ADARs act as potent regulators of circular transcriptome in cancer

Abstract

Circular RNAs (circRNAs) are produced by head-to-tail back-splicing which is mainly facilitated by base-pairing of reverse complementary matches (RCMs) in circRNA flanking introns. Adenosine deaminases acting on RNA (ADARs) are known to bind double-stranded RNAs for adenosine to inosine (A-to-I) RNA editing. Here we characterize ADARs as potent regulators of circular transcriptome by identifying over a thousand of circRNAs regulated by ADARs in a bidirectional manner through and beyond their editing function. We find that editing can stabilize or destabilize secondary structures formed between RCMs via correcting A:C mismatches to I(G)-C pairs or creating I(G).U wobble pairs, respectively. We provide experimental evidence that editing also favors the binding of RNA-binding proteins such as PTBP1 to regulate back-splicing. These ADARs-regulated circRNAs which are ubiquitously expressed in multiple types of cancers, demonstrate high functional relevance to cancer. Our findings support a hitherto unappreciated bidirectional regulation of circular transcriptome by ADARs and highlight the complexity of cross-talk in RNA processing and its contributions to tumorigenesis.

ADAR1-Mediated RNA Editing and Its Role in Cancer

“…Currently, dysregulated levels of non-coding RNAs (ncRNAs) appear to be reported for every type of cancer, and non-coding transcripts are expected to be the next class of diagnostic and therapeutic tools in oncology ( Song et al, 2016 ; Shen et al, 2022 ). In addition to RNA editing mediated amino acid substitutions in specific genes contributing to cancer, elevated ADAR1 editing of non-coding RNAs, can also promote cancer progression ( Qi et al, 2014 ; Ramírez-Moya et al, 2020 ).…”

“…In addition, ADAR1 has been described to repress circRNA production intensely, and its A-I editing process usually occurs near reverse complementary matches (RCMs) in circRNA flanking introns, A structure essential for circRNA cyclization ( Shi et al, 2017 ; Ma et al, 2020 ). Through this editing, secondary structures between RCMs could be stronger or weaker respectively depending on whether correcting A:C was mismatched to I(G)-C pairs or I(G) U pairs ( Shen et al, 2022 ).…”

“…ADAR1 can edit reverse complementary matches (RCM) of ADAR1-regulated circRNAs, altering the secondary structure formed between RCMs within the flanking introns and enhancing the binding of RNA-binding proteins (RBPs) to the site of action ( Kristensen et al, 2019 ; Shen et al, 2022 ). And the different expression of ADAR1 leads to editing dysregulation of A-to-I RNA editome in multiple cancers, such as HCC, ESCC, CRC, and GC ( Qin et al, 2014 ; Han et al, 2020 ; Song et al, 2021 ).…”

“…Mammals have three ADAR genes, ADAR1 (also called ADAR, DRADA), ADAR2 (also called ADARB1), and ADAR3 (also called ADARB2), with specific structure, location, and function differences ( Xu and Öhman, 2018 ; Shen et al, 2022 ). Currently, ADAR1 and ADAR2 have been shown to be expressed throughout most tissues and to be catalytically active, and the former mediates more editing events ( Hogg et al, 2011 ).…”

Analyses of circRNA expression throughout circadian rhythm reveal a strong link between Cdr1as and light-induced phase shifts in the SCN

“…As of now, it is clear that many RNA species, both protein-coding and non-coding, play an essential role in the maintenance of the circadian rhythm [Menet et al ., 2012; Pembroke et al ., 2015; Zhou et al ., 2021; Kadener et al ., 2009]. However, circRNAs, an alternative form of RNA splicing products, dependent on temperature and RNA-editing [Ivanov et al ., 2015; Ashwal-Fluss et al ., 2014; Rybak-Wolf et al ., 2015; Shen et al ., 2022], have not been well studied throughout daily activities and circadian rhythm.…”