DEK binds to pre-mRNAs and regulated alternative splicing of Hippo signaling genes in HeLa cell [RIP-seq]

Purpose: Explore how DEK genome widely bind RNA and affect the alternative splicing in cancer Methods: DEK was overexpressed by transfecting HeLa cells with a DEK-overexpressing plasmid and RNA_seq was used to analyze gene expression profile and splicing pattern of DEK overexpression and control cells. Then, an improved RIP-seq was conducted to explore genome-widely binding characteristic of DEK in HeLa cell. Bioinformatics analysis and qPCR/RIP-PCR were performed to identify and validate the bound and regulated targets of DEK, respectively Results:The results showed DEK overexpression did not affect transcript level expression of those high expressed genes (with FPKM > 1), but splicing pattern of 411 genes (RASGs) was regulated by DEK in HeLa cells, which were enriched in Hippo signaling pathway. Moreover, DEK broadly bind the RNA of a total of 11, 112 genes, with a biased binding the GGUAA motifs at the CDS and intronic regions Conclusions: our results indicated DEK could broadly bind and regulate the pre-mRNA splicing process, which provide new insights of mechanisms that DEK functions in various biological processes including cancer Overall design: RIP-seq was conducted to explore genome-widely binding characteristics of DEK in HeLa cell