{"doi":"10.1111/nph.70221","title":"At‐ <scp>RS31</scp> orchestrates hierarchical cross‐regulation of splicing factors and integrates alternative splicing with <scp>TOR</scp> ‐ <scp>ABA</scp> 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.","journal":"New Phytologist","year":2025,"id":511556,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":15,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9433,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":677068,"name":"Peter Venhuizen","orcid":"0000-0003-2835-1833","position":1,"is_corresponding":false},{"id":1338800,"name":"Martin Lewinski","orcid":"0000-0002-2692-3319","position":2,"is_corresponding":false},{"id":677072,"name":"Ezequiel Petrillo","orcid":"0000-0002-0025-3708","position":3,"is_corresponding":false},{"id":809025,"name":"Yamile Márquez","orcid":"0000-0003-1686-5992","position":4,"is_corresponding":false},{"id":1338801,"name":"Armin Fuchs","orcid":"0009-0004-3378-3707","position":5,"is_corresponding":false},{"id":269433,"name":"Debashish Ray","orcid":null,"position":6,"is_corresponding":false},{"id":1338802,"name":"Barbara A. Nimeth","orcid":"0000-0001-8692-8413","position":7,"is_corresponding":false},{"id":677065,"name":"Stefan Riegler","orcid":"0000-0003-3413-1343","position":8,"is_corresponding":false},{"id":1338803,"name":"Sophie Franzmeier","orcid":"0000-0002-1265-6790","position":9,"is_corresponding":false},{"id":1370302,"name":"Florencia S. Rodríguez","orcid":null,"position":10,"is_corresponding":false},{"id":1370303,"name":"Federico Emanuel Aballay","orcid":null,"position":11,"is_corresponding":false},{"id":1369586,"name":"Rocío Soledad Tognacca","orcid":"0000-0001-9678-3676","position":12,"is_corresponding":false},{"id":167489,"name":"Hong Zheng","orcid":null,"position":13,"is_corresponding":false},{"id":43029,"name":"Timothy R. Hughes","orcid":"0000-0002-8721-4719","position":14,"is_corresponding":false},{"id":267869,"name":"Quaid Morris","orcid":"0000-0002-2760-6999","position":15,"is_corresponding":false},{"id":677071,"name":"Andrea Barta","orcid":"0000-0002-8851-406X","position":16,"is_corresponding":false},{"id":617894,"name":"Dorothee Staiger","orcid":"0000-0002-1341-1381","position":17,"is_corresponding":false},{"id":677070,"name":"Maria Kalyna","orcid":"0000-0003-4702-7625","position":18,"is_corresponding":false},{"id":617891,"name":"Tino Köster","orcid":"0000-0003-3984-9813","position":0,"is_corresponding":true}],"reference_count":129,"raw_metadata":null,"created_at":"2026-07-19T02:47:55.918021Z","pmid":"40415535","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}