ArticleBMC plant biology2011
Assessing the contribution of alternative splicing to proteome diversity in Arabidopsis thaliana using proteomics data.
Article in BMC plant biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed, 41 citations in OpenAlex.
- Impact of alternative splicing on Arabidopsis proteome.Nucleic acids research · 2026Article
- Impact of alternative splicing on Arabidopsis proteome.bioRxiv : the preprint server for biology · 2025Article
- Do not panic: An intron-centric guide to alternative splicing.The Plant cell · 2023Review
- The Importance of a Genome-Wide Association Analysis in the Study of Alternative Splicing Mutations in Plants with a Special Focus on Maize.International journal of molecular sciences · 2022Review
- Principles and correction of 5'-splice site selection.RNA biology · 2022Review
- IsoResolve: predicting splice isoform functions by integrating gene and isoform-level features with domain adaptation.Bioinformatics (Oxford, England) · 2021Article
- A Functional Kinase Is Necessary for Cyclin-Dependent Kinase G1 (CDKG1) to Maintain Fertility at High Ambient Temperature inFrontiers in plant science · 2020Article
- The alternative splicing ofPlant signaling & behavior · 2019Article
- Glycosylphosphatidylinositol-Anchored Proteins inFrontiers in plant science · 2019Review
- Unexpected conservation of the RNA splicing apparatus in the highly streamlined genome of Galdieria sulphuraria.BMC evolutionary biology · 2018Article
- Alternative splicing shapes transcriptome but not proteome diversity in Physcomitrella patens.Scientific reports · 2017Article
- 50/50 Expressional Odds of Retention Signifies the Distinction between Retained Introns and Constitutively Spliced Introns inFrontiers in plant science · 2017Article
- CoSpliceNet: a framework for co-splicing network inference from transcriptomics data.BMC genomics · 2016Article
- Article
- Spliceosomal introns in the 5' untranslated region of plant BTL RING-H2 ubiquitin ligases are evolutionary conserved and required for gene expression.BMC plant biology · 2013Article
- Targeting a heterologous protein to multiple plant organelles via rationally designed 5' mRNA tags.Journal of biological engineering · 2013Article
- Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq.Molecular & cellular proteomics : MCP · 2013Article
- The rice resistance protein pair RGA4/RGA5 recognizes the Magnaporthe oryzae effectors AVR-Pia and AVR1-CO39 by direct binding.The Plant cell · 2013Article
- Function of alternative splicing.Gene · 2013Review
- Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data.PLoS computational biology · 2013Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundLarge-scale analyses of genomics and transcriptomics data have revealed that alternative splicing (AS) substantially increases the complexity of the transcriptome in higher eukaryotes. However, the extent to which this complexity is reflected at the level of the proteome remains unclear. On the basis of a lack of conservation of AS between species, we previously concluded that AS does not frequently serve as a mechanism that enables the production of multiple functional proteins from a single gene. Following this conclusion, we hypothesized that the extent to which AS events contribute to the proteome diversity in Arabidopsis thaliana would be lower than expected on the basis of transcriptomics data. Here, we test this hypothesis by analyzing two large-scale proteomics datasets from Arabidopsis thaliana.
resultsA total of only 60 AS events could be confirmed using the proteomics data. However, for about 60% of the loci that, based on transcriptomics data, were predicted to produce multiple protein isoforms through AS, no isoform-specific peptides were found. We therefore performed in silico AS detection experiments to assess how well AS events were represented in the experimental datasets. The results of these in silico experiments indicated that the low number of confirmed AS events was the consequence of a limited sampling depth rather than in vivo under-representation of AS events in these datasets.
conclusionAlthough the impact of AS on the functional properties of the proteome remains to be uncovered, the results of this study indicate that AS-induced diversity at the transcriptome level is also expressed at the proteome level.
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