Alternative Splicing Dynamics in Plant Stress Responses

Alternative splicing remodels pre‐mRNA transcripts to generate diverse mRNA isoforms that fine‐tune gene expression under environmental stress. In plants, splicing decisions—such as exon skipping, intron retention and micro‐exon inclusion—mediate rapid regulatory responses to light, temperature fluctuations, water deficit and other stressors. These dynamic adjustments influence transcript stability, translational potential and protein diversity, enabling stress adaptation at both cellular and whole‐plant levels. Emerging evidence reveals that splicing regulators respond to abiotic cues through changes in expression, post‐translational modification and subcellular localisation, orchestrating stress‐specific splicing programmes. Such programmes modulate key regulators of photomorphogenesis, thermotolerance, cold acclimation and developmental transitions, underscoring the global significance of splicing control for crop resilience.

Research from Nature Portfolio

Recent studies have elucidated how light and developmental cues interact with the splicing machinery to regulate stress responses. In one investigation, light‐induced changes in intron retention were shown to be controlled by the spliceosome and COP1‐mediated degradation of a plant‐specific spliceosomal component, leading to nucleus retention of intron‐retained transcripts in light signalling genes and thereby modulating seedling photomorphogenesis. Another report identified an RNA‐binding protein that is essential for retention of micro‐ and small exons in transcripts of floral homeotic genes; this factor binds poly‐purine motifs and associates with spliceosome components to ensure correct exon inclusion, linking splicing regulation to flower development and broader environmental response pathways.

Alternative Splicing Dynamics in Plant Stress Responses publication trend

The graph below shows the total number of articles in alternative splicing dynamics in plant stress responses across all publications each year (not limited to Nature Index journals).

Technical terms

Alternative splicing: The process by which different combinations of exons and introns are joined to produce multiple mRNA isoforms from a single gene.

Intron retention: A form of alternative splicing in which introns are retained in the mature mRNA, often leading to nuclear sequestration or degradation.

Exon skipping: A splicing event where one or more exons are omitted from the mature transcript, altering protein‐coding potential.

Micro‐exon: A very short exon (typically under 51 nucleotides) whose inclusion or exclusion can have significant functional effects on protein domains.

Spliceosome: A large ribonucleoprotein complex that recognises splice sites and catalyses the removal of introns from pre‐mRNA.

Serine/arginine‐rich (SR) proteins: A family of splicing factors that recognise splicing enhancers and regulate splice site selection under stress conditions.

References

1. Light regulates nuclear detainment of intron-retained transcripts through COP1-spliceosome to modulate photomorphogenesis. Nature Communications (2024).
2. Regulation of micro- and small-exon retention and other splicing processes by GRP20 for flower development. Nature Plants (2024).
3. A plant-specific clade of serine/arginine-rich proteins regulates RNA splicing homeostasis and thermotolerance in tomato. Nucleic Acids Research (2024).
4. Nucleo-cytoplasmic distribution of SAP18 reveals its dual function in splicing regulation and heat-stress response in Arabidopsis. Plant Communications (2024).
5. Rapid and Dynamic Alternative Splicing Impacts the Arabidopsis Cold Response Transcriptome. The Plant Cell (2018).