Quantitative predictions of protein interactions with long noncoding RNAs
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- dc.contributor.author Cirillo, Davideca
- dc.date.accessioned 2018-01-24T12:32:06Z
- dc.date.available 2018-01-24T12:32:06Z
- dc.date.issued 2016
- dc.description.abstract Long noncoding RNAs (lncRNAs, which comprise 68% of the human transcriptome with average length of 1,000 nt) interact with various RNA-binding proteins (RBPs) to mediate cellular functions. Here we introduce Global Score as a tool to predict protein interactions with lncRNAs (http://service.tartaglialab.com/new_submission/globalscore). We used enhanced CLIP (eCLIP) to test the binding of the lncRNA Xist to the RBPs HnrnpK (Global Score of 0.99), Ptbp1 (0.99), Lbr (0.79), HnrnpU (Saf-A) (0.66), Spen (Sharp) (0.59) and negative control Dkc1 (0.01). Global Score prediction correlates with the eCLIP binding profile (Pearson correlation = 0.93). As for the binding sites, Spen and HnrnpK, Ptbp1, and Lbr interact respectively with Xist A, B, and E repeats and adjacent regions, while HnrnpU binds across the whole transcript, and Dkc1 does not interact with Xist.ca
- dc.identifier.doi https://doi.org/10.34810/data428
- dc.identifier.uri http://hdl.handle.net/10230/33743
- dc.language.iso engca
- dc.publisher Universitat Pompeu Fabraca
- dc.relation Publicació relacionada: Cirillo, Davide. Prediction of protein and nucleic acid interactions. 2016. http://hdl.handle.net/10803/403537
- dc.relation.isreferencedby http://hdl.handle.net/10803/403537
- dc.rights CC0 1.0 Universalca
- dc.rights.accessRights info:eu-repo/semantics/openAccessca
- dc.rights.uri http://creativecommons.org/publicdomain/zero/1.0/ca
- dc.title Quantitative predictions of protein interactions with long noncoding RNAsca
- dc.type info:eu-repo/semantics/otherca
- dc.type Dataset