green, M.R. Interaction of U2AF65 RS region with pre-mRNA branch point and promotion of base pairing with U2 snRNA. Science 273, 1706–1709 (1996).

    Article  CAS  Google Scholar 

  • Anderson, K. & Moore, M.J. Bimolecular exon ligation by the human spliceosome. Science 276, 1712–1716 (1997).

    Article  CAS  Google Scholar 

  • Krainer, A.R. & Maniatis, T. Multiple factors including the small nuclear ribonucleoproteins U1 and U2 are necessary for pre-mRNA splicing in vitro. Cell 42, 725–736 (1985).

    Article  CAS  Google Scholar 

  • Shen, H. & Green, M.R. RS domains contact splicing signals and promote splicing by a common mechanism in yeast through humans. Genes Dev. 20, 1755–1765 (2006).

    Article  CAS  Google Scholar 

  • Konarska, M.M., Vilardell, J. & Query, C.C. Repositioning of the reaction intermediate within the catalytic center of the spliceosome. Mol. Cell 21, 543–553 (2006).

    Article  CAS  Google Scholar 

  • Wyatt, J.R., Sontheimer, E.J. & Steitz, J.A. Site-specific cross-linking of mammalian U5 snRNP to the 5′ splice site before the first step of pre-mRNA splicing. Genes Dev. 6, 2542–2553 (1992).

    Article  CAS  Google Scholar 

  • Sontheimer, E.J. & Steitz, J.A. The U5 and U6 small nuclear RNAs as active site components of the spliceosome. Science 262, 1989–1996 (1993).

    Article  CAS  Google Scholar 

  • Abmayr, S.M., Reed, R. & Maniatis, T. Identification of a functional mammalian spliceosome containing unspliced pre-mRNA. Proc. Natl. Acad. Sci. USA 85, 7216–7220 (1988).

    Article  CAS  Google Scholar 

  • Newman, A.J. & Norman, C. U5 snRNA interacts with exon sequences at 5′ and 3′ splice sites. Cell 68, 743–754 (1992).

    Article  CAS  Google Scholar 

  • Nilsen, T.W. RNA-RNA interactions in nuclear pre-mRNA splicing. in RNA Structure and Function (eds. Simons, R.W. & Grunberg-Manago, M.) 279–307 (Cold Spring Harbor Laboratory Press, New York, 1998).

    Google Scholar 

  • Burge, C.B., Tuschl, T.H. & Sharp, P.A. Splicing of precursors to mRNAs by the spliceosomes. in The RNA World (eds. Gesteland, R.F., Cech, T.R. & Atkins, J.F.) 525–560 (Cold Spring Harbor Laboratory Press, New York, 1999).

    Google Scholar 

  • Collins, C.A. & Guthrie, C. The question remains: is the spliceosome a ribozyme? Nat. Struct. Biol. 7, 850–854 (2000).

    Article  CAS  Google Scholar 

  • O'Keefe, R.T. & Newman, A.J. Functional analysis of the U5 snRNA loop 1 in the second catalytic step of yeast pre-mRNA splicing. EMBO J. 17, 565–574 (1998).

    Article  CAS  Google Scholar 

  • Zillmann, M., Zapp, M.L. & Berget, S.M. Gel electrophoretic isolation of splicing complexes containing U1 small nuclear ribonucleoprotein particles. Mol. Cell. Biol. 8, 814–821 (1988).

    Article  CAS  Google Scholar 

  • Dauksaite, V. & Akusjarvi, G. Human splicing factor ASF/SF2 encodes for a repressor domain required for its inhibitory activity on pre-mRNA splicing. J. Biol. Chem. 277, 12579–12586 (2002).

    Article  CAS  Google Scholar 

  • Caceres, J.F. & Krainer, A.R. Functional analysis of pre-mRNA splicing factor SF2/ASF structural domains. EMBO J. 12, 4715–4726 (1993).

    Article  CAS  Google Scholar 

  • Kan, J.L. & Green, M.R. Pre-mRNA splicing of IgM exons M1 and M2 is directed by a juxtaposed splicing enhancer and inhibitor. Genes Dev. 13, 462–471 (1999).

    Article  CAS  Google Scholar 

  • Valcarcel, J., Martinez, C. & Green, M.R. Functional analysis of splicing factors and regulators. in mRNA Formation and Function (ed. Richter, J.D.) 31–53 (Academic Press, New York, 1997).

    Chapter  Google Scholar 

  • Zamore, P.D. & Green, M.R. Identification, purification, and biochemical characterization of U2 small nuclear ribonucleoprotein auxiliary factor. Proc. Natl. Acad. Sci. USA 86, 9243–9247 (1989).

    Article  CAS  Google Scholar 

  • Wu, S. & Green, M.R. Identification of a human protein that recognizes the 3′ splice site during the second step of pre-mRNA splicing. EMBO J. 16, 4421–4432 (1997).

    Article  CAS  Google Scholar