SINEUP long non-coding RNA acts via PTBP1 and HNRNPK to promote translational initiation assembly [eCLIP-seq]

We found novel functional long non-coding RNAs (lncRNAs) that contain a SINE element, and which up-regulate the translation of target mRNA, named SINEUPs. To investigate the network of translational regulation, we focused on the sub-cellular distribution of target mRNAs and SINEUP RNAs and SINEUP RNA binding proteins (RBPs). We identified PTBP1 and HNRNPK as essential RBPs. These proteins contributed to SINEUP RNA sub-cellular distribution and to assembly of translational initiation complexes, leading to enhancement of the target mRNA translation. To prove the SINEUP RBPs binding regions on SINEUP-GFP transcripts, we performed seCLIP; single-end enhanced crosslinking and immunoprecipitation assay to determine the specific binding sites of PTBP1 and HNRNPK on SINEUP-GFP RNA. These findings will promote a better understanding of the mechanisms on the fate of regulatory RNAs implicated in efficient protein translation. Overall design: To identfy binding sites of PTBP1 and HNRNPK on SINEUP RNA by eCLIP analysis in HEK293T/17 cell.