At‐ <scp>RS31</scp> orchestrates hierarchical cross‐regulation of splicing factors and integrates alternative splicing with <scp>TOR</scp> ‐ <scp>ABA</scp> pathways

Alternative splicing is essential for plants, enabling a single gene to produce multiple transcript variants to boost functional diversity and fine-tune responses to environmental and developmental cues. Arabidopsis thaliana At-RS31, a plant-specific splicing factor in the Serine/Arginine-rich (SR) protein family, responds to light and the Target of Rapamycin (TOR) signalling pathway, yet its downstream targets and regulatory impact remain unknown. To identify At-RS31 targets, we applied individual-nucleotide resolution crosslinking and immunoprecipitation (iCLIP) and RNAcompete assays. Transcriptomic analyses of At-RS31 mutant and overexpressing plants further revealed its effects on alternative splicing. iCLIP identified 4034 At-RS31 binding sites across 1421 genes, enriched in CU-rich and CAGA RNA motifs. Comparative iCLIP and RNAcompete data indicate that the arginine/serine (RS) domain of At-RS31 may influence its binding specificity in planta, underscoring the value of combining in vivo and in vitro approaches. Transcriptomic analysis showed that At-RS31 modulates diverse splicing events, particularly intron retention and exitron splicing, and influences other splicing modulators, acting as a hierarchical regulator. By regulating stress response genes and genes in both TOR and abscisic acid signalling pathways, At-RS31 may help integrate these signals, balancing plant growth with environmental adaptability through alternative splicing.

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Publication Details

Journal
New Phytologist
Published
2025-05-26
DOI
https://doi.org/10.1111/nph.70221
Citations
11
Primary Topic
RNA Research and Splicing
Type
article
Field-Weighted Citation Impact
8.87

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article

At‐ RS31 orchestrates hierarchical cross‐regulation of splicing factors and integrates alternative splicing with TOR ‐ ABA pathways

Barbara A. Nimeth, Hong Zheng, Stefan Riegler, Florencia S. Rodríguez et al.
11 citations
New Phytologist
RNA Research and Splicing
8.87
article

At‐ RS31 orchestrates hierarchical cross‐regulation of splicing factors and integrates alternative splicing with TOR ‐ ABA pathways

Barbara A. Nimeth, Hong Zheng, Stefan Riegler, Florencia S. Rodríguez, Quaid Morris, Dorothee Staiger, Tino Köster, Andrea Barta, Rocío Soledad Tognacca, Peter Venhuizen, Maria Kalyna, Timothy R. Hughes, Martin Lewinski, Sophie Franzmeier, Federico Emanuel Aballay, Ezequiel Petrillo, Yamile Márquez, Armin Fuchs, Debashish Ray
article en
11 citations

Abstract

Alternative splicing is essential for plants, enabling a single gene to produce multiple transcript variants to boost functional diversity and fine-tune responses to environmental and developmental cues. Arabidopsis thaliana At-RS31, a plant-specific splicing factor in the Serine/Arginine-rich (SR) protein family, responds to light and the Target of Rapamycin (TOR) signalling pathway, yet its downstream targets and regulatory impact remain unknown. To identify At-RS31 targets, we applied individual-nucleotide resolution crosslinking and immunoprecipitation (iCLIP) and RNAcompete assays. Transcriptomic analyses of At-RS31 mutant and overexpressing plants further revealed its effects on alternative splicing. iCLIP identified 4034 At-RS31 binding sites across 1421 genes, enriched in CU-rich and CAGA RNA motifs. Comparative iCLIP and RNAcompete data indicate that the arginine/serine (RS) domain of At-RS31 may influence its binding specificity in planta, underscoring the value of combining in vivo and in vitro approaches. Transcriptomic analysis showed that At-RS31 modulates diverse splicing events, particularly intron retention and exitron splicing, and influences other splicing modulators, acting as a hierarchical regulator. By regulating stress response genes and genes in both TOR and abscisic acid signalling pathways, At-RS31 may help integrate these signals, balancing plant growth with environmental adaptability through alternative splicing.

New PhytologistVol. 247(2)
Institute of Molecular Biotechnology (AT), Memorial Sloan Kettering Cancer Center (US), University of Toronto (CA), Bielefeld University (DE), Cornell University (US), Max Perutz Labs (AT), Kettering University (US), Instituto de Neurología de Buenos Aires (AR)
James Hutton Institute, Deutsche Forschungsgemeinschaft, International Centre for Genetic Engineering and Biotechnology, Austrian Science Fund, National Institutes of Health, Canadian Institutes of Health Research, National Cancer Institute
Life in Land
Openalex Percentile: Top 2%
RNA Research and Splicing
8.87
DOIOpen Access PDFOpenAlex
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