ArticlePlant physiology2013
Genome-wide detection of condition-sensitive alternative splicing in Arabidopsis roots.
Article in Plant physiology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
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Who cites it
73 citing papers in PubMed, 119 citations in OpenAlex.
- Alternative splicing acts as a strategic switch for heat shock network diversification under escalating heat stress.Plant cell reports · 2026Article
- A functional atlas of transposon-encoded products and their integration into host networks.Nature communications · 2026Article
- Spliceosome buffers cryptic genetic variation to enforce phenotypic robustness inScience advances · 2026Article
- Phosphorus starvation-induced alternative splicing landscape of rice confirms the regulatory function of Pup1 QTL.BMC plant biology · 2025Article
- Dynamic Coordination of Alternative Splicing and Subgenome Expression Bias Underlies Rusty Root Symptom Response inPlants (Basel, Switzerland) · 2025Article
- Comprehensive mapping of Arabidopsis alternative splicing landscape reveals key insights into plant development and immunity.The plant genome · 2025Article
- Camelina circRNA landscape: Implications for gene regulation and fatty acid metabolism.The plant genome · 2025Article
- Shedding light on iron nutrition: exploring intersections of transcription factor cascades in light and iron deficiency signaling.Journal of experimental botany · 2025Review
- Multiple strategies, including 6mA methylation, affecting plant alternative splicing in allopolyploid peanut.Plant biotechnology journal · 2024Article
- Exploring salt tolerance mechanisms using machine learning for transcriptomic insights: case study inHorticulture research · 2024Article
- FER-like iron deficiency-induced transcription factor (FIT) accumulates in nuclear condensates.The Journal of cell biology · 2024Article
- Transcriptomic Analyses Reveal Insights into the Shared Regulatory Network of Phenolic Compounds and Steviol Glycosides inInternational journal of molecular sciences · 2024Article
- Responsive Alternative Splicing Events ofInternational journal of molecular sciences · 2024Article
- Mapping intron retention events contributing to complex traits using splice quantitative trait locus.Plant methods · 2023Article
- The Splicing Factor OsSCL26 Regulates Phosphorus Homeostasis in Rice.Plants (Basel, Switzerland) · 2023Article
- The Splicing Factor SR45 Negatively Regulates Anthocyanin Accumulation under High-Light Stress inLife (Basel, Switzerland) · 2023Article
- Alternative splicing shapes the transcriptome complexity in blackgram [Vigna mungo (L.) Hepper].Functional & integrative genomics · 2023Article
- Multilayered regulation of iron homeostasis in Arabidopsis.Frontiers in plant science · 2023Review
- Article
- Alternative Splicing and Its Roles in Plant Metabolism.International journal of molecular sciences · 2022Review
13 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 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Iron (Fe) deficiency is a world-wide nutritional disorder in both plants and humans, resulting from its restricted bioavailability for plants and, subsequently, low Fe concentration in edible plant parts. Plants have evolved sophisticated mechanisms to alleviate Fe deficiency, with the aim of recalibrating metabolic fluxes and maintaining cellular Fe homeostasis. To analyze condition-sensitive changes in precursor mRNA (pre-mRNA) splicing pattern, we mapped the transcriptome of Fe-deficient and Fe-sufficient Arabidopsis (Arabidopsis thaliana) roots using the RNA sequencing technology and a newly developed software toolbox, the Read Analysis & Comparison Kit in Java (RACKJ). In alternatively spliced genes, stress-related Gene Ontology categories were overrepresented, while housekeeping cellular functions were mainly transcriptionally controlled. Fe deficiency increased the complexity of the splicing pattern and triggered the differential alternative splicing of 313 genes, the majority of which had differentially retained introns. Several genes with important functions in Fe acquisition and homeostasis were both differentially expressed and differentially alternatively spliced upon Fe deficiency, indicating a complex regulation of gene activity in Fe-deficient conditions. A comparison with a data set for phosphate-deficient plants suggests that changes in splicing patterns are nutrient specific and not or not chiefly caused by stochastic fluctuations. In sum, our analysis identified extensive posttranscriptional control, biasing the abundance and activity of proteins in a condition-dependent manner. The production of a mixture of functional and nonfunctional transcripts may provide a means to fine-tune the abundance of transcripts with critical importance in cellular Fe homeostasis. It is assumed that differential gene expression and nutrient deficiency-induced changes in pre-mRNA splicing represent parallel, but potentially interacting, regulatory mechanisms.
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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.