Perturbation of transcription elongation influences the fidelity of internal exon inclusion in Saccharomyces cerevisiae

RNA

Volumn 9, Issue 8, 2003, Pages 993-1006

  Howe, Kenneth James ^a   Kane, Caroline M ^a   Ares Jr , Manuel ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

6 azauracil; Exon definition; Intron definition; RPB2; Yeast

Indexed keywords

DNA; ELONGATION FACTOR; ELONGATION FACTOR TFIIS; RNA POLYMERASE; SMALL NUCLEAR RNA; UNCLASSIFIED DRUG;

ARTICLE; EXON; GENE MUTATION; LAC GENE; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; REPRESSOR GENE; RNA SPLICING; RNA TRANSCRIPTION; SACCHAROMYCES CEREVISIAE; SPLICEOSOME;

BASE SEQUENCE; DNA PRIMERS; DYNEIN ATPASE; EXONS; INTRONS; MUTAGENESIS, SITE-DIRECTED; MUTATION; PHENANTHROLINES; RNA PRECURSORS; RNA SPLICING; RNA, MESSENGER; SACCHAROMYCES CEREVISIAE; TRANSCRIPTIONAL ELONGATION FACTORS;

SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 0041305816     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.5390803     Document Type: Article

References (70)

1. Abovich, N. and Rosbash, M. 1997. Cross-intron bridging interactions in the yeast commitment complex are conserved in mammals. Cell 89: 403-412.
2. Abovich, N., Liao, X.C., and Rosbash, M. 1994. The yeast MUD2 protein: An interaction with PRP11 defines a bridge between commitment complexes and U2 snRNP addition. Genes & Dev. 8: 843-854.
3. Aebi, M. and Weissman, S.M. 1987. Precision and orderliness in splicing. Trends Genet. 3: 102-107.
4. Archambault, J., Lacroute, F., Ruet, A., and Friesen, J.D. 1992. Genetic interaction between transcription elongation factor TFIIS and RNA polymerase II. Mol. Cell. Biol. 12: 4142-4152.
5. Ares Jr., M. and Igel, A.H. 1990. Lethal and temperature-sensitive mutations and their suppressors identify an essential structural element in U2 small nuclear RNA. Genes & Dev. 4: 2132-2145.
6. Ares Jr., M., Grate, L., and Pauling, M.H. 1999. A handful of intron-containing genes produces the lion's share of yeast mRNA. RNA 5: 1138-1139.
7. Bentley, D. 2002. The mRNA assembly line: Transcription and processing machines in the same factory. Curr. Opin. Cell. Biol. 14: 336-342.
8. Berget, S.M. 1995. Exon recognition in vertebrate splicing. J. Biol. Chem. 270: 2411-2414.
9. Blandin, G., Durrens, P., Tekaia, F., Aigle, M., Bolotin-Fukuhara, M., Bon, E., Casaregola, S., de Montigny, J., Gaillardin, C., Lepingle, A., et al. 2000. Genomic exploration of the hemiascomycetous yeasts, 4: The genome of Saccharomyces cerevisiae revisited. FEBS Lett. 487: 31-36.
10. Brow, D.A. 2002. Allosteric cascade of spliceosome activation. Annu. Rev. Genet. 36: 333-360.
11. Cadwell, R.C. and Joyce, G.F. 1992. Randomization of genes by PCR mutagenesis. PCR Methods Appl. 2: 28-33.
12. Carlo, T., Sterner, D.A., and Berget, S.M. 1996. An intron splicing enhancer containing a G-rich repeat facilitates inclusion of a vertebrate micro-exon. RNA 2: 342-353.
13. Carlo, T., Sierra, R., and Berget, S.M. 2000. A 5′ splice site-proximal enhancer binds SF1 and activates exon bridging of a microexon. Mol. Cell. Biol. 20: 3988-3995.
14. Christie, K.R., Awrey, D.E., Edwards, A.M., and Kane, C.M. 1994. Purified yeast RNA polymerase II reads through intrinsic blocks to elongation in response to the yeast TFIIS analogue, P37. J. Biol. Chem. 269: 936-943.
15. Clarke, L. and Carbon, J. 1976. A colony bank containing synthetic Col El hybrid plasmids representative of the entire E. coli genome. Cell 9: 91-99.
16. Cramer, P., Pesce, C.G., Baralle, F.E., and Kornblihtt, A.R. 1997. Functional association between promoter structure and transcript alternative splicing. Proc. Natl. Acad. Sci. 94: 11456-11460.
17. Davie, J.K. and Kane, C.M. 2000. Genetic interactions between TFIIS and the Swi-Snf chromatin-remodeling complex. Mol. Cell. Biol. 20: 5960-5973.
18. Davis, C.A., Grate, L., Spingola, M., and Ares Jr., M. 2000. Test of intron predictions reveals novel splice sites, alternatively spliced mRNAs and new introns in meiotically regulated genes of yeast. Nucleic Acids Res. 28: 1700-1706.
19. Dick, T., Surana, U., and Chia, W. 1996. Molecular and genetic characterization of SLC1, a putative Saccharomyces cerevisiae homolog of the metazoan cytoplasmic dynein light chain 1. Mol. Gen. Genet. 251: 38-43.
20. Exinger, F. and Lacroute, F. 1992. 6-Azauracil inhibition of GTP biosynthesis in Saccharomyces cerevisiae. Curr. Genet. 22: 9-11.
21. Fong, Y.W. and Zhou, Q. 2001. Stimulatory effect of splicing factors on transcriptional elongation. Nature 414: 929-933.
22. Fouser, L.A. and Friesen, J.D. 1986. Mutations in a yeast intron demonstrate the importance of specific conserved nucleotides for the two stages of nuclear mRNA splicing. Cell 45: 81-93.
23. Franklin, T.J. and Cook, J.M. 1969. The inhibition of nucleic acid synthesis by mycophenolic acid. Biochem. J. 113: 515-524.
24. Furger, A., O'Sullivan, J.M., Binnie, A., Lee, B.A., and Proudfoot, N.J. 2002. Promoter proximal splice sites enhance transcription. Genes & Dev. 16: 2792-2799.
25. Good, L. and Nazar, R.N. 1992. An improved thermal cycle for two-step PCR-based targeted mutagenesis. Nucleic Acids Res. 20: 4934.
26. Grate, L. and Ares Jr., M. 2002. Searching yeast intron data at Ares lab Web site. Methods Enzymol. 350: 380-392.
27. Hamer, D.H., Thiele, D.J., and Lemontt, J.E. 1985. Function and autoregulation of yeast copperthionein. Science 228: 685-690.
28. - mutant. Proc. Natl. Acad. Sci. 90: 7034-7038.
29. Hill, J., Ian, K.A., Donald, G., and Griffiths, D.E. 1991. DMSO-enhanced whole cell yeast transformation. Nucleic Acids Res. 19: 5791.
30. Howe, K.J. 2002. RNA polymerase II conducts a symphony of pre-mRNA processing activities. Biochim. Biophys. Acta 1577: 308-324.
31. Howe, K.J. and Ares Jr., M. 1997. Intron self-complementarity enforces exon inclusion in a yeast pre-mRNA. Proc. Natl. Acad. Sci. 94: 12467-12472.
32. Izban, M.G. and Luse, D.S. 1992. The RNA polymerase II ternary complex cleaves the nascent transcript in a 3′-5′ direction in the presence of elongation factor SII. Genes & Dev. 6: 1342-1356.
33. Kadener, S., Cramer, P., Nogues, G., Cazalla, D., de la Mata, M., Fededa, J.P., Werbajh, S.E., Srebrow, A., and Kornblihtt, A.R. 2001. Antagonistic effects of T-Ag and VP16 reveal a role for RNA pol II elongation on alternative splicing. EMBO J. 20: 5759-5768.
34. Kadener, S., Fededa, J.P., Rosbash, M., and Kornblihtt, A.R. 2002. Regulation of alternative splicing by a transcriptional enhancer through RNA pol II elongation. Proc. Natl. Acad. Sci. 99: 8185-8190.
35. Kwek, K.Y., Murphy, S., Furger, A., Thomas, B., O'Gorman, W., Kimura, H., Proudfoot, N.J., and Akoulitchev, A. 2002. U1 snRNA associates with TFIIH and regulates transcriptional initiation. Nat. Struct. Biol. 9: 800-805.
36. Lei, E.P. and Silver, P.A. 2002. Intron status and 3′-end formation control cotranscriptional export of mRNA. Genes & Dev. 16: 2761-2766.
37. Lei, E.P., Krebber, H., and Silver, P.A. 2001. Messenger RNAs are recruited for nuclear export during transcription. Genes & Dev. 15: 1771-1782.
38. Lennon III, J.C., Wind, M., Saunders, L., Hock, M.B., and Reines, D. 1998. Mutations in RNA polymerase II and elongation factor SII severely reduce mRNA levels in Saccharomyces cerevisiae. Mol. Cell. Biol. 18: 5771-5779.
39. Lesser, C.F. and Guthrie, C. 1993. Mutational analysis of pre-mRNA splicing in Saccharomyces cerevisiae using a sensitive new reporter gene, CUP1. Genetics 133: 851-863.
40. Lindstrom, D.L., Squazzo, S.L., Muster, N., Burckin, T.A., Wachter, K.C., Emigh, C.A., McCleery, J.A., Yates III, J.R., and Hartzog, G.A. 2003. Dual roles for Spt5 in pre-mRNA processing and transcription elongation revealed by identification of Spt5-associated proteins. Mol. Cell. Biol. 23: 1368-1378.
41. Lopez, A.J. 1998. Alternative splicing of pre-mRNA: Developmental consequences and mechanisms of regulation. Annu. Rev. Genet. 32: 279-305.
42. Lopez, P.J. and Seraphin, B. 2000. Uncoupling yeast intron recognition from transcription with recursive splicing. EMBO Rep. 1: 334-339.
43. Luukkonen, B.G. and Seraphin, B. 1998. Construction of an in vivo-regulated U6 snRNA transcription unit as a tool to study U6 function. RNA 4: 231-238.
44. Miraglia, L., Seiwert, S., Igel, A.H., and Ares Jr., M. 1991. Limited functional equivalence of phylogenetic variation in small nuclear RNA: Yeast U2 RNA with altered branchpoint complementarity inhibits splicing and produces a dominant lethal phenotype. Proc. Natl. Acad. Sci. 88: 7061-7065.
45. Nakanishi, T., Nakano, A., Nomura, K., Sekimizu, K., and Natori, S. 1992. Purification, gene cloning, and gene disruption of the transcription elongation factor S-II in Saccharomyces cerevisiae. J. Biol. Chem. 267: 13200-13204.
46. Nakanishi, T., Shimoaraiso, M., Kubo, T., and Natori, S. 1995. Structure-function relationship of yeast S-II in terms of stimulation of RNA polymerase II, arrest relief, and suppression of 6-azauracil sensitivity. J. Biol. Chem. 270: 8991-8995.
47. Neugebauer, K.M. 2002. On the importance of being co-transcriptional. J. Cell. Sci. 115: 3865-3871.
48. Newman, A.J., Lin, R.J., Cheng, S.C., and Abelson, J. 1985. Molecular consequences of specific intron mutations on yeast mRNA splicing in vivo and in vitro. Cell 42: 335-344.
49. Nogues, G., Kadener, S., Cramer, P., Bentley, D., and Kornblihtt, A.R. 2002. Transcriptional activators differ in their abilities to control alternative splicing. J. Biol. Chem. 277: 43110-43114.
50. Parker, R., Siliciano, P.G., and Guthrie, C. 1987. Recognition of the TACTAAC box during mRNA splicing in yeast involves base pairing to the U2-like snRNA. Cell 49: 229-239.
51. Powell, W. and Reines, D. 1996. Mutations in the second largest subunit of RNA polymerase II cause 6-azauracil sensitivity in yeast and increased transcriptional arrest in vitro. J. Biol. Chem. 271: 6866-6873.
52. Proudfoot, N.J., Furger, A., and Dye, M.J. 2002. Integrating mRNA processing with transcription. Cell 108: 501-512.
53. Rain, J.C. and Legrain, P. 1997. In vivo commitment to splicing in yeast involves the nucleotide upstream from the branch site conserved sequence and the Mud2 protein. EMBO J. 16: 1759-1771.
54. Reines, D., Ghanouni, P., Li, Q.Q., and Mote Jr., J. 1992. The RNA polymerase II elongation complex: Factor-dependent transcription elongation involves nascent RNA cleavage. J. Biol. Chem. 267: 15516-15522.
55. Reines, D., Ghanouni, P., Gu, W., Mote Jr., J., and Powell, W. 1993. Transcription elongation by RNA polymerase II: Mechanism of SII activation. Cell. Mol. Biol. Res. 39: 331-338.
56. Robberson, B.L., Cote, G.J., and Berget, S.M. 1990. Exon definition may facilitate splice site selection in RNAs with multiple exons. Mol. Cell. Biol. 10: 84-94.
57. Roberts, G.C., Gooding, C., Mak, H.Y., Proudfoot, N.J., and Smith, C.W. 1998. Co-transcriptional commitment to alternative splice site selection. Nucleic Acids Res. 26: 5568-5572.
58. Sambrook, J., Fritsch, E.F., and Maniatis, T. 1989. Molecular cloning: A laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
59. Santiago, T.C., Purvis, I.J., Bettany, A.J., and Brown, A.J. 1986. The relationship between mRNA stability and length in Saccharomyces cerevisiae. Nucleic Acids Res. 14: 8347-8360.
60. Sherman F. Getting started with yeast. Methods Enzymol. 194: 3-21.
61. Sikorski, R.S. and Hieter, P. 1989. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122: 19-27.
62. Smith, C.W. and Valcarcel, J. 2000. Alternative pre-mRNA splicing: The logic of combinatorial control. Trends Biochem. Sci. 25: 381-388.
63. Staley, J.P. and Guthrie, C. 1998. Mechanical devices of the spliceosome: Motors, clocks, springs, and things. Cell 92: 315-326.
64. Talerico, M. and Berget, S.M. 1990. Effect of 5′ splice site mutations on splicing of the preceding intron. Mol. Cell. Biol. 10: 6299-6305.
65. -. 1994. Intron definition in splicing of small Drosophila introns. Mol. Cell. Biol. 14: 3434-3445.
66. Tian, H. 2001. RNA ligands generated against complex nuclear targets indicate a role for U1 snRNP in co-ordinating transcription and RNA splicing. FEBS Lett. 509: 282-286.
67. Treich, I., Carles, C., Sentenac, A., and Riva, M. 1992. Determination of lysine residues affinity labeled in the active site of yeast RNA polymerase IIB by mutagenesis. Nucleic Acids Res. 20: 4721-4725.
68. Uptain, S.M., Kane, C.M., and Chamberlin, M.J. 1997. Basic mechanisms of transcript elongation and its regulation. Annu. Rev. Biochem. 66: 117-172.
69. Vijayraghavan, U., Parker, R., Tamm, J., Iimura, Y., Rossi, J., Abelson, J., and Guthrie, C. 1986. Mutations in conserved intron sequences affect multiple steps in the yeast splicing pathway, particularly assembly of the spliceosome. EMBO J. 5: 1683-1695.
70. Yan, D. and Ares Jr., M. 1996. Invariant U2 RNA sequences bordering the branchpoint recognition region are essential for interaction with yeast SF3a and SF3b subunits. Mol. Cell. Biol. 16: 818-828.