Pre-mRNA Topology Is Important for 3′-End Formation in Saccharomyces cerevisiae and Mammals

REFERENCES

• Abe, A., Y. Hiraoka, and T. Fukasawa. 1990. Signal sequence for generation of mRNA 3′ end in the Saccharomyces cerevisiae GAL7 gene. EMBO J. 9:3691–3697.
   PubMedGoogle Scholar
• Ahmed, Y. F., G. M. Gilmartin, S. M. Hanly, J. R. Nevins, and W. C. Greene. 1991. The HTLV-1 Rex response element mediates a novel form of mRNA polyadenylation. Cell 64:727–737.
   PubMedGoogle Scholar
• Brown, P. H., L. S. Tiley, and B. R. Cullen. 1991. Effect of RNA secondary structure on polyadenylation site selection. Genes Dev. 5:1277–1284.
   PubMedGoogle Scholar
• Bullock, W. O., J. M. Fernandez, and J. M. Short. 1987. XL1-Blue: a high efficiency plasmid transforming recA Escherichia coli strain with beta-galactosidase selection. BioTechniques 5:376–378.
   Web of Science ®Google Scholar
• Burgers, P. M. J., and B. L. Yoder. 1993. ATP-independent loading of the proliferating cell nuclear antigen requires DNA ends. J. Biol. Chem. 268:19923–19926.
   PubMedGoogle Scholar
• Butler, J. S., and T. Platt. 1988. RNA processing generates the mature 3′ end of yeast CYC1 messenger RNA in vitro. Science 242:1270–1274.
   PubMedGoogle Scholar
• Butler, J. S., P. P. Sadhale, and T. Platt. 1990. RNA processing in vitro produces mature 3′ ends of a variety of Saccharomyces cerevisiae mRNAs. Mol. Cell. Biol. 10:2599–2605.
   PubMedGoogle Scholar
• Buzayan, J. M., W. L. Gerlach, and G. Bruening. 1986. Non-enzymatic cleavage and ligation of RNAs complementary to a plant virus satellite RNA. Nature (London) 323:349–353.
   Web of Science ®Google Scholar
• Chen, C. Y., and P. Sarnow. 1995. Initiation of protein synthesis by the eukaryotic translational apparatus on circular RNAs. Science 268:415–417.
   PubMed Web of Science ®Google Scholar
• Chen, E. Y., and P. Seeburg. 1985. Supercoil sequencing: a fast and simple method for sequencing plasmid DNA. DNA 4:165–170.
   PubMedGoogle Scholar
• Chen, J., and C. Moore. 1992. Separation of factors required for cleavage and polyadenylation of yeast pre-mRNA. Mol. Cell. Biol. 12:3470–3481.
   PubMedGoogle Scholar
• Dandekar, T., and M. W. Hentze. 1995. Finding the hairpin in the haystack: searching for RNA motifs. Trends Genet. 11:45–50.
   PubMedGoogle Scholar
• Dignam, J. D., R. M. Lebovitz, and R. G. Roeder. 1983. Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res. 11:1475–1489.
   PubMed Web of Science ®Google Scholar
• Domdey, H., B. Apostol, R.-J. Lin, A. Newman, E. Brody, and J. Abelson. 1984. Lariat structures are in vivo intermediates in yeast pre-mRNA splicing. Cell 39:611–621.
   PubMed Web of Science ®Google Scholar
• Dominski, Z., and R. Kole. 1994. Identification and characterization by antisense oligonucleotides of exon and intron sequences required for splicing. Mol. Cell. Biol. 14:7445–7454.
   PubMed Web of Science ®Google Scholar
• Gil, A., and N. J. Proudfoot. 1984. A sequence downstream of AAUAAA is required for rabbit β-globin mRNA 3′-end formation. Nature (London) 312:473–474.
   PubMed Web of Science ®Google Scholar
• Gil, A., and N. J. Proudfoot. 1987. Position-dependent sequence elements downstream of AAUAAA are required for efficient rabbit β-globin mRNA 3′-end formation. Cell 49:399–406.
   PubMed Web of Science ®Google Scholar
• Gilmartin, G. M., F. Schaufele, G. Schaffner, and M. L. Birnstiel. 1988. Functional analysis of the sea urchin U7 small nuclear RNA. Mol. Cell. Biol. 8:1076–1084.
   PubMed Web of Science ®Google Scholar
• Goodall, G. J., K. Wiebauer, and W. Filipowicz. 1990. Analysis of pre-mRNA processing in transfected plant protoplasts. Methods Enzymol. 181:148–161.
   PubMedGoogle Scholar
• Gunderson, S. I., K. Beyer, G. Martin, W. Keller, W. C. Boelens, and I. W. Mattaj. 1994. The human U1A snRNP protein regulates polyadenylation via a direct interaction with poly(A) polymerase. Cell 76:531–554.
   PubMed Web of Science ®Google Scholar
• Guo, Z., and F. Sherman. 1995. 3′-end-forming signals of yeast mRNA. Mol. Cell. Biol. 15:5983–5990.
   PubMedGoogle Scholar
• Heidmann, S., B. Obermaier, K. Vogel, and H. Domdey. 1992. Identification of pre-mRNA polyadenylation sites in Saccharomyces cerevisiae. Mol. Cell. Biol. 12:4215–4229.
   PubMedGoogle Scholar
• Heidmann, S., C. Schindewolf, G. Stumpf, and H. Domdey. 1994. Flexibility and interchangeability of polyadenylation signals in Saccharomyces cerevisiae. Mol. Cell. Biol. 14:4633–4642.
   PubMedGoogle Scholar
• Henikoff, S., and E. H. Cohen. 1984. Sequences responsible for transcription termination on a gene segment in Saccharomyces cerevisiae. Mol. Cell. Biol. 4:1515–1520.
   PubMedGoogle Scholar
• Herendeen, D. R., and T. J. Kelly. 1996. DNA polymerase III: running rings around the fork. Cell 84:5–8.
   PubMedGoogle Scholar
• Humphrey, T., G. Christofori, V. Lucijanic, and W. Keller. 1987. Cleavage and polyadenylation of messenger RNA precursors in vitro occurs within large and specific 3′ processing complexes. EMBO J. 6:4159–4168.
   PubMedGoogle Scholar
• Hyman, L. E., S. H. Seiler, J. Whoriskey, and C. L. Moore. 1991. Point mutations upstream of the yeast ADH2 poly(A) site significantly reduce the efficiency of 3′-end formation. Mol. Cell. Biol. 11:2004–2012.
   PubMedGoogle Scholar
• Irniger, S., C. M. Egli, and G. H. Braus. 1991. Different classes of polyadenylation sites in the yeast Saccharomyces cerevisiae. Mol. Cell. Biol. 11:3060–3069.
   PubMedGoogle Scholar
• Irniger, S., H. Sanfaçon, C. M. Egli, and G. H. Braus. 1992. Different sequence elements are required for function of the cauliflower mosaic virus polyadenylation site in Saccharomyces cerevisiae compared with in plants. Mol. Cell. Biol. 12:2322–2330.
   PubMedGoogle Scholar
• Keller, W. 1995. No end yet to messenger RNA 3′ processing! Cell 81:829–832.
   PubMed Web of Science ®Google Scholar
• Konarska, M., W. Filipowicz, H. Domdey, and H. Gross. 1981. Binding of ribosomes to linear and circular forms of the 5′-terminal leader fragment of tobacco-mosaic-virus RNA. Eur. J. Biochem. 114:221–227.
   PubMedGoogle Scholar
• Kondrakhin, Y. V., V. V. Shamin, and N. A. Kolchanov. 1994. Construction of a generalized consensus matrix for recognition of vertebrate pre-mRNA 3′-terminal processing sites. CABIOS 10:597–603.
   PubMedGoogle Scholar
• Kong, X.-P., R. Onrust, M. O’Donnell, and J. Kuriyan. 1992. Three-dimensional structure of the β-subunit of E. coli DNA polymerase III holoenzyme: a sliding DNA clamp. Cell 69:425–437.
   PubMed Web of Science ®Google Scholar
• Kozak, M. 1979. Inability of circular mRNA to attach to eukaryotic ribosomes. Nature (London) 280:82–85.
   PubMed Web of Science ®Google Scholar
• Kozak, M. 1989. Circumstances and mechanisms of inhibition of translation by secondary structure in eucaryotic mRNAs. Mol. Cell. Biol. 9:5134–5142.
   PubMed Web of Science ®Google Scholar
• Kuriyan, J., and M. O’Donnell. 1993. Sliding clamps of DNA polymerases. J. Mol. Biol. 234:915–925.
   PubMed Web of Science ®Google Scholar
• McDevitt, M. A., R. P. Hart, W. W. Wong, and J. R. Nevins. 1986. Sequences capable of restoring poly(A) site function define two distinct downstream elements. EMBO J. 5:2907–2913.
   PubMed Web of Science ®Google Scholar
• McDevitt, M. A., M. J. Imperiale, H. Ali, and J. R. Nevins. 1984. Requirement of a downstream sequence for generation of a poly(A) addition site. Cell 37:993–999.
   PubMed Web of Science ®Google Scholar
• McLauchlan, J., D. Gaffney, J. L. Whitton, and J. B. Clements. 1985. The consensus sequence YGTGTTYY located downstream from the AATAAA signal is required for efficient formation of mRNA 3′ termini. Nucleic Acids Res. 13:1347–1368.
   PubMed Web of Science ®Google Scholar
• Melton, D. A., P. A. Krieg, M. R. Rebagliati, T. Maniatis, K. Zinn, and M. R. Green. 1984. Efficient in vitro synthesis of biologically active RNA and RNA hybridization probes from plasmids containing a bacteriophage SP6 promoter. Nucleic Acids Res. 12:7035–7056.
   PubMed Web of Science ®Google Scholar
• Minvielle-Sebastia, L., P. J. Preker, and W. Keller. 1994. RNA14 and RNA15 proteins as components of a yeast pre-mRNA 3′-end processing factor. Science 266:1702–1705.
   PubMed Web of Science ®Google Scholar
• Moore, M. J., and P. A. Sharp. 1992. Site specific modification of pre-mRNA: the 2′-hydroxyl groups at the splice sites. Science 256:992–997.
   PubMed Web of Science ®Google Scholar
• Orkin, S. H., T.-C. Cheng, S. E. Antonarakis, and H. H. Kazazian. 1985. Thalassemia due to a mutation in the cleavage-polyadenylation signal of the human β-globin gene. EMBO J. 4:453–456.
   PubMed Web of Science ®Google Scholar
• Padgett, R. A., P. J. Grabowsky, M. M. Konarska, S. Seiler, and P. A. Sharp. 1986. Splicing of messenger RNA precursors. Annu. Rev. Biochem. 55:1119–1150.
   PubMed Web of Science ®Google Scholar
• Proudfoot, N. J. 1991. Poly(A) signals. Cell 64:671–674.
   PubMed Web of Science ®Google Scholar
• Proudfoot, N. J., and G. G. Brownlee. 1974. Sequence at the 3′ end of globin mRNA shows homology with immunoglobulin light chain mRNA. Nature (London) 252:359–362.
   PubMed Web of Science ®Google Scholar
• Russo, P., W.-Z. Li, D. M. Hampsey, K. S. Zaret, and F. Sherman. 1991. Distinct cis-acting signals enhance 3′ endpoint formation of CYC1 mRNA in the yeast Saccharomyces cerevisiae. EMBO J. 10:563–571.
   PubMedGoogle Scholar
• Sadhale, P. P., and T. Platt. 1992. Unusual aspects of in vitro RNA processing in the 3′ regions of the GAL1, GAL7, and GAL10 genes in Saccharomyces cerevisiae. Mol. Cell. Biol. 12:4262–4270.
   PubMedGoogle Scholar
• Schindewolf, C., S. Braun, and H. Domdey. In vitro generation of a circular exon from a linear pre-mRNA transcript. Nucleic Acids Res., in press.
   Google Scholar
• Schindewolf, C., and H. Domdey. 1995. Splicing of a circular yeast pre-mRNA in vitro. Nucleic Acids Res. 23:1133–1139.
   PubMedGoogle Scholar
• Stukenberg, P. T., P. S. Studwell-Vaughan, and M. O’Donnell. 1991. Mechanism of the sliding β-clamp of DNA polymerase III holoenzyme. J. Biol. Chem. 266:11328–11334.
   PubMed Web of Science ®Google Scholar
• Uhlenbeck, O. C., and R. I. Gumport. 1982. T4 RNA ligase, p. 31–58. In P. D. Boyer (ed.), The enzymes. Academic Press, New York.
   Google Scholar
• Wahle, E., and W. Keller. 1992. The biochemistry of 3′-end cleavage and polyadenylation of messenger RNA precursors. Annu. Rev. Biochem. 61:419–440.
   PubMed Web of Science ®Google Scholar
• Wahle, E., and W. Keller. 1993. RNA-protein interactions in mRNA 3′-end formation. Mol. Biol. Rep. 18:157–161.
   PubMedGoogle Scholar
• Yisraeli, J. K., and D. A. Melton. 1989. Synthesis of long, capped transcripts in vitro by SP6 and T7 RNA polymerases. Methods Enzymol. 180:42–50.
   PubMedGoogle Scholar
• Zaret, K. S., and F. Sherman. 1982. DNA sequence required for efficient transcription termination in yeast. Cell 28:563–573.
   PubMed Web of Science ®Google Scholar