Small changes in ambient temperature affect alternative splicing in Arabidopsis thaliana

Plant Signaling and Behavior

Volumn 8, Issue 7, 2013, Pages

  Streitner, Corinna ^a   Simpson, Craig G ^b   Shaw, Paul ^b   Danisman, Selahattin ^a   Brown, John W S ^b,c   Staiger, Dorothee ^a,d  

^a BIELEFELD UNIVERSITY   (Germany)

^b SCOTTISH CROP RESEARCH INSTITUTE   (United Kingdom)

^c UNIVERSITY OF DUNDEE   (United Kingdom)

^d CeBiTec   (Germany)

Author keywords

Alternative splicing; Posttranscriptional regulation; RNA binding proteins; Temperature

Indexed keywords

EID: 84879745557     PISSN: 15592316     EISSN: 15592324     Source Type: Journal    
DOI: 10.4161/psb.24638     Document Type: Article

References (31)

1. Reddy AS. Alternative splicing of pre-messenger RNAs in plants in the genomic era. Annu Rev Plant Biol 2007; 58:267-94; http://dx.doi.org/10.1146/annurev.arplant.58.032806.103754
2. Syed NH, Kalyna M, Marquez Y, Barta A, Brown JWS. Alternative splicing in plants--coming of age. Trends Plant Sci 2012; 17:616-23; http://dx.doi.org/10.1016/j.tplants.2012.06.001
3. McGlincy NJ, Smith CW. Alternative splicing resulting in nonsense-mediated mRNA decay: what is the meaning of nonsense? Trends Biochem Sci 2008; 33:385-93; http://dx.doi.org/10.1016/j.tibs.2008.06.001
4. Yang X, Zhang H, Li L. Alternative mRNA process-ing increases the complexity of microRNA-based gene regulation in Arabidopsis. Plant J 2012; 70:421-31; http://dx.doi.org/10.1111/j.1365-313X.2011.04882.x
5. Staiger D, Zecca L, Wieczorek Kirk DA, Apel K, Eckstein L. The circadian clock regulated RNA-binding protein AtGRP7 autoregulates its expression by influencing alternative splicing of its own pre-mRNA. Plant J 2003; 33:361-71; http://dx.doi.org/10.1046/j.1365-313X.2003.01629.x
6. Kalyna M, Simpson CG, Syed NH, Lewandowska D, Marquez Y, Kusenda B, et al. Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis. Nucleic Acids Res 2012; 40:2454-69; http://dx.doi.org/10.1093/nar/gkr932
7. Marquez Y, Brown JWS, Simpson CG, Barta A, Kalyna M. Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis. Genome Res 2012; 22:1184-95; http://dx.doi.org/10.1101/gr.134106.111
8. Dinesh-Kumar SP, Baker BJ. Alternatively spliced N resistance gene transcripts: their possible role in tobacco mosaic virus resistance. Proc Natl Acad Sci USA 2000; 97:1908-13; http://dx.doi.org/10.1073/pnas.020367497
9. Zhang XC, Gassmann W. Alternative splicing and mRNA levels of the disease resistance gene RPS4 are induced during defense responses. Plant Physiol 2007; 145:1577-87; http://dx.doi.org/10.1104/pp.107.108720
10. Staiger D, Korneli C, Lummer M, Navarro L. Emerging role for RNA-based regulation in plant immunity. New Phytol 2013; 197:394-404; http://dx.doi.org/10.1111/nph.12022
11. Iida K, Seki M, Sakurai T, Satou M, Akiyama K, Toyoda T, et al. Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences. Nucleic Acids Res 2004; 32:5096-103; http://dx.doi.org/10.1093/nar/gkh845
12. Carvalho R, Feijao C, Duque P. On the physi-ological significance of alternative splicing events in higher plants. Protoplasma 2012; 249:1-12;
13. Reddy ASN, Rogers MF, Richardson DN, Hamilton M, Ben-Hur A. Deciphering the plant splicing code: experimental and computational approaches for pre-dicting alternative splicing and splicing regulatory ele-ments. Front Plant Sci 2012; 3:18; http://dx.doi.org/10.3389/fpls.2012.00018
14. Barta A, Kalyna M, Reddy AS. Implementing a ratio-nal and consistent nomenclature for serine/arginine-rich protein splicing factors (SR proteins) in plants. Plant Cell 2010; 22:2926-9; http://dx.doi.org/10.1105/tpc.110.078352
15. Wachter A, Rühl C, Stauffer E. The role of polypy-rimidine tract-binding proteins and other hnRNP proteins in plant splicing regulation. Front Plant Sci 2012; 3:81; http://dx.doi.org/10.3389/fpls.2012.00081
16. Heintzen C, Nater M, Apel K, Staiger D. AtGRP7, a nuclear RNA-binding protein as a component of a circadian-regulated negative feedback loop in Arabidopsis thaliana. Proc Natl Acad Sci USA 1997; 94:8515-20; http://dx.doi.org/10.1073/pnas.94.16.8515
17. Heintzen C, Melzer S, Fischer R, Kappeler S, Apel K, Staiger D. A light-and temperature-entrained circadian clock controls expression of transcripts encoding nuclear proteins with homology to RNA-binding proteins in meristematic tissue. Plant J 1994; 5:799-813; http://dx.doi.org/10.1046/j.1365-313X.1994.5060799.x
18. Streitner C, Köster T, Simpson CG, Shaw P, Danisman S, Brown JWS, et al. An hnRNP-like RNA-binding protein affects alternative splicing by in vivo interaction with transcripts in Arabidopsis thaliana. Nucleic Acids Res 2012; 40:11240-55; http://dx.doi.org/10.1093/nar/gks873
19. Schöning JC, Streitner C, Meyer IM, Gao Y, Staiger D. Reciprocal regulation of glycine-rich RNA-binding proteins via an interlocked feedback loop coupling alternative splicing to nonsense-mediat-ed decay in Arabidopsis. Nucleic Acids Res 2008; 36:6977-87; http://dx.doi.org/10.1093/nar/gkn847
20. Simpson CG, Fuller J, Maronova M, Kalyna M, Davidson D, McNicol J, et al. Monitoring changes in alternative precursor messenger RNA splicing in multiple gene transcripts. Plant J 2008; 53:1035-48; http://dx.doi.org/10.1111/j.1365-313X.2007.03392.x
21. Rühl C, Stauffer E, Kahles A, Wagner G, Drechsel G, Rätsch G, et al. Polypyrimidine tract binding protein homologs from Arabidopsis are key regulators of alternative splicing with implications in fundamental developmental processes. Plant Cell 2012; 24:4360-75; http://dx.doi.org/10.1105/tpc.112.103622
22. Filichkin SA, Priest HD, Givan SA, Shen R, Bryant DW, Fox SE, et al. Genome-wide mapping of alter-native splicing in Arabidopsis thaliana. Genome Res 2010; 20:45-58; http://dx.doi.org/10.1101/gr.093302.109
23. James AB, Syed NH, Bordage S, Marshall J, Nimmo GA, Jenkins GI, et al. Alternative splicing medi-ates responses of the Arabidopsis circadian clock to temperature changes. Plant Cell 2012; 24:961-81; http://dx.doi.org/10.1105/tpc.111.093948
24. James AB, Syed NH, Brown JW, Nimmo HG. Thermoplasticity in the plant circadian clock: how plants tell the time-perature. Plant Signal Behav 2012; 7:1219-23; http://dx.doi.org/10.4161/psb.21491
25. Tanabe N, Yoshimura K, Kimura A, Yabuta Y, Shigeoka S. Differential expression of alternatively spliced mRNAs of Arabidopsis SR protein homologs, atSR30 and atSR45a, in response to environmen-tal stress. Plant Cell Physiol 2007; 48:1036-49; http://dx.doi.org/10.1093/pcp/pcm069
26. Lazar G, Goodman HM. The Arabidopsis splicing factor SR1 is regulated by alternative splicing. Plant Mol Biol 2000; 42:571-81; http://dx.doi.org/10.1023/A:1006394207479
27. Balasubramanian S, Weigel D. Temperature Induced Flowering in Arabidopsis thaliana. Plant Signal Behav 2006; 1:227-8; http://dx.doi.org/10.4161/psb.1.5.3452
28. Balasubramanian S, Sureshkumar S, Lempe J, Weigel D. Potent induction of Arabidopsis thaliana flower-ing by elevated growth temperature. PLoS Genet 2006; 2:e106; http://dx.doi.org/10.1371/journal.pgen.0020106
29. Yan K, Liu P, Wu CA, Yang GD, Xu R, Guo QH, et al. Stress-induced alternative splicing provides a mechanism for the regulation of microRNA process-ing in Arabidopsis thaliana. Mol Cell 2012; 48:521-31; http://dx.doi.org/10.1016/j.molcel.2012.08.032
30. Li F, Zheng Q, Vandivier LE, Willmann MR, Chen Y, Gregory BD. Regulatory impact of RNA second-ary structure across the Arabidopsis transcriptome. Plant Cell 2012; 24:4346-59; http://dx.doi.org/10.1105/tpc.112.104232
31. Duque P. A role for SR proteins in plant stress responses. Plant Signal Behav 2011; 6:49-54; http://dx.doi.org/10.4161/psb.6.1.14063