8
Views
21
CrossRef citations to date
0
Altmetric
Article

A Conditional Role of U2AF in Splicing of Introns with Unconventional Polypyrimidine Tracts

&
Pages 7334-7344 | Received 10 Apr 2007, Accepted 09 Aug 2007, Published online: 27 Mar 2023

REFERENCES

  • Abovich, N., X. C. Liao, and M. Rosbash. 1994. The yeast MUD2 protein: an interaction with PRP11 defines a bridge between commitment complexes and U2 snRNP addition. Genes Dev. 8:843–854.
  • Abovich, N., and M. Rosbash. 1997. Cross-intron bridging interactions in the yeast commitment complex are conserved in mammals. Cell 89:403–412.
  • Banerjee, H., A. Rahn, W. Davis, and R. Singh. 2003. Sex lethal and U2 small nuclear ribonucleoprotein auxiliary factor (U2AF65) recognize polypyrimidine tracts using multiple modes of binding. RNA 9:88–99.
  • Banerjee, H., A. Rahn, B. Gawande, S. Guth, J. Valcárcel, and R. Singh. 2004. The conserved RNA Recognition Motif 3 of U2 snRNA Auxiliary Factor (U2AF65) is essential in vivo but dispensable for activity in vitro. RNA 10:240–253.
  • Bennett, M., S. Michaud, J. Kingston, and R. Reed. 1992. Protein components specifically associated with prespliceosome and spliceosome complexes. Genes Dev. 6:1986–2000.
  • Berglund, J. A., N. Abovich, and M. Rosbash. 1998. A cooperative interaction between U2AF65 and mBBP/SF1 facilitates branchpoint region recognition. Genes Dev. 12:858–867.
  • Black, D. L. 2003. Mechanisms of alternative pre-messenger RNA splicing. Annu. Rev. Biochem. 72:291–336.
  • Côté, J., J. Beaudoin, R. Tacke, and B. Chabot. 1995. The U1 small nuclear ribonucleoprotein/5′ splice site interaction affects U2AF65 binding to the downstream 3′ splice site. J. Biol. Chem. 270:4031–4036.
  • Crispino, J. D., B. J. Blencowe, and P. A. Sharp. 1994. Complementation by SR proteins of pre-mRNA splicing reactions depleted of U1 snRNP. Science 265:1866–1869.
  • Fleckner, J., M. Zhang, J. Valcárcel, and M. R. Green. 1997. U2AF65 recruits a novel human DEAD box protein required for the U2 snRNP-branchpoint interaction. Genes Dev. 11:1864–1872.
  • Förch, P., L. Merendino, C. Martinez, and J. Valcárcel. 2003. U2 small nuclear ribonucleoprotein particle (snRNP) auxiliary factor of 65 kDa, U2AF65, can promote U1 snRNP recruitment to 5′ splice sites. Biochem. J. 372:235–240.
  • Förch, P., O. Puig, N. Kedersha, C. Martinez, S. Granneman, B. Seraphin, P. Anderson, and J. Valcárcel. 2000. The apoptosis-promoting factor TIA-1 is a regulator of alternative pre- mRNA splicing. Mol. Cell 6:1089–1098.
  • Friedl, J. E. F. 1997. Mastering regular expressions. O'Reilly and Associates, Sebastopol, CA.
  • Golling, G., A. Amsterdam, Z. Sun, M. Antonelli, E. Maldonado, W. Chen, S. Burgess, M. Haldi, K. Artzt, S. Farrington, S. Y. Lin, R. M. Nissen, and N. Hopkins. 2002. Insertional mutagenesis in zebrafish rapidly identifies genes essential for early vertebrate development. Nat. Genet. 31:135–140.
  • Gozani, O., J. Potashkin, and R. Reed. 1998. A potential role for U2AF-SAP 155 interactions in recruiting U2 snRNP to the branch site. Mol. Cell. Biol. 18:4752–4760.
  • Granadino, B., L. O. F. Penalva, M. R. Green, J. Valcárcel, and L. Sanchez. 1997. Distinct mechanisms of splicing regulation in vivo by the Drosophila protein Sex-lethal. Proc. Natl. Acad. Sci. USA 94:7343–7348.
  • Guth, S., and J. Valcárcel. 2000. Kinetic role for mammalian SF1/BBP in spliceosome assembly and function after polypyrimidine tract recognition by U2AF. J. Biol. Chem. 275:38059–38066.
  • Habara, Y., S. Urushiyama, T. Tani, and Y. Ohshima. 1998. The fission yeast prp10(+) gene involved in pre-mRNA splicing encodes a homologue of highly conserved splicing factor, SAP155. Nucleic Acids Res. 26:5662–5669.
  • Hastings, M. L., and A. R. Krainer. 2001. Pre-mRNA splicing in the new millennium. Curr. Opin. Cell Biol. 13:302–309.
  • Hertel, K. J., K. W. Lynch, and T. Maniatis. 1997. Common themes in the function of transcription and splicing enhancers. Curr. Opin. Cell Biol. 9:350–357.
  • Hollins, C., D. A. Zorio, M. MacMorris, and T. Blumenthal. 2005. U2AF binding selects for the high conservation of the C. elegans 3′ splice site. RNA 11:248–253.
  • Huang, T., J. Vilardell, and C. C. Query. 2002. Pre-spliceosome formation in S. pombe requires a stable complex of SF1-U2AF(59)-U2AF(23). EMBO J. 21:5516–5526.
  • Jurica, M. S., and M. J. Moore. 2003. Pre-mRNA splicing: awash in a sea of proteins. Mol. Cell 12:5–14.
  • Kanaar, R., S. E. Roche, E. L. Beall, M. R. Green, and D. C. Rio. 1993. The conserved pre-mRNA splicing factor U2AF from Drosophila: requirement for viability. Science 262:569–573.
  • Kennedy, C. F., A. Kramer, and S. M. Berget. 1998. A role for SRp54 during intron bridging of small introns with pyrimidine tracts upstream of the branch point. Mol. Cell. Biol. 18:5425–5434.
  • Kent, O. A., D. B. Ritchie, and A. M. Macmillan. 2005. Characterization of a U2AF-independent commitment complex (E′) in the mammalian spliceosome assembly pathway. Mol. Cell. Biol. 25:233–240.
  • Kielkopf, C. L., S. Lucke, and M. R. Green. 2004. U2AF homology motifs: protein recognition in the RRM world. Genes Dev. 18:1513–1526.
  • Kupfer, D. M., S. D. Drabenstot, K. L. Buchanan, H. Lai, H. Zhu, D. W. Dyer, B. A. Roe, and J. W. Murphy. 2004. Introns and splicing elements of five diverse fungi. Eukaryot. Cell 3:1088–1100.
  • Levine, M., and R. Tjian. 2003. Transcription regulation and animal diversity. Nature 424:147–151.
  • Li, Y., and B. J. Blencowe. 1999. Distinct factor requirements for exonic splicing enhancer function and binding of U2AF to the polypyrimidine tract. J. Biol. Chem. 274:35074–35079.
  • Lützelberger, M., E. Backstrom, and G. Akusjarvi. 2005. Substrate-dependent differences in U2AF requirement for splicing in adenovirus-infected cell extracts. J. Biol. Chem. 280:25478–25484.
  • MacMillan, A. M., P. S. McCaw, J. D. Crispino, and P. A. Sharp. 1997. SC35-mediated reconstitution of splicing in U2AF-depleted nuclear extract. Proc. Natl. Acad. Sci. USA 94:133–136.
  • Merendino, L., S. Guth, D. Bilbao, C. Martinez, and J. Valcárcel. 1999. Inhibition of msl-2 splicing by Sex-lethal reveals interaction between U2AF35 and the 3′ splice site AG. Nature 402:838–841.
  • Moore, M. J. 2000. Intron recognition comes of AGe. Nat. Struct. Biol. 7:14–16.
  • Patterson, B., and C. Guthrie. 1991. A U-rich tract enhances usage of an alternative 3′ splice site in yeast. Cell 64:181–187.
  • Potashkin, J., K. Naik, and K. Wentz-Hunter. 1993. U2AF homolog required for splicing in vivo. Science 262:573–575.
  • Ptashne, M., and A. Gann. 1997. Transcriptional activation by recruitment. Nature 386:569–577.
  • Puig, O., A. Gottschalk, P. Fabrizio, and B. Seraphin. 1999. Interaction of the U1 snRNP with nonconserved intronic sequences affects 5′ splice site selection. Genes Dev. 13:569–580.
  • Rain, J. C., Z. Rafi, Z. Rhani, P. Legrain, and A. Kramer. 1998. Conservation of functional domains involved in RNA binding and protein-protein interactions in human and Saccharomyces cerevisiae pre-mRNA splicing factor SF1. RNA 4:551–565.
  • Reed, R. 2000. Mechanisms of fidelity in pre-mRNA splicing. Curr. Opin. Cell Biol. 12:340–345.
  • Romfo, C. M., S. Lakhe-Reddy, and J. A. Wise. 1999. Molecular genetic analysis of U2AF59 in Schizosaccharomyces pombe: differential sensitivity of introns to mutational inactivation. RNA 5:49–65.
  • Rudner, D. Z., K. S. Breger, R. Kanaar, M. D. Adams, and D. C. Rio. 1998. RNA binding activity of heterodimeric splicing factor U2AF: at least one RS domain is required for high-affinity binding. Mol. Cell. Biol. 18:4004–4011.
  • Rudner, D. Z., R. Kanaar, K. S. Breger, and D. C. Rio. 1996. Mutations in the small subunit of the Drosophila U2AF splicing factor cause lethality and developmental defects. Proc. Natl. Acad. Sci. USA 93:10333–10337.
  • Rutz, B., and B. Seraphin. 2000. A dual role for BBP/ScSF1 in nuclear pre-mRNA retention and splicing. EMBO J. 19:1873–1886.
  • Seraphin, B., and M. Rosbash. 1989. Identification of functional U1 snRNA-pre-mRNA complexes committed to spliceosome assembly and splicing. Cell 59:349–358.
  • Shen, H., and M. R. Green. 2004. A pathway of sequential arginine-serine-rich domain-splicing signal interactions during mammalian spliceosome assembly. Mol. Cell 16:363–373.
  • Singh, R., H. Banerjee, and M. R. Green. 2000. Differential recognition of the polypyrimidine-tract by the general splicing factor U2AF65 and the splicing repressor sex-lethal. RNA 6:901–911.
  • Singh, R., and J. Valcárcel. 2005. Building specificity with nonspecific RNA-binding proteins. Nat. Struct. Mol. Biol. 12:645–653.
  • Singh, R., J. Valcárcel, and M. R. Green. 1995. Distinct binding specificities and functions of higher eukaryotic polypyrimidine tract-binding proteins. Science 268:1173–1176.
  • Smith, C. W., T. T. Chu, and B. Nadal-Ginard. 1993. Scanning and competition between AGs are involved in 3′ splice site selection in mammalian introns. Mol. Cell. Biol. 13:4939–4952.
  • Tange, T. O., C. K. Damgaard, S. Guth, J. Valcárcel, and J. Kjems. 2001. The hnRNP A1 protein regulates HIV-1 tat splicing via a novel intron silencer element. EMBO J. 20:5748–5758.
  • Tarn, W. Y., and J. A. Steitz. 1994. SR proteins can compensate for the loss of U1 snRNP functions in vitro. Genes Dev. 8:2704–2717.
  • Valcárcel, J., R. K. Gaur, R. Singh, and M. R. Green. 1996. Interaction of U2AF65 RS region with pre-mRNA branch point and promotion of base pairing with U2 snRNA. Science 273:1706–1709.
  • Valcárcel, J., R. Singh, P. D. Zamore, and M. R. Green. 1993. The protein Sex-lethal antagonizes the splicing factor U2AF to regulate alternative splicing of transformer pre-mRNA. Nature 362:171–175.
  • Webb, C. J., S. Lakhe-Reddy, C. M. Romfo, and J. A. Wise. 2005. Analysis of mutant phenotypes and splicing defects demonstrates functional collaboration between the large and small subunits of the essential splicing factor U2AF in vivo. Mol. Biol. Cell 16:584–596.
  • Webb, C. J., and J. A. Wise. 2004. The splicing factor U2AF small subunit is functionally conserved between fission yeast and humans. Mol. Cell. Biol. 24:4229–4240.
  • Wentz-Hunter, K., and J. Potashkin. 1995. The evolutionary conservation of the splicing apparatus between fission yeast and man. Nucleic Acids Symp. Ser. 33:226–228.
  • Will, C. L., C. Schneider, R. Reed, and R. Luhrmann. 1999. Identification of both shared and distinct proteins in the major and minor spliceosomes. Science 284:2003–2005.
  • Wood, V., et al. 2002. The genome sequence of Schizosaccharomyces pombe. Nature 415:871–880.
  • Wu, J. Y., and T. Maniatis. 1993. Specific interactions between proteins implicated in splice site selection and regulated alternative splicing. Cell 75:1061–1070.
  • Wu, S., C. M. Romfo, T. W. Nilsen, and M. R. Green. 1999. Functional recognition of the 3′ splice site AG by the splicing factor U2AF35. Nature 402:832–835.
  • Zamore, P. D., J. G. Patton, and M. R. Green. 1992. Cloning and domain structure of the mammalian splicing factor U2AF. Nature 355:609–614.
  • Zhang, D., and M. Rosbash. 1999. Identification of eight proteins that cross-link to pre-mRNA in the yeast commitment complex. Genes Dev. 13:581–592.
  • Zhang, W. J., and J. Y. Wu. 1996. Functional properties of p54, a novel SR protein active in constitutive and alternative splicing. Mol. Cell. Biol. 16:5400–5408.
  • Zorio, D. A., and T. Blumenthal. 1999. Both subunits of U2AF recognize the 3′ splice site in Caenorhabditis elegans. Nature 402:835–838.
  • Zorio, D. A., and T. Blumenthal. 1999. U2AF35 is encoded by an essential gene clustered in an operon with RRM/cyclophilin in Caenorhabditis elegans. RNA 5:487–494.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.