Features of evolutionarily conserved alternative splicing events between Brassica and Arabidopsis
Article first published online: 2 APR 2013
© 2013 The Authors. New Phytologist © 2013 New Phytologist Trust
Volume 199, Issue 1, pages 252–263, July 2013
How to Cite
Darracq, A. and Adams, K. L. (2013), Features of evolutionarily conserved alternative splicing events between Brassica and Arabidopsis. New Phytologist, 199: 252–263. doi: 10.1111/nph.12238
- Issue published online: 28 MAY 2013
- Article first published online: 2 APR 2013
- Manuscript Accepted: 18 FEB 2013
- Manuscript Received: 30 NOV 2012
- Natural Science and Engineering Council of Canada
- 2006. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 22: 1600–1607. , , .
- 2006. UPF1 is required for nonsense-mediated mRNA decay (NMD) and RNAi in Arabidopsis. Plant Journal 47: 480–489. , , , .
- 2004. How did alternative splicing evolve? Nature Reviews Genetics 5: 773–782. .
- 2008. Characterization and comparison of intron structure and alternative splicing between Medicago truncatula, Populus trichocarpa, Arabidopsis and rice. Plant Molecular Biology 67: 499–510. , , , .
- 2008. Genome-wide analyses of alternative splicing in plants: opportunities and challenges. Genome Research 18: 1381–1392. , , .
- 2003. Alternative splicing and evolution. BioEssays 25: 1031–1034. , , .
- 2006. Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis. BMC Genomics 7: 327. , , , , .
- 2011. BRAD, the genetics and genomics database for Brassica plants. BMC Plant Biology 11: 136. , , , , , , , , .
- 2012. Biased gene fractionation and dominant gene expression among the subgenomes of Brassica rapa. PLoS ONE 7: e36442. , , , , , , , .
- 2010. Alternative splicing expands the repertoire of dominant JAZ repressors of jasmonate signaling. Plant Journal 63: 613–622. , , , , , , .
- 2000. Alternatively spliced N resistance gene transcripts: their possible role in tobacco mosaic virus resistance. Proceedings of the National Academy of Sciences, USA 97: 1908–1913. , .
- 1998. Multiple forms of the U2 small nuclear ribonucleoprotein auxiliary factor U2AF subunits expressed in higher plants. Journal of Biological Chemistry 273: 34603–34610. , , , .
- 1998. Biological sequence analysis: probabilistic models of proteins and nucleic acids. Cambridge, UK: Academic Press. , , , .
- 2010. The Pfam protein families database. Nucleic Acids Research 38: D211–D222. , , , , , , , , .
- 2005. Cullins 3a and 3b assemble with members of the broad complex/tramtrack/bric-a-brac (BTB) protein family to form essential ubiquitin-protein ligases (E3s) in Arabidopsis. Journal of Biological Chemistry 280: 18810–18821. , , , , , , .
- 2002. Plant development: regulation by protein degradation. Science 297: 793–797. , .
- 2005. UPF3 suppresses aberrant spliced mRNA in Arabidopsis. Plant Journal 43: 530–540. , .
- 2006. Survey of conserved alternative splicing events of mRNAs encoding SR proteins in land plants. Molecular Biology and Evolution 23: 1085–1094. , .
- 2006. The serine/arginine-rich protein family in rice plays important roles in constitutive and alternative splicing of pre-mRNA. Plant Cell 18: 146–158. , , .
- 2006. Evolutionary conservation and regulation of particular alternative splicing events in plant SR proteins. Nucleic Acids Research 34: 4395–4405. , , , .
- 2012. Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis. Nucleic Acids Research 40: 2454–2469. , , , , , , , , , et al.
- 2003. Alternative splicing and proteome diversity in plants: the tip of the iceberg has just emerged. Trends in Plant Science 8: 468–471. .
- 2010. Alternative splicing and evolution: diversification, exon definition and function. Nature Reviews Genetics 11: 345–355. , , .
- 2009. Ets-1 p27: a novel Ets-1 isoform with dominant-negative effects on the transcriptional properties and the subcellular localization of Ets-1 p51. Oncogene 28: 2087–2099. , , , , , , , , .
- 2010. Conserved alternative splicing of Arabidopsis transthyretin-like determines protein localization and S-allantoin synthesis in peroxisomes. Plant Cell 22: 1564–1574. , , , , .
- 2003. Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proceedings of the National Academy of Sciences, USA 100: 189–192. , , .
- 2006. A subgroup of myb transcription factor genes undergoes highly conserved alternative splicing in Arabidopsis and rice. Journal of Experimental Botany 57: 1263–1273. , , , , , , , , .
- 2008. Role of Arabidopsis RAP2.4 in regulating light- and ethylene-mediated developmental processes and drought stress tolerance. Molecular Plant 1: 42–57. , , .
- 1996. Pre-mRNA splicing in plants: characterization of ser/arg splicing factors. Proceedings of the National Academy of Sciences, USA 93: 3074–3079. , , , .
- 2010. Function annotation of rice transcriptome at single nucleotide resolution by RNA-seq. Genome Research 20: 1238–1249. , , , , , , , , , et al.
- 2011. Multi-domain conformational selection underlies pre-mRNA splicing regulation by U2AF. Nature 475: 408–411. , , , , , , , , .
- 2002. Functional significance of the alternative transcript processing of the Arabidopsis floral promoter FCA. Plant Cell 14: 877–888. , , , , , .
- 2012. Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis. Genome Research 22: 1184–1195. , , , , .
- 2009. Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication. Genome Biology 10: R111. , , , , , , , , , et al.
- 2004. Intron retention is a major phenomenon in alternative splicing in Arabidopsis. Plant Journal 39: 877–885. , , , , , .
- 2010. Expansion of the eukaryotic proteome by alternative splicing. Nature 463: 457–463. , .
- 2001. The crystal structures of glutathione S-transferases isozymes 1–3 and 1–4 from Anopheles dirus species b. Protein Science 10: 2176–2185. , , , , , .
- 2008. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nature Genetics 40: 1413–1415. , , , , .
- 2008. Rubisco regulation: a role for inhibitors. Journal of Experimental Botany 59: 1569–1580. , , , , .
- 2001. Crystal structures of two human pyrophosphorylase isoforms in complexes with UDPGlc(Gal)NAc: role of the alternatively spliced insert in the enzyme oligomeric assembly and active site architecture. EMBO Journal 20: 6191–6202. , , , , , , , , .
- 2007. Alternative splicing of pre-messenger RNAs in plants in the genomic era. Annual Review of Plant Biology 58: 267–294. .
- 2009. Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks. Plant Physiology 150: 889–903. , , , , , , , .
- 1998. Protein targeting to the thylakoid membrane. Annual Review of Plant Biology 49: 97–126. .
- 2008. Reciprocal regulation of glycine-rich RNA-binding proteins via an interlocked feedback loop coupling alternative splicing to nonsense-mediated decay in Arabidopsis. Nucleic Acids Research 36: 6977–6987. , , , , .
- 2009. Comparative analysis indicates that alternative splicing in plants has a limited role in functional expansion of the proteome. BMC Genomics 10: 154. , , , .
- 2004. How prevalent is functional alternative splicing in the human genome? Trends in Genetics 20: 68–71. , , .
- 2003. The circadian clock regulated RNA-binding protein AtGRP7 autoregulates its expression by influencing alternative splicing of its own pre-mRNA. Plant Journal 33: 361–371. , , , , .
- 2005. Function of alternative splicing. Gene 344: 1–20. , , , , , , , .
- 2011. Regulation of protein function by ‘microproteins’. EMBO Reports 12: 35–42. , .
- 2009. The spliceosome: design principles of a dynamic RNP machine. Cell 136: 701–718. , , .
- 1989. Characterization of cDNA clones encoding the extrinsic 23 kDa polypeptide of the oxygen-evolving complex of photosystem II in pea. Plant Molecular Biology 13: 573–582. , , , , .
- 2006. Genomewide comparative analysis of alternative splicing in plants. Proceedings of the National Academy of Sciences, USA 103: 7175–7180. , .
- 2008. Cross-species EST alignments reveal novel and conserved alternative splicing events in legumes. BMC Plant Biology 8: 17. , , , .
- 2009. Arabidopsis thaliana BTB/POZ-math proteins interact with members of the ERF/AP2 transcription factor family. FEBS Journal 276: 6624–6635. , .
- 2004. The impact of very short alternative splicing on protein structures and functions in the human genome. Trends in Genetics 20: 232–236. , , , , , .
- 1989. Alternative mRNA splicing generates the two ribulosebisphosphate carboxylase/oxygenase activase polypeptides in spinach and Arabidopsis. Plant Cell 1: 815–825. , , .
- 2005. Gmap: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 21: 1859–1875. , .
- 2000. Three-amino acid extension loop homeodomain proteins Meis2 and TGIF differentially regulate transcription. Journal of Biological Chemistry 275: 20734–20741. , , , , , .
- 2010. Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Research 20: 646–654. , , , , , , , , , et al.
- 2009. Two alternatively spliced isoforms of the Arabidopsis SR45 protein have distinct roles during normal plant development. Plant Physiology 150: 1450–1458. , .
- 2009. Sim4 cc: a cross-species spliced alignment program. Nucleic Acids Research 37: e80. , , , .
- 2011. Extensive changes to alternative splicing patterns following allopolyploidy in natural and resynthesized polyploids. Proceedings of the National Academy of Sciences, USA 108: 16122–16127. , , .