Tumor-associated intronic editing of HNRPLL generates a novel splicing variant linked to cell proliferation

Abstract

Processing of the eukaryotic transcriptome is a dynamic regulatory mechanism that confers genetic diversity, and splicing and adenosine to inosine (A-to-I) RNA editing are well-characterized examples of such processing. Growing evidence reveals the cross-talk between the splicing and RNA editing, but there is a paucity of substantial evidence for its mechanistic details and contribution in a physiological context. Here, our findings demonstrate that tumor-associated differential RNA editing, in conjunction with splicing machinery, regulates the expression of variants of <i>HNRPLL</i>, a gene encoding splicing factor. We discovered an <i>HNRPLL</i> transcript variant containing an additional exon 12A (<i>E12A</i>), which is a substrate of ADAR1 and ADAR2. <u>A</u>denosine <u>d</u>eaminases <u>a</u>cting on <u>R</u>NA (ADAR) direct deaminase-dependent expression of the <i>E12A</i> transcript, and ADAR-mediated regulation of <i>E12A</i> is largely splicing-based, and does not affect the stability or nucleocytoplasmic distribution of the transcript. Furthermore, ADAR-mediated modification of exon 12A generates an enhancer for the oncogenic splicing factor SRSF1 and consequently promotes the frequency of alternative splicing. Gene expression profiling by RNA-seq revealed that <i>E12A</i> acts distinctly from HNRPLL and regulates a set of growth-related genes, such as cyclin <i>CCND1</i> and growth factor receptor <i>TGFBR1</i> Accordingly, silencing <i>E12A</i> expression leads to impaired clonogenic ability and enhanced sensitivity to doxorubicin, thus highlighting the significance of this alternative isoform in tumor cell survival. In summary, we present the interplay of RNA editing and splicing as a regulatory mechanism of gene expression and also its physiological relevance. These findings extend our understanding of transcriptional dynamics and provide a mechanistic explanation to the link of RNA editors to tumorigenesis.