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Relative nuclear enrichment of lncRNAs compared to mRNAs is a prevalent phenomenon but the molecular mechanisms governing their nuclear retention in cells remain largely unknown. Here in this study, we harness the recently released eCLIP data for a large number of RNA-binding proteins (RBPs) in K562 and HepG2 cells and utilize multiple bioinformatics methods to comprehensively survey the roles of RBPs in lncRNA nuclear retention. We identify an array of splicing RBPs that bind to nuclear-enriched lincRNAs (large intergenic non-coding RNAs) thus may act as trans-factors regulating their nuclear retention. Further analyses reveal that these RBPs may bind with distinct core motifs, flanking sequence compositions, or secondary structures to drive lincRNA nuclear retention. Moreover, network analyses uncover potential co-regulatory RBP clusters and the physical interaction between HNRNPU and SAFB2 proteins in K562 cells is further experimentally verified. Altogether, our analyses reveal previously unknown factors and mechanisms that govern lincRNA nuclear localization in cells.<\/jats:p>","DOI":"10.1093\/bib\/bbab195","type":"journal-article","created":{"date-parts":[[2021,4,29]],"date-time":"2021-04-29T19:12:27Z","timestamp":1619723547000},"source":"Crossref","is-referenced-by-count":35,"title":["Large scale RNA-binding proteins\/LncRNAs interaction analysis to uncover lncRNA nuclear localization mechanisms"],"prefix":"10.1093","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7593-8085","authenticated-orcid":false,"given":"Yile","family":"Huang","sequence":"first","affiliation":[{"name":"Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yulong","family":"Qiao","sequence":"additional","affiliation":[{"name":"Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yu","family":"Zhao","sequence":"additional","affiliation":[{"name":"Department of Orthaepedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China"},{"name":"Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China"},{"name":"School of Medicine, Sun Yat-sen University, Guangzhou, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuying","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jie","family":"Yuan","sequence":"additional","affiliation":[{"name":"Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiajian","family":"Zhou","sequence":"additional","affiliation":[{"name":"Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China"},{"name":"Dermatology Hospital, Southern Medical University, Guangzhou, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5547-9501","authenticated-orcid":false,"given":"Hao","family":"Sun","sequence":"additional","affiliation":[{"name":"Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China"},{"name":"Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5474-2905","authenticated-orcid":false,"given":"Huating","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Orthaepedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China"},{"name":"Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,5,31]]},"reference":[{"key":"2021110814415159800_ref1","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1038\/nature21374","article-title":"An atlas of human long non-coding RNAs with accurate 5\u2032 ends","volume":"543","author":"Hon","year":"2017","journal-title":"Nature"},{"key":"2021110814415159800_ref2","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1038\/nrm.2017.104","article-title":"The 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