The effect of U1 snRNA binding free energy on the selection of 5′ splice sites

Biochemical and Biophysical Research Communications

Volumn 333, Issue 1, 2005, Pages 64-69

  Bi, Jianning ^a   Xia, Huiyu ^a   Li, Fei ^a   Zhang, Xuegong ^a   Li, Yanda ^a  

^a TSINGHUA UNIVERSITY   (China)

Author keywords

Alternative splicing; Free energy; U1 snRNA

Indexed keywords

SMALL NUCLEAR RNA;

5' UNTRANSLATED REGION; ALTERNATIVE RNA SPLICING; ARTICLE; ENERGY; EXON; GENOME ANALYSIS; PRIORITY JOURNAL; REGULATORY MECHANISM; RNA BINDING;

ALTERNATIVE SPLICING; BINDING SITES; COMPUTER SIMULATION; ENERGY TRANSFER; MODELS, CHEMICAL; MODELS, GENETIC; MODELS, MOLECULAR; MODELS, STATISTICAL; RNA SPLICE SITES; RNA, SMALL NUCLEAR; SEQUENCE ANALYSIS, RNA; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 20444462332     PISSN: 0006291X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbrc.2005.05.078     Document Type: Article

References (24)

1. D. Black Protein diversity from alternative splicing: a challenge for bioinformatics and post-genome biology Cell 103 2000 367 370
2. B. Modrek, and C. Lee A genomic view of alternative splicing Nat. Genet. 30 2002 13 19
3. D. Brett, H. Pospisil, J. Valcarcel, J. Reich, and P. Bork Alternative splicing and genome complexity Nat. Genet. 30 2001 29 30
4. D. Black Mechanisms of alternative pre-messenger RNA splicing Annu. Rev. Biochem. 72 2003 291 336
5. J. Kralovicova, S. Houngninou-Molango, A. Kramer, and I. Vorechovsky Branch site hyplotypes that control alternative splicing Hum. Mol. Genet. 13 2004 3189 3202
6. Z. Wang, M. Rolish, G. Yeo, V. Tung, M. Mawson, and C. Burge Systematic identification and analysis of exonic splicing silencers Cell 119 2004 831 845
7. E. Ibrahim, T. Schaal, K. Hertel, R. Reed, and T. Maniatis Serine/arginine-rich protein-dependent suppression of exon skipping by exonic splicing enhancers PNAS 102 2005 5002 5007
8. E. Miriami, H. Margalit, and R. Sperling Conserved sequence elements associated with exon skipping Nucleic Acids Res. 31 2003 1974 1983
9. S. Kadener, J. Fededa, M. Rosbash, and A. Kornblihtt Regulation of alternative splicing by a transcriptional enhancer through RNA pol II elongation PNAS 99 2002 8185 8190
10. B. Tasic, C. Nabholz, K. Baldwin, Y. Kim, E. Rueckert, S. Ribich, P. Cramer, Q. Wu, R. Axel, and T. Maniatis Promoter choice determines splice site selection in protocadherin alpha and gamma pre-mRNA splicing Mol. Cell 10 2002 21 33
11. R. Sorek, G. Lev-Maor, M. Reznik, T. Dagan, F. Belinky, D. Graur, and G. Ast Minimal conditions for exonization of intronic sequences: 5′ splice site formation in Alu exons Mol. Cell 14 2004 221 231
12. H. Mahloogi, and M. Behe Oligoadenosin tracts favor nucleosome formation Biochem. Biophys. Res. Commun. 235 1997 663 668
13. A. Golshani, V. Kolev, R. Mironova, M.G. AbouHaidar, and I.G. Ivanov Enhancing activity of ε in Escherichia coli and Agrobacterium tumefaciens cells Biochem. Biophys. Res. Commun. 269 2000 508 512
14. B.C. Morrish1, and M.G. Rumsby The 5′ UTR of protein kinase C ε confers translational regulation in vitro and in vivo Biochem. Biophys. Res. Commun. 283 2001 1091 1098
15. M. Rehmsmeier, P. Steffen, M. Hochsmann, and R. Giegerich Fast and effective prediction of microRNA/target duplexes RNA 10 2004 1507 1517
16. G. Ruvkun Glimpses of a tiny RNA world Science 294 2001 797 799
17. M. Lund, and J. Kjems Defining a 5′ splice site by functional selection in the presence and absence of U1 snRNA 5′ end RNA 8 2002 166 179
18. J.P. Staley, and C. Guthrie An RNA switch at the 5′ splice site requires ATP and the DEAD box protein Prp28p Mol. Cell 3 1999 55 64
19. C. Lee, L. Atanelov, B. Modrek, and Y. Xing ASAP: the alternative splicing annotation project Nucleic Acids Res. 31 2003 101 105
20. M. Freund, C. Asang, S. Kammler, C. Konermann, J. Krummheuer, M. Hipp, I. Meyer, W. Gierling, S. Theiss, T. Preuss, D. Schindler, J. Kjems, and H. Schaal A novel approach to describe a U1 snRNA binding site Nucleic Acids Res. 31 2003 6963 6975
21. C.I. Castillo-Davis, S.L. Mekhedov, D.L. Hartl, E.V. Koonin, and F.A. Kondrashov Selection for short introns in highly expressed genes Nat. Genet. 31 2002 415 418
22. M. Zuker Mfold web server for nucleic acid folding and hybridization prediction Nucleic Acids Res. 31 2003 3406 3415
23. B.-C. Kim, H.-J. Lee, S.H. Park, S.R. Lee, T.S. Karpova, J.G. McNally, A. Felici, D.K. Lee, and S.-J. Kim Jab1/CSN5, a component of the COP9 signalosome, regulates transforming growth factor β signaling by binding to Smad7 and promoting its degradation Mol. Cell. Biol. 24 2004 2251 2262
24. D.A. Thompson, and R.J. Weigel hAG-2, the human homologue of the Xenopus laevis cement gland gene XAG-2, Is coexpressed with estrogen receptor in breast cancer cell lines Biochem. Biophys. Res. Commun. 251 1998 111 116