Distal regulation of alternative splicing by splicing enhancer in equine β-casein intron 1

RNA

Volumn 12, Issue 3, 2006, Pages 498-507

  Lenasi, Tina ^a,b   Peterlin, B Matija ^b   Dovc, Peter ^a  

^a UNIVERSITY OF LJUBLJANA   (Slovenia)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Alternative splicing; Casein gene; Cotranscriptional processing; Splicing enhancer; Weak exon

Indexed keywords

BETA CASEIN; FIBRONECTIN; MESSENGER RNA; RNA POLYMERASE II;

ALTERNATIVE RNA SPLICING; ARTICLE; EXON; INTRON; PRIORITY JOURNAL; PROMOTER REGION; REGULATORY MECHANISM; RNA TRANSCRIPTION; TRANSCRIPTION REGULATION;

ALTERNATIVE SPLICING; ANIMALS; BASE SEQUENCE; CASEINS; DNA; ENHANCER ELEMENTS (GENETICS); EXONS; FEMALE; GLOBINS; HORSES; HUMANS; INTRONS; MOLECULAR SEQUENCE DATA; MUTAGENESIS; POLYMORPHISM, GENETIC; RNA PRECURSORS;

EQUIDAE;

EID: 33344460783     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.7261206     Document Type: Article

References (45)

1. Adamson, T.E., Shutt, D.C., and Price, D.H. 2005. Functional coupling of cleavage and polyadenylation with transcription of mRNA. J. Biol. Chem. 280: 32262-32271.
2. Baraniak, A.P., Lasda, E.L., Wagner, E.J., and Garcia-Blanco, M.A. 2003. A stem structure in fibroblast growth factor receptor 2 transcripts mediates cell-type-specific splicing by approximating intronic control elements. Mol. Cell. Biol. 23: 9327-9337.
3. Bird, G., Zorio, D.A., and Bentley, D.L. 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.
4. Black, D.L. 2000. Protein diversity from alternative splicing: A challenge for bioinformatics and post-genome biology. Cell 103: 367-370.
5. _. 2003. Mechanisms of alternative pre-messenger RNA splicing. Annu. Rev. Biochem. 72: 291-336.
6. Buratti, E. and Baralle, F.E. 2004. Influence of RNA secondary structure on the pre-mRNA splicing process. Mol. Cell. Biol. 24: 10505-10514.
7. Buratti, E., Muro, A.F., Giombi, M., Gherbassi, D., Iaconcig, A., and Baralle, F.E. 2004. RNA folding affects the recruitment of SR proteins by mouse and human polypurinic enhancer elements in the fibronectin EDA exon. Mol. Cell. Biol. 24: 1387-1400.
8. Caceres, J.F. and Kornblihtt, A.R. 2002. Alternative splicing: Multiple control mechanisms and involvement in human disease. Trends Genet. 18: 186-193.
9. Caputi, M., Casari, G., Guenzi, S., Tagliabue, R., Sidoli, A., Melo, C.A., and Baralle F.E. 1994. A novel bipartite splicing enhancer modulates the differential processing of the human fibronectin EDA exon. Nucleic Acids Res. 22: 1018-1022.
10. 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.
11. Cramer, P., Bushnell, D.A., and Kornberg, R.D. 2001. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science 292: 1863-1876.
12. de la Mata, M., Alonso, C.R., Kadener, S., Fededa, J.P., Blaustein, M., Pelisch, F., Cramer, P., Bentley, D., and Kornblihtt, A.R. 2003. A slow RNA polymerase II affects alternative splicing in vivo. Mol. Cell 12: 525-532.
13. Fairbrother, W.G., Yeh, R.F., Sharp, P.A., and Burge, C.B. 2002. Predictive identification of exonic splicing enhancers in human genes. Science 297: 1007-1013.
14. Fededa, J.P., Petrillo, E., Gelfa, M.S., Neverov, A.D., Kadener, S., Nogues, G., Pelisch, F., Baralle, F.E., Muro, A.F., and Kornblihtt, A.R. 2005. A polar mechanism coordinates different regions of alternative splicing within a single gene. Mol. Cell 19: 393-404.
15. Flaherty, S.M., Fortes, P., Izaurralde, E., Mattaj, I.W., and Gilmartin, G.M. 1997. Participation of the nuclear cap binding complex in pre-mRNA 3′ processing. Proc. Natl. Acad. Sci. 94: 11893-11898.
16. 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.
17. Fong, Y.W. and Zhou, Q. 2001. Stimulatory effect of splicing factors on transcriptional elongation. Nature 414: 929-933.
18. Goldfarb, A. 1981. Changes in the promoter range of RNA polymerase resulting from bacteriophage T4-induced modification of core enzyme. Proc. Natl. Acad. Sci. 78: 3454-3458.
19. Goldstrohm, A.C., Greenleaf. A.L., and Garcia-Blanco, M.A. 2001. Cotranscriptional splicing of pre-messenger RNAs: Considerations for the mechanism of alternative splicing. Gene 277: 31-47.
20. Graveley, B.R. 2000. Sorting out the complexity of SR protein functions. RNA 6: 1197-1211.
21. Hirose, Y. and Manley, J.L. 2000. RNA polymerase II and the integration of nuclear events. Genes & Dev. 14: 1415-1429.
22. Howe, K.J. 2002. RNA polymerase II conducts a symphony of premRNA processing activities. Biochim. Biophys. Acta 1577: 308-324.
23. Johnsen, L.B., Rasmussen, L.K., Petersen, T.E., and Berglund, L. 1995. Characterization of three types of human a s1-casein mRNA transcripts. Biochem. J. 309: 237-242.
24. 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.
25. Komarnitsky, P., Cho, E.J., and Buratowski, S. 2000. Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription. Genes & Dev. 14: 2452-2460.
26. Kornblihtt, A.R., de la Mata, M., Fededa, J.P., Munoz, M.J., and Nogues, G. 2004. Multiple links between transcription and splicing. RNA 10: 1489-1498.
27. Lenasi, T., Rogelj, I., and Dovc, P. 2003. Characterization of equine cDNA sequences for αS1-, β- and κ-casein. J. Dairy. Res. 70: 29-36.
28. Lewis, J.D. and Izaurralde, E. 1997. The role of the cap structure in RNA processing and nuclear export. Eur. J. Biochem. 247: 461-469.
29. Lewis, J.D., Izaurralde, E., Jarmolowski, A., McGuigan, C., and Mattaj, I.W. 1996. A nuclear cap-binding complex facilitates association of U1 snRNP with the cap-proximal 5′ splice site. Genes. & Dev. 10: 1683-1698.
30. Liu, H.X., Zhang, M., and Krainer, A.R. 1998. Identification of functional exonic splicing enhancer motifs recognized by individual SR proteins. Genes & Dev. 12: 1998-2012.
31. Maniatis, T. and Reed, R. 2002. An extensive network of coupling among gene expression machines. Nature 416: 499-506.
32. Maniatis, T. and Tasic, B. 2002. Alternative pre-mRNA splicing and proteome expansion in metazoans. Nature 418: 236-243.
33. Matter, N., Herrlich, P., and Konig, H. 2002. Signal-dependent regulation of splicing via phosphorylation of Sam68. Nature 420: 691-695.
34. 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.
35. Michel, Y.M., Poncet, D., Piron, M., Kean, K.M., and Borman, A.M. 2000. Cap-Poly(A) synergy in mammalian cell-free extracts. Investigation of the requirements for poly(A)-mediated stimulation of translation initiation. J. Biol. Chem. 275: 32268-32276.
36. Milenkovic, D., Martin, P., Guerin, G., and Leroux, C. 2002. A specific pattern of splicing for the horse αS1-Casein mRNA and partial genomic characterization of the relevant locus. Genet. Sel. Evol. 34: 509-519.
37. Muro, A.F., Caputi, M., Pariyarath, R., Pagani, F., Buratti, E., and Baralle, F.E. 1999. Regulation of fibronectin EDA exon alternative splicing: Possible role of RNA secondary structure for enhancer display. Mol. Cell. Biol. 19: 2657-2671.
38. Neugebauer, K.M. and Roth, M.B. 1997. Transcription units as RNA processing units. Genes. & Dev. 11: 3279-3285.
39. Pagani, F., Stuani, C., Zuccato, E., Kornblihtt, A.R., and Baralle, F.E. 2003. Promoter architecture modulates CFTR exon 9 skipping. J. Biol. Chem. 278: 1511-1517.
40. Schaal, T.D. and Maniatis, T. 1999. Multiple distinct splicing enhancers in the protein-coding sequences of a constitutively spliced premRNA. Mol. Cell. Biol. 19: 261-273.
41. Ule, J., Jensen, K.B., Ruggiu, M., Mele, A., Ule, A., and Darnel, R.B. 2003. CLIP identifies Nova-regulated RNA networks in the brain. Science 302: 1212-1215.
42. Weeks, J.R., Hardin, S.E., Shen, J., Lee, J.M., and Greenleaf, A.L. 1993. Locus-specific variation in phosphorylation state of RNA polymerase II in vivo: Correlations with gene activity and transcript processing. Genes & Dev. 7: 2329-2344.
43. Wetterberg, I., Zhao, J., Masich, S., Wieslander, L., and Skoglund, U. 2001. In situ transcription and splicing in the Balbiani ring 3 gene. EMBO J. 20: 2564-2574.
44. Zeng, C. and Berget, S.M. 2000. Participation of the C-terminal domain of RNA polymerase II in exon definition during premRNA splicing. Mol. Cell. Biol. 20: 8290-8301.
45. Zhang, W., Liu, H., Han, K., and Grabowski, P.J. 2002. Regionspecific alternative splicing in the nervous system: Implications for regulation by the RNA-binding protein NAPOR. RNA 8: 671-685.