Circular versus linear RNA topology: different modes of RNA–RNA interactions in vitro and in human cells

Abstract

Circular RNA is progressively reported to occur in various species including mammals where it is thought to be involved in the post-transcriptional regulation of gene expression, partly via interactions with microRNA. Here, we asked whether the circular topology causes functional differences to linear forms when interacting with short RNA strands in vitro and in human cells. Kinetic studies with human bladder cancer-derived synthetic circular RNA versus linear transcripts, respectively, with short oligoribonucleotides showed similar association rates for both topologies. Conversely, a substantial topology-related difference was measured for the activation entropy and the activation enthalpy of RNA–RNA annealing. This finding strongly indicates a significant difference of the mechanism of RNA–RNA interactions. To investigate whether these characteristics of circular RNA are biologically meaningful we performed transient transfection experiments with a microRNA-regulated expression system for luciferase in bladder cancer-derived cells. We co-transfected linear or circular RNA containing one microRNA binding site for the target-suppressing microRNA mlet7a. Here, the circular isoform showed a strongly increased competition with microRNA function versus linear versions. In summary, this study suggests novel topology-related characteristics of RNA–RNA interactions involving circRNA in vitro and in living cells.

CircRNA-0100 positively regulates the differentiation of cashmere goat SHF-SCs into hair follicle lineage via sequestering miR-153-3p to heighten the KLF5 expression

“…CircRNA-producing host genes tend to be longer than average with more exons; moreover, reverse-splicing acceptor exons are highly enriched at the ordinal position 2 of the host genes (Ragan et al, 2019). CircRNAs were progressively identified in various species, and they are thought to be deeply implicated in the gene expression through post-transcriptional regulation (Petkovic et al, 2021). Increasing lines of evidence indicate that many cir-cRNAs play important biological roles by serving as miRNA "sponges" to regulate protein function or by being translated into polypeptides with a physiological function (Hansen et al, 2013;Guo et al, 2014;Kristensen et al, 2019).…”

Influence of RNA circularity on Target RNA-Directed MicroRNA Degradation

“…The extra rigidity of circRNAs could preclude the conformational change of AGO, thus bypassing TDMD while remaining bound to the RISC complex. A recent report might be consistent with this view by showing differences between the thermodynamic properties of linear and circular RNA in binding to complementary short RNAs, favouring a model where circRNAs might bind to miRNAs more efficiently than their cognate linear RNAs (Petkovic et al, 2021). An alternative explanation could relate to the differential ability of distinct RNA species in recruiting TDMD machinery factors such as ZSWIM8.…”