Chemically-induced cellular stress signals are transmitted to alternative splicing via UsnRNA levels to alter gene expression in Arabidopsis thaliana

TL;DR

This study shows that cellular stress in plants can change gene expression by altering alternative splicing, which is influenced by UsnRNA levels and SRD2-mediated transcription.

Contribution

The study reveals a novel mechanism linking cellular stress to alternative splicing through UsnRNA levels and SRD2 in Arabidopsis.

Findings

Stress treatments altered AS patterns and U1 snRNA levels in Arabidopsis.

The srd2-1 mutant showed hypersensitivity to stress, with AS changes at lower stress concentrations.

Cellular stress influences gene expression via AS regulation, partially mediated by UsnRNA levels.

Abstract

Alternative pre-mRNA splicing (AS) is a crucial regulatory layer of gene expression in eukaryotes. AS patterns can change in response to abiotic and biotic stress, allowing cellular functions to adapt to environmental conditions. Here, we examined the effects of cellular stress-inducing chemicals on AS-mediated gene regulation in Arabidopsis thaliana by investigating the alternatively spliced forms of SERINE-ARGININE PROTEIN30 (SRp30) and U1-70 K, encoding splicing factors, as well as ASCORBATE PEROXIDASE3 (APX3) and FOLYLPOLYGLUTAMATE SYNTHASE3 (FPGS3), encoding enzymes important for stress responses. Disrupting key cellular activities, including nitric oxide metabolism, ATPase activity, plastid function, and genome stability, affected AS patterns in Arabidopsis. Stress treatment altered the abundance of uridine-rich small nuclear RNAs (UsnRNAs), especially U1 snRNAs, which are essential non-coding RNA components of U1 small nuclear ribonucleoproteins (U1 snRNPs), suggesting that abnormalities in AS are partially mediated by changes in U1 snRNA levels. The shoot redifferentiation defectice2-1 (srd2-1) mutant defective for snRNA transcription was hypersensitive for stress treatment, since it showed changes in AS patterns at lower concentrations of stress inducers to compare with the wild type. Together, our data suggest that cellular stress can influence gene expression in plants by regulating AS, which is partially regulated by UsnRNA levels through the SRD2-mediated snRNA transcription.

The online version contains supplementary material available at 10.1007/s11103-025-01575-9.

In plants, cellular stress differentially changes gene expression by regulating alternative splicing, which is regulated by UsnRNA levels through SRD2-mediated transcription.

The online version contains supplementary material available at 10.1007/s11103-025-01575-9.

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