{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T04:13:06Z","timestamp":1789704786090,"version":"4.0.1"},"reference-count":182,"publisher":"MDPI AG","issue":"17","license":[{"start":{"date-parts":[[2026,8,27]],"date-time":"2026-08-27T00:00:00Z","timestamp":1787788800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["2244127"],"award-info":[{"award-number":["2244127"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"award":["2244127"],"award-info":[{"award-number":["2244127"]}],"id":[{"id":"https:\/\/ror.org\/021nxhr62","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Cells"],"abstract":"<jats:p>RNA-binding proteins (RBPs) are essential regulators of RNA metabolism and gene expression, influencing processes such as splicing, stability, localization, and translation. Despite their critical roles in health and disease, including cancer, identifying RNA\u2013protein interactions remains challenging due to technical limitations and biases of existing methods. Here we review and compare experimental techniques\u2014including in vitro affinity purification, in vivo crosslinking, and proximity labeling\u2014and computational prediction tools for RBP identification. We assess their strengths, limitations, and applicability across biological contexts, emphasizing the benefits of integrating experimental and computational strategies. Our analysis provides practical guidelines for selecting appropriate methodologies tailored to different cell types and research goals. These insights aim to facilitate more accurate mapping of RNA\u2013protein interactomes, thereby advancing understanding of RBP functions and supporting the development of novel therapeutic interventions targeting RNA\u2013protein complexes.<\/jats:p>","DOI":"10.3390\/cells15171546","type":"journal-article","created":{"date-parts":[[2026,8,27]],"date-time":"2026-08-27T10:58:21Z","timestamp":1787828301000},"page":"1546","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Experimental and Computational Approaches to Identify RNA\u2013Protein Interactions"],"prefix":"10.3390","volume":"15","author":[{"given":"Brigette","family":"Romero","sequence":"first","affiliation":[{"name":"Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jadira Aurora","family":"Fuentes Bautista","sequence":"additional","affiliation":[{"name":"Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victoria","family":"Beringer","sequence":"additional","affiliation":[{"name":"Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maryia","family":"Hrynashka","sequence":"additional","affiliation":[{"name":"Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7518-0400","authenticated-orcid":false,"given":"Vijay","family":"Parashar","sequence":"additional","affiliation":[{"name":"Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9039-6149","authenticated-orcid":false,"given":"Mona","family":"Batish","sequence":"additional","affiliation":[{"name":"Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,27]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"101318","DOI":"10.1016\/j.isci.2020.101318","article-title":"MS2-TRIBE Evaluates Both Protein-RNA Interactions and Nuclear Organization of Transcription by RNA Editing","volume":"23","author":"Biswas","year":"2020","journal-title":"iScience"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Konde, O.M., Balela, W.B., and Tshitenge, T.B. 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