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However, nucleotide features that determine these distinct distributions of lncRNAs and mRNAs have yet to be fully addressed. Here, we develop RNAlight, a machine learning model based on LightGBM, to identify nucleotide k-mers contributing to the subcellular localizations of mRNAs and lncRNAs. With the Tree SHAP algorithm, RNAlight extracts nucleotide features for cytoplasmic or nuclear localization of RNAs, indicating the sequence basis for distinct RNA subcellular localizations. By assembling k-mers to sequence features and subsequently mapping to known RBP-associated motifs, different types of sequence features and their associated RBPs were additionally uncovered for lncRNAs and mRNAs with distinct subcellular localizations. Finally, we extended RNAlight to precisely predict the subcellular localizations of other types of RNAs, including snRNAs, snoRNAs and different circular RNA transcripts, suggesting the generality of using RNAlight for RNA subcellular localization prediction.<\/jats:p>","DOI":"10.1093\/bib\/bbac509","type":"journal-article","created":{"date-parts":[[2022,10,26]],"date-time":"2022-10-26T10:52:00Z","timestamp":1666781520000},"source":"Crossref","is-referenced-by-count":39,"title":["RNAlight: a machine learning model to identify nucleotide features determining RNA subcellular localization"],"prefix":"10.1093","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8459-3784","authenticated-orcid":false,"given":"Guo-Hua","family":"Yuan","sequence":"first","affiliation":[{"name":"CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences , Chinese Academy of Sciences, Shanghai 200031 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5230-4119","authenticated-orcid":false,"given":"Ying","family":"Wang","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences , Chinese Academy of Sciences, Shanghai 200031 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6432-8310","authenticated-orcid":false,"given":"Guang-Zhong","family":"Wang","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences , Chinese Academy of Sciences, Shanghai 200031 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8833-7473","authenticated-orcid":false,"given":"Li","family":"Yang","sequence":"additional","affiliation":[{"name":"Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University , Shanghai 200032 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,12,3]]},"reference":[{"key":"2023011917140788900_ref1","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1016\/j.tcb.2009.02.001","article-title":"RNA localization and polarity: from A(PC) to Z(BP)","volume":"19","author":"Mili","year":"2009","journal-title":"Trends Cell 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