ArticleGenome biology2021
Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions highlight major functional differences with animals.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 107 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
107 citing papers in PubMed, 200 citations in OpenAlex.
- Interpretable machine learning enables de novo mapping of cell type-specific RNA splicing regulation from scRNA-seq data.Nature communications · 2026Article
- Changes in Alternative Splicing are Associated with Insecticide Response and Resistance.Genome biology and evolution · 2026Article
- Long-Read RNA Sequencing Reveals an Isoform Switching Pattern in Healthy Microglial Cell Lines Exposed to Radiotherapy.Non-coding RNA · 2026Article
- Intron retention dominates alternative splicing reprogramming during anaerobic stress in Chlamydomonas reinhardtii.Planta · 2026Article
- RNA regulation in plants.Science China. Life sciences · 2026Review
- Transcriptome assemblies for two drug-type cannabis chemotypes by long-read RNA sequencing.The plant genome · 2026Article
- Phosphate starvation induces root cell-type-specific transcriptional responses and alternative splicing.The New phytologist · 2026Article
- UniSplicer: A deep-learning framework for accurate splice-site prediction and splice-altering mutation detection across diverse taxa.Plant communications · 2026Article
- Comprehensive review and assessment of multi-species splicing variant prediction: task-specific deep learning models and genomic foundation models.Briefings in bioinformatics · 2026Review
- Differential splicing fine-tunes guard cell gene expression and is required for drought tolerance in Arabidopsis thaliana.The Plant journal : for cell and molecular biology · 2026Article
- Impact of alternative splicing on Arabidopsis proteome.Nucleic acids research · 2026Article
- Splicing as an integrative layer linking cell cycle regulation, epigenetic dynamics, and environmental responses in plants.Frontiers in plant science · 2026Review
- Pre-mRNA splicing and its regulation in microalgae and cyanobacteria.Advanced biotechnology · 2025Review
- Identification of the Splicing FactorInternational journal of molecular sciences · 2025Article
- Impact of U2-type introns on splice site prediction in A. thaliana species using deep learning.BMC bioinformatics · 2025Article
- MONOPTEROS isoform MP11ir plays a role during somatic embryogenesis in Arabidopsis thaliana.Plant physiology · 2025Article
- Phenotypic impact of individual conserved neuronal microexons and their master regulators in zebrafish.eLife · 2025Article
- Alternative splicing in plant stress responses: potential application for crop improvement.Planta · 2025Review
- Conservation and Remodeling of Alternative Splicing Landscapes in the Evolution ofPlants (Basel, Switzerland) · 2025Article
- Article
47 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAlternative splicing (AS) is a widespread regulatory mechanism in multicellular organisms. Numerous transcriptomic and single-gene studies in plants have investigated AS in response to specific conditions, especially environmental stress, unveiling substantial amounts of intron retention that modulate gene expression. However, a comprehensive study contrasting stress-response and tissue-specific AS patterns and directly comparing them with those of animal models is still missing.
resultsWe generate a massive resource for Arabidopsis thaliana, PastDB, comprising AS and gene expression quantifications across tissues, development and environmental conditions, including abiotic and biotic stresses. Harmonized analysis of these datasets reveals that A. thaliana shows high levels of AS, similar to fruitflies, and that, compared to animals, disproportionately uses AS for stress responses. We identify core sets of genes regulated specifically by either AS or transcription upon stresses or among tissues, a regulatory specialization that is tightly mirrored by the genomic features of these genes. Unexpectedly, non-intron retention events, including exon skipping, are overrepresented across regulated AS sets in A. thaliana, being also largely involved in modulating gene expression through NMD and uORF inclusion.
conclusionsNon-intron retention events have likely been functionally underrated in plants. AS constitutes a distinct regulatory layer controlling gene expression upon internal and external stimuli whose target genes and master regulators are hardwired at the genomic level to specifically undergo post-transcriptional regulation. Given the higher relevance of AS in the response to different stresses when compared to animals, this molecular hardwiring is likely required for a proper environmental response in A. thaliana.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.