Control of alternative pre-mRNA splicing by RNA pol II elongation: Faster is not always better

IUBMB Life

Volumn 55, Issue 4-5, 2003, Pages 235-241

  Nogués, Guadalupe ^a   Kadener, Sebastián ^a,b   Cramer, Paula ^a,c   De la Mata, Manuel ^a   Fededa, Juan Pablo ^a   Blaustein, Matías ^a   Srebrow, Anabella ^a   Kornblihtt, Alberto R ^a  

^a UNIVERSIDAD DE BUENOS AIRES   (Argentina)

^b BRANDEIS UNIVERSITY   (United States)

^c HARVARD UNIVERSITY   (United States)

Author keywords

Alternative splicing; Elongation; mRNA processing; RNA polymerase II; Transcription

Indexed keywords

CALCITONIN GENE RELATED PEPTIDE; FIBRONECTIN; HERMES ANTIGEN; MESSENGER RNA; PROTEIN; PROTEOME; TRANSCRIPTION FACTOR;

ALTERNATIVE RNA SPLICING; ANIMAL CELL; CONTROLLED STUDY; CYSTIC FIBROSIS; DNA TEMPLATE; GENE CONTROL; GENE FUNCTION; GENETIC CODE; GENETIC TRANSCRIPTION; MAMMALIAN GENETICS; NONHUMAN; PROMOTER REGION; PROTEIN RNA BINDING; PROTEOMICS; REGULATORY MECHANISM; REVIEW;

ALTERNATIVE SPLICING; ANIMALS; MODELS, GENETIC; RNA POLYMERASE II; RNA PRECURSORS; RNA, MESSENGER; RNA-BINDING PROTEINS; TRANSCRIPTION, GENETIC;

ANIMALIA; MAMMALIA;

EID: 0038491212     PISSN: 15216543     EISSN: None     Source Type: Journal    
DOI: 10.1080/1521654031000119830     Document Type: Review

References (48)

1. Bentley, D. (2002) The mRNA assembly line: transcription and processing machines in the same factory. Curr. Op. Cell Biol. 14, 336-342.
2. Travers, A. (1999) Chromatin modification by DNA tracking. Proc. Natl. Acad. Sci. USA 96, 13634-13637.
3. Maniatis, T., and Reed, R. (2002) An extensive network of coupling among gene expression machines. Nature 416, 499-506.
4. Proudfoot, N. J., Furger, A., and Dye, M. J. (2002) Integrating mRNA processing with transcription. Cell 108, 501-512.
5. Neugebauer, K. M. (2002) On the importance of being cotranscriptional. J. Cell Sci. 115, 3865.
6. McCracken, S., Fong, N., Yankulov, K., Ballantyne, S., Pan, G., Greenblatt, J., Patterson, S. D., Wickens, M., and Bentley, D. L. (1997) The C-terminal domain of RNA polymerase II couples mRNA processing to transcription. Nature 385, 357-361.
7. Fong, N., and Bentley, D. L. (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.
8. Schroeder, S., Schwer, B., Shuman, S., and Bentley, D. L. (2000) Dynamic association of capping enzymes with transcribing RNA polymerase II. Genes Dev. 14, 2435-2440.
9. Licatalosi, D. D., Geiger, G., Minet, M., Schroeder, S., Cilli, K., McNeil, J. B., and Bentley, D. L. (2002) Functional interaction of yeast pre-mRNA 3′ end processing factors with RNA polymerase II Mol. Cell 9, 1101-1111.
10. Misteli. T., and Spector, D. L. (1999) RNA polymerase II targets pre-mRNA splicing factors to transcription sites in vivo. Mol. Cell 3, 697-705.
11. Black, D. L. (2000) Protein diversity from alternative splicing: a challenge for bioinformatics and post-genome biology. Cell 103, 367-370.
12. Gutman, A., and Kornblihtt, A. R. (1987) Identification of a third region of cell-specific alternative splicing in human fibronectin mRNA. Proc. Natl. Acad. Sci. USA 84, 7179-7182.
13. Schmucker, D., Clemens, J. C., Shu. H., Worby, C. A., Xiao, J., Muda, M., Dixon, J. E., and Zipursky, S. L. (2000) Drosophila DSCAM is an axon guidance receptor exhibiting extraordinary molecular diversity. Cell 101, 671-684.
14. Croft, L., Schandorff, S., Clark, F., Burrage, K., Arctander, P., and Mattick, J. S. (2000) ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome. Nature Genet. 24, 340-341.
15. Mouse Genome Sequencing Consortium. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520-562.
16. Hanamura, A., Cáceres, J. F., Mayeda, A., Franza, Jr. B. R., and Krainer, A. R. (1998) Regulated tissue-specific expression of antagonistic pre-mRNA splicing factors. RNA 4, 430-444.
17. Misteli, T., Cáceres, J. F., and Spector, D. L. (1997) The dynamics of a pre-mRNA splicing factor in living cells. Nature 387, 523-527.
18. Phair, R. D., and Misteli, T. (2000) High mobility of proteins in the mammalian cell nucleus. Nature 404, 604-609.
19. Neugebauer, K. M., and Roth, M. B. (1997) Distribution of pre-mRNA splicing factors at sites of RNA polymerase II transcription. Genes Dev. 11, 1148-1159.
20. 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. USA 94, 11456-11460.
21. Cramer, P., Cáceres, J. F., Cazalla, D., Kadener, S., Muro, A. F., Baralle, F. E., and Kornblihtt, A. R. (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.
22. Kadener, S., Cramer, P., Nogués, G., Cazalla, D., de la Mata, M., Fededa, J. P., Werbajh, S., Srebrow, A., and Kornblihtt, A. R. (2001) EMBO J. 20, 5759-5768.
23. Aboeuf, D., Hönig, A., Berget, S. M., and O'Malley, B. W. (2002) Coordinate regulation of transcription and splicing by steroid receptor coregulators. Science 298, 416-419.
24. Pagani, F., Stuani, C., Kornblihtt, A. R., and Baralle, F. E. (2003) Promoter architecture modulates CFTR exon 9 skipping. J. Biol. Chem. 278, 1511-1517.
25. Blau, J., Xiao, H., McCracken, S., O'Hare, P., Greenblatt, J., and Bentley, D. (1996) Three functional classes of transcriptional activation domains. Mol. Cell. Biol. 16, 2044-2055.
26. Nogués, 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.
27. Yankulov, K., Blau, J., Purton, T., Roberts, S., and Bentley, D. L. (1994) Transcriptional elongation by RNA polymerase II is stimulated by transactivators. Cell 77, 749-759.
28. 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. USA 99. 8185-8190.
29. Ge, H., Si, Y., and Wolffe, A. P. (1998) A novel transcriptional coactivator, p52, functionally interacts with the essential splicing factor ASF/SF2. Mol. Cell 2, 751-759.
30. Lai, M. C., Teh, B. H., and Tarn, W. Y. (1999) A human papillomavirus E2 transcriptional activator. The interactions with cellular splicing factors and potential function in pre-mRNA processing. J. Biol. Chem. 274, 11832-11841.
31. Monsalve, M., Wu, Z., Adelmant, G., Puigserver, P., Fan, M., and Spiegelman, B. M. (2000) Direct coupling of transcription and mRNA processing through the thermogenic coactivator PGC-1. Mol. Cell 6, 307-316.
32. Davies, R. C., Calvio, C., Bratt, E., Larsson, S. H., Lamond, A. I., and Hastie, N. D. (1998) WTI interacts with the splicing factor U2AF65 in an isoform-dependent manner and can be incorporated into spliceosomes. Genes Dev. 12, 3217-3225.
33. Nayler, O., Stratling, W., O. Stratline, W., Bourquin, J. P., Stagljar, I., Lindemann, L., Jasper, H., Hartmann, A. M., Fackelmayer, F. O., Ullrich A., and Stamm, S. (1998) SAF-B protein couples transcription and pre-mRNA splicing to SAR/MAR elements. Nucleic Acids Res. 26, 3542-3549.
34. Morris, D. P., and Greenleaf, A. L. (2000) The splicing factor, Prp40, binds the phosphorylated carboxyl-terminal domain of RNA polymerase II. J. Biol. Chem. 275, 39935-39943.
35. Myers, J. K., Morris, D. P., Greenleaf, A. L., and Oas, T. G. (2001) Phosphorylation of RNA polymerase II CTD fragments results in tight binding to the WW domain from the yeast prolyl isomerase Ess1. Biochemistry 40, 8479-8486.
36. Carty, S. M., Goldstrohm, A. C., Sune, C., Garcia-Blanco, M. A., and Greenleaf, A. L. (2000) Protein-interaction modules that organize nuclear function: FF domains of CA150 bind the phosphoCTD of RNA polymerase II. Proc. Natl. Acad. Sci. U.S.A. 97, 9015-9020.
37. Yuryev, A., Patturajan, M., Litingtung, Y., Joshi, R. V., Gentile, C., Gebara, M., and Corden, J. L. (1996) The C-terminal domain of the largest subunit of RNA polymerase II interacts with a novel set of serine/arginine-rich proteins. Proc. Natl. Acad. Sci. U.S.A 93, 6975-6980.
38. Eperon, L. P., Graham, I. R., Griffiths, A. D., and Eperon, I. C. (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.
39. Roberts, G. C., Gooding, C., Mak, H. Y., Proudfoot, N. J., and Smith, C. W. J. (1998) Co-transcriptional commitment to alternative splice site selection. Nucleic Acids Res. 26, 5568-5572.
40. Price, D. H. (2000) P-TEFb, a cyclin-dependent kinase controlling elongation by RNA polymerase II. Mol. Cell. Biol. 20, 2629-3634.
41. Fong, Y. W., and Zhou, Q. (2002) Stimulatory effect of splicing factors on transcriptional elongation. Nature 414, 929-933.
42. 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.
43. Cereghini, S., and Yaniv, M. (1984) Assembly of transfected DNA into chromatin: structural changes in the origin-promoter-enhancer region upon replication. EMBO J. 3, 1243-1253.
44. Nahreini, P., and Mathews, M. B. (1995) Effect of simian virus 40 origin of replication on transcription from the Human Immunodeficiency Virus type 1 promoter. J. Virol. 69. 1296-1301.
45. Cho, E. J., Kobor, M. S., Kim, M., Greenblatt, J., and Buratowski, S. (2001) Opposing effects of Ctk1 kinase and Fcp1 phosphatase at Ser 2 of the RNA polymerase II C-terminal domain. Genes Dev. 15. 3319-3329.
46. Lindstrom, D. L., Squazzo, S. L., Muster, N., Burckin, T. A., Wachter, K. C., Emigh, C. A., McCleery, J. A., Yates, 3rd 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.
47. Weg-Remers, S., Ponta, H., Herrlich, P., and König, H. (2001) Regulation of alternative pre-mRNA splicing by the ERK MAP-kinase pathway. EMBO J. 20. 4194-4203.
48. Srebrow, A., Blaustein, M., and Kornblihtt, A. R. (2002) Regulation of fibronectin alternative splicing by a basement membrane-like extracellular matrix. FEBS Lett. 514, 285-289.