Systematic Analysis of the Impact of R-Methylation on RBPs-RNA Interactions: A Proteomic Approach.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34557518", "kind": "science-record", "revision": 8, "content_hash": "sha256:85d794680c57d37f09e43388ca98f1226f635a3beb4a8b8b15fc0e1a5705356f", "created_at": "2026-11-01T15:41:53Z", "updated_at": "2026-11-01T22:47:35Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Systematic Analysis of the Impact of R-Methylation on RBPs-RNA Interactions: A Proteomic Approach.", "doi": "10.3389/fmolb.2021.688973", "pmid": "34557518", "authors": ["Marianna Maniaci", "Francesca Ludovica Boffo", "Enrico Massignani", "Tiziana Bonaldi"], "journal": "Frontiers in molecular biosciences", "year": 2021, "abstract": "RNA binding proteins (RBPs) bind RNAs through specific RNA-binding domains, generating multi-molecular complexes known as ribonucleoproteins (RNPs). Various post-translational modifications (PTMs) have been described to regulate RBP structure, subcellular localization, and interactions with other proteins or RNAs. Recent proteome-wide experiments showed that RBPs are the most representative group within the class of arginine (R)-methylated proteins. Moreover, emerging evidence suggests that this modification plays a role in the regulation of RBP-RNA interactions. Nevertheless, a systematic analysis of how changes in protein-R-methylation can affect globally RBPs-RNA interactions is still missing. We describe here a quantitative proteomics approach to profile global changes of RBP-RNA interactions upon the modulation of type I and II protein arginine methyltransferases (PRMTs). By coupling the recently described Orthogonal Organic Phase Separation (OOPS) strategy with the Stable Isotope Labelling with Amino acids in Cell culture (SILAC) and pharmacological modulation of PRMTs, we profiled RNA-protein interaction dynamics in dependence of protein-R-methylation. Data are available via ProteomeXchange with identifier PXD024601.", "claims": [{"id": "claim-method", "statement": "To determine whether the abundance of the interface proteins was significantly affected by PRMT inhibitors compared to their expression level in the corresponding whole cell extracts, Fisher’s exact tests were performed with Python SciPy package.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34557518", "locator": "sections[18] \"Statistical Analysis of the Stable Isotope Labelling with Amino acids in Cell Culture -Based Quantitative Proteomics Data\" paragraph 2", "quote": "To determine whether the abundance of the interface proteins was significantly affected by PRMT inhibitors compared to their expression level in the corresponding whole cell extracts, Fisher’s exact tests were performed with Python SciPy package."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. 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We describe here a quantitative proteomics approach to profile global changes of RBP-RN", "NA complexes, coupling it with triple SILAC- proteomics and the use of PRMT inhibitors, in HeLa cerv", "actions were then selected for subsequent MS-proteomics analysis: proteins were in solution Trypsin-"], "order_basis": "paper_text_order:34", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ds in Cell Culture Labelling HeLa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) al", "roteomics and the use of PRMT inhibitors, in HeLa cervical cancer cells. 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