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The effect of U1 snRNA binding free energy on the selection of 5' splice sites.
Biochem Biophys Res Commun. 2005 Jul 22; 333(1):64-9.BB

Abstract

The importance of U1 snRNA binding free energy in the regulation of alternative splicing has been studied in some genes with site-directed mutagenesis. Here we report a large-scale analysis of its impact on 5' splice site (5'ss) selection in human genome. The results show that free energy exerts different effects on alternative 5'ss choice in different situations and -8.1 kcal/mol is a threshold. When both free energies of two competing 5'ss are larger than -8.1 kcal/mol, the 5'ss with lower free energy is more frequently used. However, in other pairs of 5'ss, lower-free-energy 5'ss does not seem to be favored and even the other 5'ss is used more frequently, which suggests that very low binding free energy would impair splicing. Some observations hold true only for those alternative 5' splicing with short alternative exons (<50nt), which implies a complex mechanism of 5'ss selection involving both U1 snRNA binding free energy and regulatory factors.

Authors+Show Affiliations

MOE Key Laboratory of Bioinformatics, Department of Automation, Tsinghua University, Beijing, China.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

15936716

Citation

Bi, Jianning, et al. "The Effect of U1 snRNA Binding Free Energy On the Selection of 5' Splice Sites." Biochemical and Biophysical Research Communications, vol. 333, no. 1, 2005, pp. 64-9.
Bi J, Xia H, Li F, et al. The effect of U1 snRNA binding free energy on the selection of 5' splice sites. Biochem Biophys Res Commun. 2005;333(1):64-9.
Bi, J., Xia, H., Li, F., Zhang, X., & Li, Y. (2005). The effect of U1 snRNA binding free energy on the selection of 5' splice sites. Biochemical and Biophysical Research Communications, 333(1), 64-9.
Bi J, et al. The Effect of U1 snRNA Binding Free Energy On the Selection of 5' Splice Sites. Biochem Biophys Res Commun. 2005 Jul 22;333(1):64-9. PubMed PMID: 15936716.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - The effect of U1 snRNA binding free energy on the selection of 5' splice sites. AU - Bi,Jianning, AU - Xia,Huiyu, AU - Li,Fei, AU - Zhang,Xuegong, AU - Li,Yanda, PY - 2005/05/05/received PY - 2005/05/13/accepted PY - 2005/6/7/pubmed PY - 2005/8/16/medline PY - 2005/6/7/entrez SP - 64 EP - 9 JF - Biochemical and biophysical research communications JO - Biochem. Biophys. Res. Commun. VL - 333 IS - 1 N2 - The importance of U1 snRNA binding free energy in the regulation of alternative splicing has been studied in some genes with site-directed mutagenesis. Here we report a large-scale analysis of its impact on 5' splice site (5'ss) selection in human genome. The results show that free energy exerts different effects on alternative 5'ss choice in different situations and -8.1 kcal/mol is a threshold. When both free energies of two competing 5'ss are larger than -8.1 kcal/mol, the 5'ss with lower free energy is more frequently used. However, in other pairs of 5'ss, lower-free-energy 5'ss does not seem to be favored and even the other 5'ss is used more frequently, which suggests that very low binding free energy would impair splicing. Some observations hold true only for those alternative 5' splicing with short alternative exons (<50nt), which implies a complex mechanism of 5'ss selection involving both U1 snRNA binding free energy and regulatory factors. SN - 0006-291X UR - https://www.unboundmedicine.com/medline/citation/15936716/The_effect_of_U1_snRNA_binding_free_energy_on_the_selection_of_5'_splice_sites_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0006-291X(05)01068-5 DB - PRIME DP - Unbound Medicine ER -