{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,6]],"date-time":"2026-02-06T02:51:11Z","timestamp":1770346271534,"version":"3.49.0"},"reference-count":25,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2024,2,6]],"date-time":"2024-02-06T00:00:00Z","timestamp":1707177600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Bioinform."],"abstract":"<jats:p>In the past, several methods have been developed for predicting the single-label subcellular localization of messenger RNA (mRNA). However, only limited methods are designed to predict the multi-label subcellular localization of mRNA. Furthermore, the existing methods are slow and cannot be implemented at a transcriptome scale. In this study, a fast and reliable method has been developed for predicting the multi-label subcellular localization of mRNA that can be implemented at a genome scale. Machine learning-based methods have been developed using mRNA sequence composition, where the XGBoost-based classifier achieved an average area under the receiver operator characteristic (AUROC) of 0.709 (0.668\u20130.732). In addition to alignment-free methods, we developed alignment-based methods using motif search techniques. Finally, a hybrid technique that combines the XGBoost model and the motif-based approach has been developed, achieving an average AUROC of 0.742 (0.708\u20130.816). Our method\u2014MRSLpred\u2014outperforms the existing state-of-the-art classifier in terms of performance and computation efficiency. A publicly accessible webserver and a standalone tool have been developed to facilitate researchers (webserver: <jats:ext-link>https:\/\/webs.iiitd.edu.in\/raghava\/mrslpred\/<\/jats:ext-link>).<\/jats:p>","DOI":"10.3389\/fbinf.2024.1341479","type":"journal-article","created":{"date-parts":[[2024,2,6]],"date-time":"2024-02-06T05:04:55Z","timestamp":1707195895000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":5,"title":["MRSLpred\u2014a hybrid approach for predicting multi-label subcellular localization of mRNA at the genome scale"],"prefix":"10.3389","volume":"4","author":[{"given":"Shubham","family":"Choudhury","sequence":"first","affiliation":[]},{"given":"Nisha","family":"Bajiya","sequence":"additional","affiliation":[]},{"given":"Sumeet","family":"Patiyal","sequence":"additional","affiliation":[]},{"given":"Gajendra P. S.","family":"Raghava","sequence":"additional","affiliation":[]}],"member":"1965","published-online":{"date-parts":[[2024,2,6]]},"reference":[{"key":"B1","doi-asserted-by":"crossref","DOI":"10.1145\/2939672.2939785","article-title":"XGBoost","author":"Chen","year":"2016"},{"key":"B2","doi-asserted-by":"publisher","first-page":"3777","DOI":"10.1091\/mbc.E15-02-0115","article-title":"Global analysis of asymmetric RNA enrichment in oocytes reveals low conservation between closely related Xenopus species","volume":"26","author":"Clau\u00dfen","year":"2015","journal-title":"Mol. Biol. Cell."},{"key":"B3","doi-asserted-by":"publisher","first-page":"D333","DOI":"10.1093\/nar\/gkab825","article-title":"RNALocate v2.0: an updated resource for RNA subcellular localization with increased coverage and annotation","volume":"50","author":"Cui","year":"2022","journal-title":"Nucleic acids Res."},{"key":"B4","doi-asserted-by":"publisher","first-page":"747","DOI":"10.3892\/ijmm.2014.1629","article-title":"Regulation of mRNA transport, localization and translation in the nervous system of mammals (Review)","volume":"33","author":"Di Liegro","year":"2014","journal-title":"Int. J. Mol. Med."},{"key":"B5","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1016\/0092-8674(91)90137-n","article-title":"Oskar organizes the germ plasm and directs localization of the posterior determinant nanos","volume":"66","author":"Ephrussi","year":"1991","journal-title":"Cell."},{"key":"B6","doi-asserted-by":"publisher","first-page":"397","DOI":"10.1074\/mcp.M113.035600","article-title":"Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics","volume":"13","author":"Fagerberg","year":"2014","journal-title":"Mol. Cell. proteomics MCP"},{"key":"B7","doi-asserted-by":"publisher","first-page":"W239","DOI":"10.1093\/nar\/gkaa385","article-title":"mRNALoc: a novel machine-learning based in-silico tool to predict mRNA subcellular localization","volume":"48","author":"Garg","year":"2020","journal-title":"Nucleic acids Res."},{"key":"B8","doi-asserted-by":"publisher","first-page":"1212","DOI":"10.1126\/science.1176488","article-title":"Subcellular mRNA localization in animal cells and why it matters","volume":"326","author":"Holt","year":"2009","journal-title":"Sci. (New York, N.Y.)"},{"key":"B9","doi-asserted-by":"publisher","first-page":"1885","DOI":"10.1101\/gad.190413.112","article-title":"\u03b2-Actin mRNA compartmentalization enhances focal adhesion stability and directs cell migration","volume":"26","author":"Katz","year":"2012","journal-title":"Genes and Dev."},{"key":"B10","doi-asserted-by":"publisher","first-page":"223","DOI":"10.1146\/annurev.cellbio.21.122303.120653","article-title":"RNA transport and local control of translation","volume":"21","author":"Kindler","year":"2005","journal-title":"Annu. Rev. Cell. Dev. Biol."},{"key":"B11","doi-asserted-by":"publisher","first-page":"533","DOI":"10.1016\/s0092-8674(02)00651-7","article-title":"Mechanisms of subcellular mRNA localization","volume":"108","author":"Kloc","year":"2002","journal-title":"Cell."},{"key":"B12","doi-asserted-by":"publisher","first-page":"174","DOI":"10.1016\/j.cell.2007.08.003","article-title":"Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function","volume":"131","author":"L\u00e9cuyer","year":"2007","journal-title":"Cell."},{"key":"B13","doi-asserted-by":"publisher","first-page":"1826","DOI":"10.1093\/bib\/bby053","article-title":"Function determinants of TET proteins: the arrangements of sequence motifs with specific codes","volume":"20","author":"Liu","year":"2019","journal-title":"Briefings Bioinforma."},{"key":"B14","doi-asserted-by":"publisher","first-page":"1080","DOI":"10.1261\/rna.060814.117","article-title":"LncATLAS database for subcellular localization of long noncoding RNAs","volume":"23","author":"Mas-Ponte","year":"2017","journal-title":"RNA (New York, N.Y.)"},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.1101\/2021.12.14.472723","article-title":"Nfeature: a platform for computing features of nucleotide sequences","author":"Mathur","year":"2021","journal-title":"bioRxiv"},{"key":"B16","doi-asserted-by":"publisher","first-page":"3263","DOI":"10.1242\/dev.078626","article-title":"Principles and roles of mRNA localization in animal development","volume":"139","author":"Medioni","year":"2012","journal-title":"Development"},{"key":"B17","doi-asserted-by":"publisher","first-page":"103298","DOI":"10.1016\/j.isci.2021.103298","article-title":"Prediction of RNA subcellular localization: learning from heterogeneous data sources","volume":"24","author":"Savulescu","year":"2021","journal-title":"iScience"},{"key":"B18","doi-asserted-by":"publisher","first-page":"2617","DOI":"10.1016\/j.ymthe.2021.04.004","article-title":"mRNALocater: enhance the prediction accuracy of eukaryotic mRNA subcellular localization by using model fusion strategy","volume":"29","author":"Tang","year":"2021","journal-title":"Mol. Ther. J. Am. Soc. Gene Ther."},{"key":"B19","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1104\/pp.19.00972","article-title":"MRNA localization in plant cells","volume":"182","author":"Tian","year":"2020","journal-title":"Plant physiol."},{"key":"B20","doi-asserted-by":"publisher","first-page":"1231","DOI":"10.1093\/bioinformatics\/btr110","article-title":"Identifying discriminative classification-based motifs in biological sequences","volume":"27","author":"Vens","year":"2011","journal-title":"Bioinformatics"},{"key":"B21","doi-asserted-by":"publisher","first-page":"e46","DOI":"10.1093\/nar\/gkab016","article-title":"DM3Loc: multi-label mRNA subcellular localization prediction and analysis based on multi-head self-attention mechanism","volume":"49","author":"Wang","year":"2021","journal-title":"Nucleic acids Res."},{"key":"B22","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/database\/bay085","article-title":"lncSLdb: a resource for long non-coding RNA subcellular localization","volume":"2018","author":"Wen","year":"2018","journal-title":"Database (Oxford)"},{"key":"B23","doi-asserted-by":"publisher","first-page":"i333","DOI":"10.1093\/bioinformatics\/btz337","article-title":"Prediction of mRNA subcellular localization using deep recurrent neural networks","volume":"35","author":"Yan","year":"2019","journal-title":"Bioinformatics"},{"key":"B24","doi-asserted-by":"publisher","first-page":"D135","DOI":"10.1093\/nar\/gkw728","article-title":"RNALocate: a resource for RNA subcellular localizations","volume":"45","author":"Zhang","year":"2017","journal-title":"Nucleic acids Res."},{"key":"B25","doi-asserted-by":"publisher","first-page":"526","DOI":"10.1093\/bib\/bbz177","article-title":"Design powerful predictor for mRNA subcellular location prediction in Homo sapiens","volume":"22","author":"Zhang","year":"2021","journal-title":"Briefings Bioinforma."}],"container-title":["Frontiers in Bioinformatics"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fbinf.2024.1341479\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,6]],"date-time":"2024-02-06T05:04:58Z","timestamp":1707195898000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fbinf.2024.1341479\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,2,6]]},"references-count":25,"alternative-id":["10.3389\/fbinf.2024.1341479"],"URL":"https:\/\/doi.org\/10.3389\/fbinf.2024.1341479","relation":{},"ISSN":["2673-7647"],"issn-type":[{"value":"2673-7647","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,2,6]]},"article-number":"1341479"}}