Linking splicing to Pol II transcription stabilizes pre-mRNAs and influences splicing patterns

PLoS Biology

Volumn 4, Issue 6, 2006, Pages 0943-0951

  Hicks, Martin J ^a   Yang, Chin Rang ^a,b,c   Kotlajich, Matthew V ^a   Hertel, Klemens J ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA PRECURSOR; RNA POLYMERASE II; BACTERIOPHAGE T7 RNA POLYMERASE; DNA DIRECTED RNA POLYMERASE; GLOBIN; MESSENGER RNA; RNA PRECURSOR; VIRUS PROTEIN;

ARTICLE; CELL NUCLEUS; CELL PROTECTION; CONCENTRATION (PARAMETERS); GENE EXPRESSION; HUMAN; HUMAN CELL; IN VITRO STUDY; PROTEIN INTERACTION; RNA DEGRADATION; RNA SPLICING; RNA SYNTHESIS; RNA TRANSCRIPTION; BIOLOGICAL MODEL; GENETIC TRANSCRIPTION; GENETICS; HELA CELL; KINETICS; METABOLISM; PHYSIOLOGY; PLASMID; RNA STABILITY; SPLICEOSOME;

DNA-DIRECTED RNA POLYMERASES; GLOBINS; HELA CELLS; HUMANS; KINETICS; MODELS, GENETIC; PLASMIDS; RNA POLYMERASE II; RNA PRECURSORS; RNA SPLICE SITES; RNA SPLICING; RNA STABILITY; RNA, MESSENGER; SPLICEOSOMES; TRANSCRIPTION, GENETIC; VIRAL PROTEINS;

EID: 33745220323     PISSN: 15457885     EISSN: 15457885     Source Type: Journal    
DOI: 10.1371/journal.pbio.0040147     Document Type: Article

References (52)

1. Black DL (2003) Mechanisms of alternative pre-messenger RNA splicing. Annu Rev Biochem 72: 291-336.
2. Black DL (2000) Protein diversity from alternative splicing: A challenge for bioinformatics and post-genome biology. Cell 103: 367-370.
3. Graveley BR (2001) Alternative splicing: Increasing diversity in the proteomic world. Trends Genet 17: 100-107.
4. Maniatis T, Tasic B (2002) Alternative pre-mRNA splicing and proteome expansion in metazoans. Nature 418: 236-243.
5. Cramer P, Pesce CG, Baralle FE, Kornblihtt AR (1997) Functional association between promoter structure and transcript alternative splicing. Proc Natl Acad Sci U S A 94: 11456-11460.
6. Auboeuf D, Honig A, Berget SM, O'Malley BW (2002) Coordinate regulation of transcription and splicing by steroid receptor coregulators. Science 298: 416-419.
7. Kornblihtt AR, de la Mata M, Fededa JP, Munoz MJ, Nogues G (2004) Multiple links between transcription and splicing. RNA 10: 1489-1498.
8. Fededa JP, Petrillo E, Gelfand MS, Neverov AD, Kadener S, et al. (2005) A polar mechanism coordinates different regions of alternative splicing within a single gene. Mol Cell 19: 393-404.
9. Maniatis T, Reed R (2002) An extensive network of coupling among gene expression machines. Nature 416: 499-506.
10. Proudfoot NJ, Furger A, Dye MJ (2002) Integrating mRNA processing with transcription. Cell 108: 501-512.
11. Neugebauer KM (2002) On the importance of being co-transcriptional. J Cell Sci 115: 3865-3871.
12. Bentley D (2002) The mRNA assembly line: Transcription and processing machines in the same factory. Curr Opin Cell Biol 14: 336-342.
13. McCracken S, Fong N, Yankulov K, Ballantyne S, Pan G, et al. (1997) The C-terminal domain of RNA polymerase II couples mRNA processing to transcription. Nature 385: 357-361.
14. McCracken S, Fong N, Rosonina E, Yankulov K, Brothers G, et al. (1997) 5′-capping enzymes are targeted to pre-mRNA by binding to the phosphorylated carboxy-terminal domain of RNA polymerase II. Genes Dev 11: 3306-3318.
15. Cho EJ, Rodriguez CR, Takagi T, Buratowski S (1998) Allosteric interactions between capping enzyme subunits and the RNA polymerase II carboxy-terminal domain. Genes Dev 12: 3482-2487.
16. Ho CK, Sriskanda V, McCracken S, Bentley D, Schwer B, et al. (1998) The guanylyltransferase domain of mammalian mRNA capping enzyme binds to the phosphorylated carboxyl-terminal domain of RNA polymerase II. J Biol Chem 273: 9577-9585.
17. Ho CK, Shuman S (1999) Distinct roles for CTD Ser-2 and Ser-5 phosphorylation in the recruitment and allosteric activation of mammalian mRNA capping enzyme. Mol Cell 3: 405-411.
18. Licatalosi DD, Geiger G, Minet M, Schroeder S, Cilli K, et al. (2002) Functional interaction of yeast pre-mRNA 3′ end processing factors with RNA polymerase II. Mol Cell 9: 1101-1111.
19. Cramer P, Caceres JF, Cazalla D, Kadener S, Muro AF, et al. (1999) Coupling of transcription with alternative splicing: RNA pol II promoters modulate SF2/ASF and 9G8 effects on an exonic splicing enhancer. Mol Cell 4: 251-258.
20. Pagani F, Stuani C, Zuccato E, Kornblihtt AR, Baralle FE (2003) Promoter architecture modulates CFTR exon 9 skipping. J Biol Chem 278: 1511-1517.
21. Robson-Dixon ND, Garcia-Blanco MA (2004) MAZ elements alter transcription elongation and silencing of the fibroblast growth factor receptor 2 exon IIIb. J Biol Chem 279: 29075-29084.
22. Hirose Y, Tacke R, Manley JL (1999) Phosphorylated RNA polymerase II stimulates pre-mRNA splicing. Genes Dev 13: 1234-1239.
23. Eperon LP, Graham IR, Griffiths AD, Eperon IC (1988) Effects of RNA secondary structure on alternative splicing of pre-mRNA: Is folding limited to a region behind the transcribing RNA polymerase? Cell 54: 393-401.
24. Roberts GC, Gooding C, Mak HY, Proudfoot NJ, Smith CW (1998) Cotranscriptional commitment to alternative splice site selection. Nucleic Acids Res 26: 5568-5572.
25. Kadener S, Fededa JP, Rosbash M, Kornblihtt AR (2002) Regulation of alternative splicing by a transcriptional enhancer through RNA pol II elongation. Proc Natl Acad Sci U S A 99: 8185-8190.
26. Nogues G, Kadener S, Cramer P, Bentley D, Kornblihtt AR (2002) Transcriptional activators differ in their abilities to control alternative splicing. J Biol Chem 277: 43110-43114.
27. de la Mata M, Alonso CR, Kadener S, Fededa JP, Blaustein M, et al. (2003) A slow RNA polymerase II affects alternative splicing in vivo. Mol Cell 12: 525-532.
28. Shilatifard A, Conaway RC, Conaway JW (2003) The RNA polymerase II elongation complex. Annu Rev Biochem 72: 693-715.
29. Skinner GM, Baumann CG, Quinn DM, Molloy JE, Hoggett JG (2004) Promoter binding, initiation, and elongation by bacteriophage T7 RNA polymerase. A single-molecule view of the transcription cycle. J Biol Chem 279: 3239-3244.
30. Audibert A, Weil D, Dautry F (2002) In vivo kinetics of mRNA splicing and transport in mammalian cells. Mol Cell Biol 22: 6706-6718.
31. Hicks MJ, Lam BJ, Hertel KJ (2005) Analyzing mechanisms of alternative pre-mRNA splicing using in vitro splicing assays. Methods 37: 306-313.
32. Black DL, Chabot B, Steitz JA (1985) U2 as well as U1 small nuclear ribonucleoproteins are involved in premessenger RNA splicing. Cell 42: 737-750.
33. Furman E, Glitz DG (1995) Purification of the spliceosome A-complex and its visualization by electron microscopy. J Biol Chem 270: 15515-15522.
34. Yang CR, Shapiro BE, Mjolsness ED, Hatfield GW (2005) An enzyme mechanism language for the mathematical modeling of metabolic pathways. Bioinformatics 21: 774-780.
35. Ibrahim EC, Schaal TD, Hertel KJ, Reed R, Maniatis T (2005) Serine/arginine-rich protein-dependent suppression of exon skipping by exonic splicing enhancers. Proc Natl Acad Sci U S A 102: 5002-5007.
36. Gornemann J, Kotovic KM, Hujer K, Neugebauer KM (2005) Cotranscriptional spliceosome assembly occurs in a stepwise fashion and requires the cap binding complex. Mol Cell 19: 53-63.
37. Lacadie SA, Rosbash M (2005) Cotranscriptional spliceosome assembly dynamics and the role of U1 snRNA: 5′ ss base pairing in yeast. Mol Cell 19: 65-75.
38. Burge CB, Tuschl T, Sharp PA (1999) Splicing of precursors to mRNAs by the spliceosome. In: Gesteland RF, Cech TR, Atkins JF, editors. The RNA world. 2nd edition. Cold Spring Harbor (New York): Cold Spring Harbor Laboratory Press. pp. 525-560.
39. Fairbrother WG, Yeh RF, Sharp PA, Burge CB (2002) Predictive identification of exonic splicing enhancers in human genes. Science 297: 1007-1013.
40. Natalizio BJ, Garcia-Blanco MA (2005) In vitro coupled transcription splicing. Methods 37: 314-322.
41. Reed R, Maniatis T (1986) A role for exon sequences and splice-site proximity in splice-site selection. Cell 46: 681-690.
42. Fox-Walsh KL, Dou Y, Lam BJ, Hung S, Baldi PF, et al. (2005) The architecture of pre-mRNAs affects mechanisms of splice-site pairing. Proc Natl Acad Sci USA 102: 16176-16181.
43. Douziech M, Forget D, Greenblatt J, Coulombe B (1999) Topological localization of the carboxyl-terminal domain of RNA polymerase II in the initiation complex. J Biol Chem 274: 19868-19873.
44. Cramer P, Bushnell DA, Kornberg RD (2001) Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science 292: 1863-1876.
45. Morris DP, Greenleaf AL (2000) The splicing factor, Prp40, binds the phosphorylated carboxyl-terminal domain of RNA polymerase II. J Biol Chem 275: 39935-39943.
46. Bird G, Zorio DA, Bentley DL (2004) RNA polymerase II carboxy-terminal domain phosphorylation is required for cotranscriptional pre-mRNA splicing and 3′ end formation. Mol Cell Biol 24: 8963-8969.
47. Fong N, Bentley DL (2001) Capping, splicing, and 3′ processing are independently stimulated by RNA polymerase II: Different functions for different segments of the CTD. Genes Dev 15: 1783-1795.
48. Bauren G, Wieslander L (1994) Splicing of Balbiani ring 1 gene pre-mRNA occurs simultaneously with transcription. Cell 76: 183-192.
49. Dignam JD, Lebovitz RM, Roeder RG (1983) Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res 11: 1475-1489.
50. Lim SR, Hertel KJ (2004) Commitment to splice-site pairing coincides with A complex formation. Mol Cell 15: 477-483.
51. Madocsai C, Lim SR, Geib T, Lam BJ, Hertel KJ (2005) Correction of SMN2 pre-mRNA splicing by antisense U7 small nuclear RNAs. Mol Ther 12: 1013-1022.
52. Shapiro BE, Levchenko A, Meyerowitz EM, Wold BJ, Mjolsness ED (2003) Cellerator: Extending a computer algebra system to include biochemical arrows for signal transduction simulations. Bioinformatics 19: 677-678.