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http://dx.doi.org/10.1007/s10059-009-0087-y

Thermodynamic Analyses of the Constitutive Splicing Pathway for Ovomucoid Pre-mRNA  

Ro-Choi, Tae Suk (Medical Research Center for Cancer Molecular Therapy, Dong-A University College of Medicine)
Choi, Yong Chun (Medical Research Center for Cancer Molecular Therapy, Dong-A University College of Medicine)
Publication Information
Molecules and Cells / v.27, no.6, 2009 , pp. 657-665 More about this Journal
Abstract
The ovomucoid pre-mRNA has been folded into mini-hairpins adaptable for the RNA recognition motif (RRM) protein binding. The number of mini-hairpins were 372 for pre-mRNA and 83-86 for mature mRNA. The spatial arrangements are, in average, 16 nucleotides per mini-hairpin which includes 7 nt in the stem, 5.6 nt in the loop and 3.7 nt in the inter-hairpin spacer. The constitutive splicing system of ovomucoid-pre-mRNA is characterized by preferred order of intron removal of 5/6 > 7/4 > 2/1 > 3. The 5' splice sites (5'SS), branch point sequences (BPS) and 3' splice sites (3'SS) were identified and free energies involved have been estimated in 7 splice sites. Thermodynamic barriers for splice sites from the least (|lowest| -Kcal) were 5, 4, 7, 6, 2, 1, and 3; i.e., -18.7 Kcal, -20.2 Kcal, -21.0 Kcal, -24.0 Kcal, - 25.4 Kcal, -26.4 Kcal and -28.2 Kcal respectively. These are parallel to the kinetic data of splicing order reported in the literature. As a result, the preferred order of intron removals can be described by a consideration of free energy changes involved in the spliceosomal assembly pathway. This finding is consistent with the validity of hnRNP formation mechanisms in previous reports.
Keywords
co-transcriptional folding; Mini-hairpins; snRNAs; U1; U2; U4; U5; U6; splicing; thermodynamics;
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1 Beyer, A.L., and Osheim, Y.N. (1990). Ultrastructural analysis of the ribonucleoprotein substrate for pre-mRNA processing. In The Eukaryotic Nucleus; Molecular Biochemistry and Macromolecular Assemblies, Vol. 2, P.R. Strauss, and S.H. Wilson, eds. (The Telford Press, Chapter 18), pp. 431-451
2 Buratti, E., and Baralle, F.E. (2004). Influence of RNA Secondary Structure on the Pre-mRNA Splicing Process. Mol. Cell. Biol. 24, 10505-10514   DOI   ScienceOn
3 Cartegni, L., Wang, J., Zhu, Z., Zhang, M.Q., and Krainer, A.R. (2003). http://rulai.cshl.edu/tools/ESE
4 Freund, M., Asang, C., Kammler, S., Konermann, C., Krummheuer, J., Hipp, M., Meyer, I., Gierling, W., Theiss, S., Preuss, T., et al. (2003). A novel approach to describe a U1 snRNA binding site. Nucleic Acids Res. 31, 6963-6975   DOI   ScienceOn
5 Freund, M., Hicks, M.J., Konermann, C., Otte, M., Hertel, K.J., and Schaal, H. (2005). Extended base pair complementarity between U1 snRNA and the 5′ splice site does not inhibit splicing in higher eukaryotes, but rather increases 5′ splicing site recognition. Nucleic Acids Res. 35, 5112-5119
6 Goguel, V., Wang, Y., and Rosbash, M. (1993). Short artificial hairpins sequester splicing signals and inhibit yeast pre-mRNA splicing. Mol. Cell. Biol. 13, 6841-6848   DOI   PUBMED   ScienceOn
7 Liu, Z.-R. (2002). p68 RNA Helicase is an essential human splicing factor that acts at the U1 snRNA-5′ splice site duplex. Mol. Cell. Biol. 22, 5443-5450   DOI   PUBMED   ScienceOn
8 Ro-Choi, T.S., and Choi, Y.C. (2007). A modeling study of cotranscriptional metabolism of hnRNP Using FMR1 gene. Mol. Cells 23, 228-238   PUBMED   ScienceOn
9 Ro-Choi, T.S., and Henning, D. (1977). Sequence of 5′ oligonucleotide of U1 RNA from Novikoff hepatoma cells. J. Biol. Chem. 252, 3814-3820   PUBMED
10 Ro-Choi, T.S., Reddy, R., Choi, Y.C., Raj, N.B., and Henning, D. (1974). Primary sequence of U1 nuclear RNA and unusual feature of 5′ end structure of LMWN RNA. Fed. Proc. Fed. Am. Soc. Exp. Biol. 33, 1548
11 Staley, J., and Guthrie, C. (1999). An RNA switch at the 5′ splice site requires ATP and the DEAD box protein Prp28p. Mol. Cell 3, 55-64   DOI   ScienceOn
12 Stein, J.P., Catterall, J.F., Kristo, P., Means, A.R., and O'Malley, B.W. (1980). Ovomucoid intervening sequences specify functional domains and generate protein polymorphism. Cell 21, 681-687   DOI   ScienceOn
13 Madhani, H.D., and Guthrie, C. (1994). Dynamic RNA-RNA interactions in the spliceosome. Ann. Rev. Genet. 28, 1-26   DOI   ScienceOn
14 Gerlinger, P., Krust, A., LeMeur, M., Perrin, F., Cochet, M., Gannon, F., Dupret, D., and Chambon, P. (1982). Multiple initiation and polyadenylation sites for the chicken ovomucoid transcription unit. J. Mol. Biol. 162, 345-364   DOI   PUBMED
15 Korf, G.M., and Stumph, W.E. (1986). Chicken U2 and U1 RNA genes are found in very different genomic environment but have similar promoter structures. Biochemistry 25, 2041-2047   DOI   ScienceOn
16 Ro-Choi, T.S. (1999). Nuclear snRNA and nuclear function (Discovery of 5′ cap structures in RNA). Crit. Rev. Eukaryot. Gene Expr. 9, 107-158   DOI   PUBMED   ScienceOn
17 Brow, D.A. (2002). Allosteric cascade of spliceosome activation. Annu. Rev. Genet. 36, 333-360   DOI   PUBMED   ScienceOn
18 Ro-Choi, T.S., and Choi, Y.C. (2003). Structural elements of dynamic RNA strings. Mol. Cells 16, 201-210
19 Xia, T., Mathews, D.H., and Turner, D.H. (2001). Thermodynamics of RNA secondary structure formation. In RNA, Chapter 2, D. Soll, S. Nishimura, and P.B. Moore, eds., pp. 21-48
20 Isaacs, N. (1995). Kinetics and thermodynamics. In the book 'Physical Organic Chemistry' Chapter 2, (England: Longman Scietific and Technical, Longman House, Burnt Mill, Harlow Essex CM20 2JE), pp. 87-128
21 von Heijine, G. (1987). Sequence analysis in molecular biology, Chapter 4, Nucleotide sequences: what you can do with your sequence once you have it (Academic Press), pp. 19-80
22 Branlant, C., Krol, A., Ebel, J.-P., Lazar, E., Gallinaro, H., Jacob, M., Sri-Widada, J., and Jeanteur, P. (1980). Nucleotide sequences of nuclear U1A RNAs from chicken, rat and man. Nucleic Acids. Res. 8, 4143-4154   DOI   ScienceOn
23 Roca, X., Sachidanandam, R., and Krainer, A. (2005). Determinants of the inherent strength of human 5′ splice sites. RNA 11, 683-698   DOI   ScienceOn
24 Skoglund, U., Andersson, K., Björkroth, B., Lamb, M.M., and Daneholt, B. (1983). Visualization of the formation and transport of a specific hnRNP particle. Cell 34, 847-855   DOI   ScienceOn
25 Catterall, J.F., Stein, J.P., Kristo, P., Means, A.R., and O'Malley, B.W. (1980). Primary sequence of ovomucoid messenger RNAas determined from cloned complementary DNA. J. Cell Biol. 87, 480-487   DOI   ScienceOn
26 Seetharaman, M., Eldho, N.V., Padgett, R.A., and Dayie, K.T. (2008). Structure of a self-splicing group II intron catalytic effector domain 5: Parallels with spliceosomal U6 RNA. RNA 12, 235-247   DOI   ScienceOn
27 Schulz, G.E., and Schirmer, R.H. (1985). Protein-Ligand Interactions. Principles of Protein Structure, Chapter 10, (New York, Berlin, Heidelberg, Tokyo: Springer-Verlag)
28 Freier, S., Kierzek, R., Jaeger, J.A., Sugimoto, N., Caruthers, M.H., Neilson, T., and Turner, D.H. (1986). Improved free-energy parameters for predictions of RNA duplex stability. Proc. Natl. Acad. Sci. USA 83, 9373-9377   DOI   ScienceOn
29 Draper, D.E. (1995). Protein-RNA recognition. Annu. Rev. Biochem.64, 593-620   DOI   PUBMED   ScienceOn
30 Auweter, S.D., Oberstrass, F.C., and Allain, F.H.-T. (2006). Sequence-specific binding of single-stranded RNA: is there a code for recognition? Nucleic Acids Res. 34, 4943-4959   DOI   ScienceOn
31 Lewin, B. (1994; 2008). RNA splicing and processing. Genes IX, Chapter 26, (Pearson Prentice Hall, Pearson Education, Inc.), pp. 667-705
32 Kim, H.-J., and Han, K. (1995). Automated modeling of the RNA folding process. Mol. Cells 5, 406-412
33 Jamison, S.F., Pasman, Z., Wang, J., Will, C., L$\ddot{u}$hrmann, R., Manley, J.L., and Garcia-Blanco, M.A. (1995). U1 snRNP-ASF/SF2 interaction and 5′ splice site recognition: characterization of required elements. Nucleic Acids Res. 23, 3260-3267   DOI   ScienceOn
34 Toor, N., Keating, K.S., Taylor, S.D., and Pyle, A.M. (2008). Crystal structure of a self-spliced group II intron. Science 320, 77-82   DOI   PUBMED   ScienceOn
35 Lund, M., and Kjems, J. (2002). Defining a 5′ splice site by functional selection in the presence and absence of U1 snRNA 5′ end. RNA 8, 166-179   DOI   ScienceOn
36 Epstein, P., Reddy, R., Henning, D., and Busch, H. (1980). The nucleotide sequence of Nuclear U6 (4.7 S) RNA. J. Biol. Chem. 255, 8901-8906   PUBMED
37 Shahied-Milam, L., Soltaninassab, S.R., Iyer, G.V., and LeStourgeon, W.M. (1998). The heterogenous nuclear ribonucleoprotein C protein tetramer binds U1, U2, and U6 snRNAs through its high affinity RNA bindinf domain (the bZIP-like motif). J. Biol Chem. 273, 21359-21367   DOI   ScienceOn
38 Berget, S.M. (1995). Exon recognition in vertebrate splicing. J. Biol. Chem. 270, 2411-2414   DOI   PUBMED
39 Rossi, F., Forne, T., Antoine, E., Tazi, J., Brunel, C., and Cathala, G. (1996). Involvement of U1 small nuclear ribonucleoproteins (snRNP). in 5′ splice site-U1 snRNP interaction. J. Biol. Chem. 271, 23985-23991   DOI   ScienceOn
40 Samarina, O.P., and Krichevskaya, A.A. (1981). Nuclear 30S RNP Particles. In the book 'The Cell Nucleus; Nuclear Particles' Part B., H. Busch, ed, (Academic Press, Inc.), pp. 1-48