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Open Life Sciences

formerly Central European Journal of Biology

Editor-in-Chief: Ratajczak, Mariusz


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Volume 7, Issue 4

Issues

Volume 10 (2015)

Natural rules for Arabidopsis thaliana pre-mRNA splicing site selection

Ning Wu / Kanyand Matand
  • Center for Biotechnology Research and Education, Langston University, Langston, Oklahoma, 73050, USA
  • Department of Biology, School of Arts and Science, Langston University, Langston, Oklahoma, 73050, USA
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/ Huijuan Wu / Baoming Li / Kayla Love / Brittany Stoutermire / Yanfeng Wu
Published Online: 2012-06-03 | DOI: https://doi.org/10.2478/s11535-012-0060-1

Abstract

The accurate prediction of plant pre-mRNA splicing sites has been studied extensively. The rules for plant pre-mRNA splicing still remain unknown. This study, based on confirmed sequence data, systematically analyzed all expressed genes on Arabidopsis thaliana chromosome IV to quantitatively explore the natural splicing rules. The results indicated that defining Arabidopsis thaliana pre-mRNA splicing sites required a combination of multiple factors including (1) relative conserved consensus sequence at splicing site; (2) individual nucleotide distribution pattern in 50 nucleotides up- and down-stream regions of splicing site; (3) quantitative analysis of individual nucleotide distribution by using the formulations concluded from this study. The combination of all these factors together can bring the accuracy of Arabidopsis thaliana splicing site recognition over 99%. The results provide additional information to the future of plant pre-mRNA splicing research.

Keywords: Arabidopsis thaliana; Pre-mRNA splicing

  • [1] Green M.R., Biochemical mechanisms of constitutive and regulated pre-mRNA splicing, Annu Rev Cell Biol., 1991, 7, 559–599 http://dx.doi.org/10.1146/annurev.cb.07.110191.003015CrossrefGoogle Scholar

  • [2] Wang Z., Burge C., Splicing regulation: from a parts list of regulatory elements to an integrated splicing code, RNA, 2008, 14, 802–813 http://dx.doi.org/10.1261/rna.876308CrossrefGoogle Scholar

  • [3] Lal S., Choi J.H., Shaw J.R., Hannah L.C., A splice site mutant of maize activates cryptic splice sites, elicits intron inclusion and exon exclusion, and permits branch point elucidation, Plant Physiol., 1999, 121, 411–418 http://dx.doi.org/10.1104/pp.121.2.411CrossrefGoogle Scholar

  • [4] Goodall G.J., Filipowicz W., Different effects of intron nucleotide composition and secondary structure on pre-mRNA splicing in monocot and dicot plants, EMBO J., 1991, 10, 2635–2644 Google Scholar

  • [5] Brown J.W., Simpson C.G., Splice site selection in plant pre-mRNA splicing, Annu Rev Plant Physiol Plant Mol Biol., 1998, 49, 77–95 http://dx.doi.org/10.1146/annurev.arplant.49.1.77CrossrefGoogle Scholar

  • [6] Simpson C.G., McQuade C., Lyon J., Brown J.W., Characterization of exon skipping mutants of the COP1 gene from Arabidopsis, Plant J., 1998, 15, 125–131 http://dx.doi.org/10.1046/j.1365-313X.1998.00184.xGoogle Scholar

  • [7] Lazar G., Goodman H.M., The Arabidopsis splicing factor SR1 is regulated by alternative splicing, Plant Mol Biol., 2000, 42, 571–581 http://dx.doi.org/10.1023/A:1006394207479Google Scholar

  • [8] Sarmah B., Chakraborty N., Chakraborty S., Datta A., Plant pre-mRNA splicing in fission yeast, Schizosaccharomyces pombe, Biochem Biophys Res Commun., 2002, 293, 1209–1216 http://dx.doi.org/10.1016/S0006-291X(02)00364-9CrossrefGoogle Scholar

  • [9] Lou H., McCullough A.J., Schuler M.A., 3′ splice site selection in dicot plant nuclei is position dependent, Mol Cell Biol, 1993, 13, 4485–4493 CrossrefGoogle Scholar

  • [10] Brendel V., Kleffe J., Prediction of locally optimal splice sites in plant pre-mRNA with applications to gene identification in Arabidopsis thaliana genomic DNA, Nucleic Acids Res, 1998, 26, 4748–4757 http://dx.doi.org/10.1093/nar/26.20.4748CrossrefGoogle Scholar

  • [11] Luehrsen K.R., Taha S., Walbot V., Nuclear premRNA processing in higher plants, Prog Nucleic Acid Res Mol Biol, 1994, 47, 149–193 http://dx.doi.org/10.1016/S0079-6603(08)60252-4CrossrefGoogle Scholar

  • [12] Hebsgaard S.M., Korning P.G., Tolstrup N., Engelbrecht J., Rouze P., Brunak S., Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information, Nucl. Ac. Res., 1996, 24, 3439–3452 http://dx.doi.org/10.1093/nar/24.17.3439CrossrefGoogle Scholar

  • [13] Guigó R., Flicek P., Abril J.F., Reymond A., Lagarde J., Denoeud F., et al., EGASP: the human ENCODE Genome Annotation Assessment Project, Genome Biol, 2006, 7, 1–31 http://dx.doi.org/10.1186/gb-2006-7-s1-s2CrossrefGoogle Scholar

  • [14] Dogan R.I., Getoor L., Wilbur J., Mount S., Features generated for computational splice-site prediction correspond to functional elements, BMC Bioinformatics, 2007, 8, 410–424 http://dx.doi.org/10.1186/1471-2105-8-410CrossrefGoogle Scholar

  • [15] White O., Soderlund C., Shanmugan P., Fields C., Information contents and dinucleotide compositions of plant intron sequences vary with evolutionary origin, Plant Mol Biol, 1992, 19, 1057–1064 http://dx.doi.org/10.1007/BF00040537CrossrefGoogle Scholar

  • [16] Kleffe J., Hermann K., Vahrson W., Wittig B., Brendel V., Logitlinear models for the prediction of splice sites in plant pre-mRNA sequences, Nucl. Ac. Res., 1996, 24, 4709–4718 http://dx.doi.org/10.1093/nar/24.23.4709CrossrefGoogle Scholar

  • [17] Carle-Urioste J.C., Brendel V., Walbot V., A combinatorial role for exon, intron and splice site sequences in splicing in maize, Plant J, 1997, 11, 1253–1263 http://dx.doi.org/10.1046/j.1365-313X.1997.11061253.xCrossrefGoogle Scholar

  • [18] Brendel V., Kleffe J., Carle-Urioste J.C., Walbot V., Prediction of splice sites in plant pre-mRNA from sequence properties, J Mol Biol, 1998, 276, 85–104 http://dx.doi.org/10.1006/jmbi.1997.1523CrossrefGoogle Scholar

About the article

Published Online: 2012-06-03

Published in Print: 2012-08-01


Citation Information: Open Life Sciences, Volume 7, Issue 4, Pages 620–625, ISSN (Online) 2391-5412, DOI: https://doi.org/10.2478/s11535-012-0060-1.

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© 2012 Versita Warsaw. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License. BY-NC-ND 3.0

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