Repression of Gene Expression by an Exogenous Sequence Element Acting in Concert with a Heterogeneous Nuclear Ribonucleoprotein-Like Protein, Nrd1, and the Putative Helicase Sen1

REFERENCES

• Alani, E., S. Subbiah, and N. Kleckner. 1989. The yeast RAD50 gene encodes a predicted 153-kD protein containing a purine nucleotide-binding domain and two large heptad-repeat regions. Genetics 122:47–57.
   PubMedGoogle Scholar
• Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403–410.
   PubMed Web of Science ®Google Scholar
• Anderson, J. T., M. R. Paddy, and M. S. Swanson. 1993. PUB1 is a major nuclear and cytoplasmic polyadenylated RNA-binding protein in Saccharomyces cerevisiae. Mol. Cell. Biol. 13:6102–6113.
   PubMedGoogle Scholar
• Anderson, J. T., S. M. Wilson, K. V. Datar, and M. S. Swanson. 1993. NAB2: a yeast nuclear polyadenylated RNA-binding protein essential for cell viability. Mol. Cell. Biol. 13:2730–2741.
   PubMed Web of Science ®Google Scholar
• Bandziulis, R. J., M. S. Swanson, and G. Dreyfuss. 1989. RNA-binding proteins as developmental regulators. Genes Dev. 3:431–437.
   PubMed Web of Science ®Google Scholar
• Birney, E., S. Kumar, and A. R. Krainer. 1993. Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors. Nucleic Acids Res. 21:5803–5816.
   PubMed Web of Science ®Google Scholar
• Brow, D. A., and C. Guthrie. 1988. Spliceosomal RNA U6 is remarkably conserved from yeast to mammals. Nature (London) 334:213–218.
   PubMed Web of Science ®Google Scholar
• Burd, C. G., and G. Dreyfuss. 1994. Conserved structures and diversity of functions of RNA-binding proteins. Science 265:615–621.
   PubMed Web of Science ®Google Scholar
• Caceres, J. F., S. Stamm, D. M. Helfman, and A. R. Krainer. 1994. Regulation of alternative splicing in vivo by overexpression of antagonistic splicing factors. Science 265:1706–1709.
   PubMed Web of Science ®Google Scholar
• Christianson, T. W., R. S. Sikorski, M. Dante, J. H. Shero, and P. Hieter. 1992. Multifunctional yeast high-copy-number shuttle vectors. Gene 110:119–122.
   PubMed Web of Science ®Google Scholar
• Czaplinski, K., Y. Weng, K. W. Hagan, and S. W. Peltz. 1995. Purification and characterization of the Upf1 protein: a factor involved in translation and mRNA degradation. RNA 1:610–623.
   PubMedGoogle Scholar
• Dahmus, M. E. 1995. Phosphorylation of the C-terminal domain of RNA polymerase II. Biochim. Biophys. Acta 1261:171–182.
   PubMedGoogle Scholar
• Darnell, J. E., Jr. 1982. Variety in the level of gene control in eukaryotic cells. Nature (London) 297:365–371.
   PubMed Web of Science ®Google Scholar
• Das, A. 1993. Control of transcription termination by RNA-binding proteins. Annu. Rev. Biochem. 62:893–930.
   PubMed Web of Science ®Google Scholar
• DeMarini, D. J., M. Winey, D. Ursic, F. Webb, and M. R. Culbertson. 1992. SEN1, a positive effector of tRNA-splicing endonuclease in Saccharomyces cerevisiae. Mol. Cell. Biol. 12:2154–2164.
   PubMed Web of Science ®Google Scholar
• Dreyfuss, G., M. J. Matunis, S. Pinol-Roma, and C. G. Burd. 1993. hnRNP proteins and the biogenesis of mRNA. Annu. Rev. Biochem. 62:289–321.
   PubMed Web of Science ®Google Scholar
• Duan, D. R., A. Pause, W. H. Burgess, T. Aso, D. Y. T. Chen, K. P. Garrett, R. C. Conaway, J. W. Conaway, W. M. Linehan, and R. D. Klausner. 1995. Inhibition of transcription by the VHL tumor suppressor gene. Science 269:1402–1406.
   PubMed Web of Science ®Google Scholar
• Elliott, D. J., F. Stutz, A. Lescure, and M. Rosbash. 1994. mRNA nuclear export. Curr. Opin. Genet. Dev. 4:305–309.
   PubMedGoogle Scholar
• Frank, D., and C. Guthrie. 1992. An essential splicing factor, SLU7, mediates 3′ splice site choice in yeast. Genes Dev. 6:2112–2124.
   PubMedGoogle Scholar
• Fry, D. C., S. A. Kuby, and A. S. Mildvan. 1986. ATP-binding site of adenylate kinase: mechanistic implications of its homology with ras-encoded p21, F1-ATPase, and other nucleotide-binding proteins. Proc. Natl. Acad. Sci. USA 83:907–911.
   PubMed Web of Science ®Google Scholar
• Fu, X. D. 1995. The superfamily of arginine/serine-rich splicing factors. RNA 1:663–680.
   PubMed Web of Science ®Google Scholar
• Good, P. J. 1995. A conserved family of elav-like genes in vertebrates. Proc. Natl. Acad. Sci. USA 92:4557–4561.
   PubMed Web of Science ®Google Scholar
• Gorbalenya, A. E., E. V. Koonin, A. P. Donchenko, and V. M. Blinov. 1989. Two related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes. Nucleic Acids Res. 17:4713–4730.
   PubMed Web of Science ®Google Scholar
• Greenblatt, J., J. R. Nodwell, and S. W. Mason. 1993. Transcriptional anti-termination. Nature (London) 364:401–406.
   PubMed Web of Science ®Google Scholar
• Guthrie, C., and G. R. Fink (ed.). 1991. Guide to yeast genetics and molecular biology, vol. 194. Academic Press, San Diego, Calif.
   Google Scholar
• Hamer, D. H., D. J. Thiele, and J. E. Lemontt. 1985. Function and autoregulation of yeast copperthionein. Science 228:685–690.
   PubMedGoogle Scholar
• Hodgman, T. C. 1988. A new superfamily of replicative proteins. Nature (London) 333:22–23.
   PubMed Web of Science ®Google Scholar
• Hoffman, C. S., and F. Winston. 1987. A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli. Gene 57:267–272.
   PubMed Web of Science ®Google Scholar
• Kenan, D. J., C. C. Query, and J. D. Keene. 1991. RNA recognition: towards identifying determinants of specificity. Trends Biochem. Sci. 16:214–220.
   PubMedGoogle Scholar
• Kibel, A., O. Iliopoulos, J. A. DeCaprio, and W. G. Kaelin. 1995. Binding of the von Hippel-Lindau tumor suppressor protein to elongin B and C. Science 269:1444–1446.
   PubMed Web of Science ®Google Scholar
• Koonin, E. V. 1992. A new group of putative RNA helicases. Trends Biochem. Sci. 17:495–497.
   PubMedGoogle Scholar
• Kunkel, T. A., J. D. Roberts, and R. A. Zakour. Rapid and efficient site-specific mutagenesis without phenotypic selection. Methods Enzymol. 154:367–382.
   PubMedGoogle Scholar
• Lee, F. J., and J. Moss. 1993. An RNA-binding protein gene (RBP1) of Saccharomyces cerevisiae encodes a putative glucose-repressible protein containing two RNA recognition motifs. J. Biol. Chem. 268:15080–15087.
   PubMedGoogle Scholar
• Leeds, P., J. M. Wood, B.-S. Lee, and M. R. Culbertson. 1992. Gene products that promote mRNA turnover in Saccharomyces cerevisiae. Mol. Cell. Biol. 12:2165–2177.
   PubMed Web of Science ®Google Scholar
• Legrain, P., and M. Rosbash. 1989. Some cis- and trans-acting mutants for splicing target pre-mRNA to the cytoplasm. Cell 57:573–583.
   PubMed Web of Science ®Google Scholar
• Lesser, C. F., and C. Guthrie. 1993. Mutational analysis of pre-mRNA splicing in Saccharomyces cerevisiae using a sensitive new reporter gene, CUP1. Genetics 133:851–863.
   PubMedGoogle Scholar
• Lesser, C. F., and C. Guthrie. 1993. Mutations in U6 snRNA that alter splice site specificity: implications for the active site. Science 262:1982–1988.
   PubMedGoogle Scholar
• Liu, X., and J. E. Mertz. 1995. HnRNP L binds a cis-acting RNA sequence element that enables intron-independent gene expression. Genes Dev. 9:1766–1780.
   PubMed Web of Science ®Google Scholar
• Matunis, M. J., E. L. Matunis, and G. Dreyfuss. 1993. PUB1: a major yeast poly(A)+ RNA-binding protein. Mol. Cell. Biol. 13:6114–6123.
   PubMedGoogle Scholar
• Mayeda, A., and A. R. Krainer. 1992. Regulation of alternative pre-mRNA splicing by hnRNP A1 and splicing factor SF2. Cell 68:365–375.
   PubMed Web of Science ®Google Scholar
• Michael, W. M., M. Choi, and G. Dreyfuss. 1995. A nuclear export signal in hnRNP A1: a signal-mediated, temperature-dependent nuclear protein export pathway. Cell 83:415–422.
   PubMed Web of Science ®Google Scholar
• Nagai, K., K. Oubridge, N. Ito, J. Avis, and P. Evans. 1995. The RNP domain: a sequence-specific RNA-binding domain involved in processing and transport of RNA. Trends Biochem. Sci. 20:235–240.
   PubMedGoogle Scholar
• Negishi, Y., Y. Nishita, Y. Saegusa, I. Kakizaki, I. Galli, F. Kihara, K. Tamai, N. Miyajima, S. M. Iguchi-Ariga, and H. Ariga. 1994. Identification and cDNA cloning of single-stranded DNA binding proteins that interact with the region upstream of the human c-myc gene. Oncogene 9:1133–1143.
   PubMedGoogle Scholar
• Nevins, J. R. 1983. The pathway of eukaryotic mRNA formation. Annu. Rev. Biochem. 52:441–466.
   PubMed Web of Science ®Google Scholar
• Page, B. D., and M. Snyder. 1992. CIK1: a developmentally regulated spindle pole body-associated protein important for microtubule functions in Saccharomyces cerevisiae. Genes Dev. 6:1414–1429.
   PubMedGoogle Scholar
• Parker, R., P. G. Siliciano, and C. Guthrie. 1987. Recognition of the TAC-TAAC box during mRNA splicing in yeast involves base pairing to the U2-like snRNA. Cell 49:229–239.
   PubMed Web of Science ®Google Scholar
• Pikielny, C. W., and M. Rosbash. 1985. mRNA splicing efficiency in yeast and the contribution of nonconserved sequences. Cell 41:119–126.
   PubMed Web of Science ®Google Scholar
• Pinol-Roma, S., and G. Dreyfuss. 1992. Shuttling of pre-mRNA binding proteins between nucleus and cytoplasm. Nature (London) 355:730–732.
   PubMed Web of Science ®Google Scholar
• Platt, T. 1994. Rho and RNA: models for recognition and response. Mol. Microbiol. 11:983–990.
   PubMed Web of Science ®Google Scholar
• Ripmaster, T. L., and J. L. Woolford, Jr. 1993. A protein containing conserved RNA-recognition motifs is associated with ribosomal subunits in Saccharomyces cerevisiae. Nucleic Acids Res. 21:3211–3216.
   PubMedGoogle Scholar
• Robinow, S., A. R. Campos, K. M. Yao, and K. White. 1988. The elav gene product of Drosophila, required in neurons, has three RNP consensus motifs. Science 242:1570–1572.
   PubMed Web of Science ®Google Scholar
• Rose, M. D., P. Novick, J. H. Thomas, D. Botstein, and G. R. Fink. 1987. A Saccharomyces cerevisiae genomic plasmid bank based on a centromere-containing shuttle vector. Gene 60:237–243.
   PubMed Web of Science ®Google Scholar
• Rothstein, R. 1991. Targeting, disruption, replacement, and allele rescue: integrative DNA transformation in yeast. Methods Enzymol. 194:281–301.
   PubMed Web of Science ®Google Scholar
• Russo, P., and F. Sherman. 1989. Transcription terminates near the poly(A) site in the CYC1 gene of the yeast Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 86:8348–8352.
   PubMedGoogle Scholar
• Schiestl, R. H., and R. D. Gietz. 1989. High efficiency transformation of intact yeast cells using single stranded nucleic acids as a carrier. Curr. Genet. 16:339–346.
   PubMed Web of Science ®Google Scholar
• Schneiter, R., T. Kadowaki, and A. M. Tartakoff. 1995. mRNA transport in yeast: time to reinvestigate the functions of the nucleus. Mol. Biol. Cell 6:357–370.
   PubMedGoogle Scholar
• Sikorski, R. S., and P. Hieter. 1989. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122:19–27.
   PubMed Web of Science ®Google Scholar
• Soulard, M., V. Della Valle, M. C. Siomi, S. Pinol-Roma, P. Codogno, C. Bauvy, M. Bellini, J. C. Lacroix, G. Monod, G. Dreyfuss, et al. 1993. hnRNP G: sequence and characterization of a glycosylated RNA-binding protein. Nucleic Acids Res. 21:4210–4217.
   PubMed Web of Science ®Google Scholar
• Spencer, C. A., and M. Groudine. 1990. Transcription elongation and eukaryotic gene regulation. Oncogene 5:777–785.
   PubMed Web of Science ®Google Scholar
• Steinmetz, E. J., and D. A. Brow. Unpublished observations.
   Google Scholar
• Story, R. M., and T. A. Steitz. 1992. Structure of the recA protein-ADP complex. Nature (London) 355:374–376.
   PubMed Web of Science ®Google Scholar
• Sun, Q., A. Mayeda, R. K. Hampson, A. R. Krainer, and F. M. Rottman. 1993. General splicing factor SF2/ASF promotes alternative splicing by binding to an exonic splicing enhancer. Genes Dev. 7:2598–2608.
   PubMed Web of Science ®Google Scholar
• Tian, Q., M. Streuli, H. Saito, S. F. Schlossman, and P. Anderson. 1991. A polyadenylate binding protein localized to the granules of cytolytic lymphocytes induces DNA fragmentation in target cells. Cell 67:629–639.
   PubMed Web of Science ®Google Scholar
• Treco, D. A. 1989. Saccharomyces cerevisiae, p. 13.12.11–13.12.13. In F. M. Ausubel, R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl (ed.), Current protocols in molecular biology. Greene Publishing Associates and Wiley Interscience, New York.
   Google Scholar
• Ursic, D., D. J. DeMarini, and M. R. Culbertson. 1995. Inactivation of the yeast Sen1 protein affects the localization of nucleolar proteins. Mol. Gen. Genet. 249:571–584.
   PubMedGoogle Scholar
• Vijayraghavan, U., R. Parker, J. Tamm, Y. Iimura, J. Rossi, J. Abelson, and C. Guthrie. 1986. Mutations in conserved intron sequences affect multiple steps in the yeast splicing pathway, particularly assembly of the spliceosome. EMBO J. 5:1683–1695.
   PubMed Web of Science ®Google Scholar
• Wilson, S. M., K. V. Datar, M. R. Paddy, J. R. Swedlow, and M. S. Swanson. 1994. Characterization of nuclear polyadenylated RNA-binding proteins in Saccharomyces cerevisiae. J. Cell Biol. 127:1173–1184.
   PubMedGoogle Scholar
• Yang, X., M. R. Bani, S. J. Lu, S. Rowan, Y. Ben-David, and B. Chabot. 1994. The A1 and A1B proteins of heterogeneous nuclear ribonucleoparticles modulate 5′ splice site selection in vivo. Proc. Natl. Acad. Sci. USA 91:6924–6928.
   PubMedGoogle Scholar
• Yuryev, A., M. Patturajan, Y. Litingtung, R. V. Joshi, C. Gentile, M. Gebara, and J. L. Corden. 1996. The CTD of RNA polymerase II interacts with a novel set of SR-like proteins. Proc. Natl. Acad. Sci. USA 93:6975–6980.
   PubMed Web of Science ®Google Scholar