Beyond Back Splicing, a Still Poorly Explored World: Non-Canonical Circular RNAs

Abstract

Most of the circRNAs reported to date originate from back splicing of a pre-mRNA, and these exonic circRNAs are termed canonical circRNAs. Our objective was to provide an overview of all other (non-canonical) circRNAs that do not originate from the junction of two exons and to characterize their common properties. Those generated through a failure of intron lariat debranching are the best known, even though studies on them are rare. These circRNAs retain the 2′–5′ bond derived from the intron lariat, and this feature probably explains the difficulties in obtaining efficient reverse transcription through the circular junction. Here, we provide an unprecedented overview of non-canonical circRNAs (lariat-derived intronic circRNAs, sub-exonic circRNAs, intron circles, tricRNAs), which all derive from non-coding sequences. As there are few data suggesting their involvement in cellular regulatory processes, we believe that it is early to propose a general function for circRNAs, even for lariat-derived circRNAs. We suggest that their small size and probably strong secondary structures could be major obstacles to their reliable detection. Nevertheless, we believe there are still several possible ways to advance our knowledge of this class of non-coding RNA.

Comparative Analysis of the Circular Transcriptome in Muscle, Liver, and Testis in Three Livestock Species

“…CE2 was also able to detect the six intronic circRNAs from the DNAH17 previously reported ( Robic et al, 2019 ) but again with a lower number of CCRs than expected. These observations confirmed that CE2 is able to detect intronic circRNAs ( Das et al, 2020 ), but as suggested previously ( Robic and Kühn, 2020 ), the strong requests on the two paired-end reads as included in the CE2 algorithm could impair the characterization of intronic circRNAs. The dataset ssc_testis_1 had also been used to describe the first sub-exonic circRNAs ( Robic et al, 2020 ).…”

“…So far, intronic circRNAs have been identified only from coding genes (reviewed by Robic and Kühn, 2020 ), but the current study shows that lncRNAs can also be involved in the production of intronic circRNAs. In pigs, this study highlighted that the lncRNAs ENSSSCG00000048463 and ENSSSCG00000041596 generated intronic circRNAs, however at a low expression level, with 6 and 11 associated CCRs, respectively.…”

“…Those annotated as “ciRNA” correspond to circRNAs localized entirely in intronic sequences and with the circRNA 5′ junction site corresponding to the intron donor site. Although the term “ciRNA” is the one proposed for intronic circular RNA by Zhang et al (2013) , the location of the 3′ junction of these circRNAs must be analyzed before to consider them as intronic circRNA ( Robic and Kühn, 2020 ).…”

“…(ii) sub-exonic, when both junctions fall strictly within a single exon. (iii) intronic, when both junctions fall within a single intron, the 5′ junction corresponding to the intron donor site and the 3′ junction located not further than 60 bp away from the intron acceptor site ( Robic and Kühn, 2020 ). CircRNA from ribosomal RNA genes were excluded from the list of sub-exonic circRNAs.…”

“…Exonic circRNAs can be produced by coding or non-coding genes ( Salzman et al, 2012 ; Barrett et al, 2017 ; Robic et al, 2020 ) and by some snRNA genes ( Kaur et al, 2018 ; Robic et al, 2020 ). Two types of circRNAs can be derived from intronic sequences (see Robic and Kühn (2020) for a review): (1) when intron lariats escape degradation due to the failure of intron debranching ( Zhang et al, 2013 ), they may become circRNA precursors of lariat-derived circRNAs and (2) for very rare introns we can observe the circularization of the entire intronic sequences as intron circle ( Taggart et al, 2017 ). These two types of intron derived circRNAs can be grouped as “intronic circRNAs.” Sub-exonic circRNAs have been characterized as including only a part of the exon of some mono-exonic genes ( Robic et al, 2020 ).…”