At-RS31 orchestrates hierarchical cross-regulation of splicing factors and integrates alternative splicing with TOR-ABA pathways Journal Article
| Authors: | Köster, T.; Venhuizen, P.; Lewinski, M.; Petrillo, E.; Marquez, Y.; Fuchs, A.; Ray, D.; Nimeth, B. A.; Riegler, S.; Franzmeier, S.; Rodríguez, F. S.; Aballay, F. E.; Tognacca, R. S.; Zheng, H.; Hughes, T.; Morris, Q.; Barta, A.; Staiger, D.; Kalyna, M. |
| Article Title: | At-RS31 orchestrates hierarchical cross-regulation of splicing factors and integrates alternative splicing with TOR-ABA pathways |
| 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. © 2025 The Author(s). New Phytologist © 2025 New Phytologist Foundation. |
| Keywords: | mutation; gene expression; protein; rna; alternative splicing; binding site; arabidopsis thaliana; abscisic acid; sr proteins; dicotyledon; iclip; aba; rnacompete; tor kinase |
| Journal Title: | New Phytologist |
| Volume: | 247 |
| Issue: | 2 |
| ISSN: | 0028646X |
| Publisher: | Unknown |
| Date Published: | 2025-01-01 |
| Start Page: | 738 |
| End Page: | 759 |
| Language: | English |
| DOI: | 10.1111/nph.70221 |
| PROVIDER: | scopus |
| DOI/URL: | |
| Notes: | Article -- Source: Scopus |
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