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 , a gene encoding splicing factor. We discovered an transcript variant containing an additional exon 12A (), which is a substrate of ADAR1 and ADAR2. denosineeaminases cting onNA (ADAR) direct deaminase-dependent expression of the transcript, and ADAR-mediated regulation of 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 acts distinctly from HNRPLL and regulates a set of growth-related genes, such as cyclin and growth factor receptor Accordingly, silencing 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.

Cis- and trans-regulations of pre-mRNA splicing by RNA editing enzymes influence cancer development

“…Of note, we found that ADAR1 and ADAR2 regulate cassette exons in both directions. However, some previously reported crosstalk splicing events, such as STAT3, hnRNPR, and hnRNPLL were not identified by our RNA-Seq analysis 20,23,24,27 , presumably due to differential expressions of editing regulators in different types of cells and the resultant absence or low level of RNA editing at particular targets 34,51 . This Fig.…”

“…Editing occurs cotranscriptionally on nascent RNA, suggesting that editing precedes splicing and may cause widespread effects on splicing 20 . As proposed by previous studies, A-to-I editing may modulate splicing through disrupting branch point sequence (BPS) 21 , creating novel 3′ splice site (3′ss) 17,20,22 , modifying auxiliary cis-acting elements 23,24 as well as affecting RNA secondary structure 25,26 . However, the majority of studies were lack of experimental validations, specific mechanisms, and functional importance of crosstalk events.…”

Estimating growth patterns and driver effects in tumor evolution from individual samples

“…Less appreciated is the role of noncoding mutations in tumor progression 36,38,39 . Interestingly, in the case of TSGs, different studies have reported the role of noncoding intronic mutations that alter correct exon splicing, resulting in faulty tumor suppression [40][41][42][43] . Similarly, in the case of oncogenes different studies have reported the potential effect of synonymous mutations 39,40,44 .…”

Adenosine deaminase acting on RNA (ADAR1), a suppressor of double-stranded RNA–triggered innate immune responses

“…Human nuclear prelamin A recognition factor transcript includes an Alu-exon that depends upon A-to-I editing for exonization in a tissue-dependent manner, again by creation of a functional 3Ј AG splice site (75). Tumor-associated intronic editing of the HNRPLL splicing factor transcript by ADAR1 p110 and ADAR2 generates a novel variant containing an additional exon 12A (76). A comprehensive survey of noncanonical splice sights using deep transcriptome profiling identified seven U2/U12like noncanonical sites that are converted to canonical sites by A-to-I editing (77).…”