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

Sze Jing Tang,Leilei Chen,Jian Han,Henry Yang,Haoqing Shen,Huiqi Hong,Daryl Jin Tai Tay,Ka Wai Leong,Omer An,Fernando Bellido Molias,Vanessa Hui En Ng,Jia Li,Priyankaa Pitcheshwar,Yangyang Song

doi:10.1038/s41467-020-14621-5

Sze Jing Tang, Leilei Chen + Show 12 more

Open Access

https://doi.org/10.1038/s41467-020-14621-5

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Abstract

RNA editing and splicing are the two major processes that dynamically regulate human transcriptome diversity. Despite growing evidence of crosstalk between RNA editing enzymes (mainly ADAR1) and splicing machineries, detailed mechanistic explanations and their biological importance in diseases, such as cancer are still lacking. Herein, we identify approximately a hundred high-confidence splicing events altered by ADAR1 and/or ADAR2, and ADAR1 or ADAR2 protein can regulate cassette exons in both directions. We unravel a binding tendency of ADARs to dsRNAs that involves GA-rich sequences for editing and splicing regulation. ADAR1 edits an intronic splicing silencer, leading to recruitment of SRSF7 and repression of exon inclusion. We also present a mechanism through which ADAR2 binds to dsRNA formed between GA-rich sequences and polypyrimidine (Py)-tract and precludes access of U2AF65 to 3′ splice site. Furthermore, we find these ADARs-regulated splicing changes per se influence tumorigenesis, not merely byproducts of ADARs editing and binding.

Highlights

RNA editing and splicing are the two major processes that dynamically regulate human transcriptome diversity
We modulated expression of ADAR1/2 in an esophageal squamous carcinoma (ESCC) cell line EC109 that has been used for RNA editing studies previously[33,34], using lentivirus-mediated silencing and overexpression (Fig. 1a), followed by transcriptomewide RNA-Seq analysis of editing sites and alternative splicing events
As previously appreciated, modification of canonical cis-acting elements by RNA editing is unlikely to be a widespread mechanism of editing-regulated splicing changes[27]; instead, RNA editing enzymes ADARs and splicing machineries may contribute to their crosstalk through acting on the same double-stranded RNA (dsRNA) regions[20,50]

Summary

Introduction

RNA editing and splicing are the two major processes that dynamically regulate human transcriptome diversity. We present a mechanism through which ADAR2 binds to dsRNA formed between GA-rich sequences and polypyrimidine (Py)-tract and precludes access of U2AF65 to 3′ splice site We find these ADARs-regulated splicing changes per se influence tumorigenesis, not merely byproducts of ADARs editing and binding. Since very few canonical cis-acting elements (5′ splice site (5′ss), 3′ss, and BPS) are affected by editing[27], we believe that ADAR proteins may regulate splicing through other mechanisms beyond their editing functions[20]. Albeit both ADAR1 and 2 edit many sites, there is very little information about the role of ADAR2 in splicing regulation. CCDC15 (coiled-coil domain containing 15) exon 9 (CCDC15-ex9) and RELL2 (receptor expressed in lymphoid tissues-like 2) exon 3 (RELL2-ex3) are chosen as exemplary targets to decipher the interplay between editing enzymes and splicing machineries, and their biological importance in cancer

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