A lncRNA, SPRIGHTLY, interacts with Polypyrimidine Tract Binding Protein 1 (PTBP1) and modulates SET And MYND Domain Containing 3 (SMYD3) exon skipping.

During the course of surveying Medulloblastoma (MB) group specific lncRNAs, we found that SPRIGHTLY was highly upregulated in group 4 cell lines and patient derived xenografts (PDX). Its knock down reduced cell proliferation, invasion, and colony formation. It binds to the intron region of SMYD3 pre-mRNA and regulates SMYD3 exon 5 skipping together with PTBP1 protein. In group 4 cell line, the increase of SMYD3 affects EGFR pathway and regulates its downstream gene transcription. Inquiring SMYD3 and SMYD3 E5D transcripts expression in the patient RNA-seq data suggests that balancing two transcripts level seems to be associated with tumor development or maintenance. Group 4 MB cell line, CHLA01-MED cells were transfected with plasmid harvoring SMYD3-Myc or SMYD3 E5 deletion-Myc gene and stable clones were selected. To knock down the SPRIGHTLY, cells were transduced with lentivirus having two gRNAs, which are targetting before and after SPRIGHTLY gene and Cas9 gene. Single clones showing reduced SPRIGHTLY expression was selected.