Figure 5.

LncRNAs and HuR interact and this interaction influences lncRNAs’ expression.

(a). In silico identification of HuR Binding Sites. Three different in silico approaches were used: RNA-Protein Interaction Prediction (RPISeq, http://pridb.gdcb.iastate.edu/RPISeq/) where a score >0.5 was considered ‘positive’ for a possible interaction (YES); RBPmap database (http://rbpmap.technion.ac.il/1541972084/results.html) which reports a prediction of the possible interaction sites (obtained with a ‘high stringency’ filter); RNAbp database (RBPDB, http://rbpdb.ccbr.utoronto.ca/index.php) which identifies the potential RNAbp binding sites (default threshold score of 0.8). (b). RNA-immunoprecipitation assay (RIP) for HuR was performed in neurospheres grown for 8 days (NSCs) and at the end of the 8-day differentiation process (DIFF). Quantification was performed by real time PCR and results are expressed as ddCt fold enrichment relative to unrelated IgG, used as IP negative control and performed in triplicate. Results are expressed as mean of three different experiments ± SD (*p < 0.05, ** p< 0.01, ***p < 0.001 vs NSCs).