ArticleBMC genomics2008
Alternative splicing at NAGNAG acceptors in Arabidopsis thaliana SR and SR-related protein-coding genes.
Article in BMC genomics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 52 citations in OpenAlex.
- Molecular Mechanisms in Responses to Combined Stresses in Strawberry.Current issues in molecular biology · 2026Review
- CAX-INTERACTING PROTEIN4 depletion causes early lethality and pre-mRNA missplicing in Arabidopsis.Plant physiology · 2024Article
- CXIP4 depletion causes early lethality and pre-mRNA missplicing in Arabidopsis.bioRxiv : the preprint server for biology · 2024Article
- Alternative splicing responses to salt stress inFrontiers in genetics · 2024Article
- Article
- Research progress on the roles of lncRNAs in plant development and stress responses.Frontiers in plant science · 2023Review
- meLife · 2022Article
- Missplicing suppressor alleles of Arabidopsis PRE-MRNA PROCESSING FACTOR 8 increase splicing fidelity by reducing the use of novel splice sites.Nucleic acids research · 2022Article
- Nucleotides in both donor and acceptor splice sites are responsible for choice in NAGNAG tandem splice sites.Cellular and molecular life sciences : CMLS · 2021Article
- BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq.BMC genomics · 2019Article
- Coordinated Regulation of Pre-mRNA Splicing by the SFPS-RRC1 Complex to Promote Photomorphogenesis.The Plant cell · 2019Article
- An eukaryotic elongation factor 2 from Medicago falcata (MfEF2) confers cold tolerance.BMC plant biology · 2019Article
- Evolution of Alternative Splicing in Eudicots.Frontiers in plant science · 2019Article
- Identification and analysis of alternative splicing events in Phaseolus vulgaris and Glycine max.BMC genomics · 2017Article
- Functions of long intergenic non-coding (linc) RNAs in plants.Journal of plant research · 2017Review
- CoSpliceNet: a framework for co-splicing network inference from transcriptomics data.BMC genomics · 2016Article
- Merging Absolute and Relative Quantitative PCR Data to Quantify STAT3 Splice Variant Transcripts.Journal of visualized experiments : JoVE · 2016Article
- Analysis of pollen-specific alternative splicing in Arabidopsis thaliana via semi-quantitative PCR.PeerJ · 2015Article
- Article
- Physiological state co-regulates thousands of mammalian mRNA splicing events at tandem splice sites and alternative exons.Nucleic acids research · 2014Article
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSeveral recent studies indicate that alternative splicing in Arabidopsis and other plants is a common mechanism for post-transcriptional modulation of gene expression. However, few analyses have been done so far to elucidate the functional relevance of alternative splicing in higher plants. Representing a frequent and universal subtle alternative splicing event among eukaryotes, alternative splicing at NAGNAG acceptors contributes to transcriptome diversity and therefore, proteome plasticity. Alternatively spliced NAGNAG acceptors are overrepresented in genes coding for proteins with RNA-recognition motifs (RRMs). As SR proteins, a family of RRM-containing important splicing factors, are known to be extensively alternatively spliced in Arabidopsis, we analyzed alternative splicing at NAGNAG acceptors in SR and SR-related genes.
resultsIn a comprehensive analysis of the Arabidopsis thaliana genome, we identified 6,772 introns that exhibit a NAGNAG acceptor motif. Alternative splicing at these acceptors was assessed using available EST data, complemented by a sequence-based prediction method. Of the 36 identified introns within 30 SR and SR-related protein-coding genes that have a NAGNAG acceptor, we selected 15 candidates for an experimental analysis of alternative splicing under several conditions. We provide experimental evidence for 8 of these candidates being alternatively spliced. Quantifying the ratio of NAGNAG-derived splice variants under several conditions, we found organ-specific splicing ratios in adult plants and changes in seedlings of different ages. Splicing ratio changes were observed in response to heat shock and most strikingly, cold shock. Interestingly, the patterns of differential splicing ratios are similar for all analyzed genes.
conclusionNAGNAG acceptors frequently occur in the Arabidopsis genome and are particularly prevalent in SR and SR-related protein-coding genes. A lack of extensive EST coverage can be compensated by using the proposed sequence-based method to predict alternative splicing at these acceptors. Our findings indicate that the differential effects on NAGNAG alternative splicing in SR and SR-related genes are organ- and condition-specific rather than gene-specific.
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