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

RNA Biol. 2021 Nov 12;18(sup2):674-683. doi: 10.1080/15476286.2021.1978214. Epub 2021 Nov 28.


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.

Keywords: Circular RNA; RNA kinetics; RNA structure; RNA thermodynamics; RNA-RNA annealing; living cells; microRNA; mlet7a.

MeSH terms

  • Base Pairing
  • Epistasis, Genetic
  • Gene Expression Regulation
  • Humans
  • Kinetics
  • MicroRNAs / chemistry
  • MicroRNAs / genetics
  • Nucleic Acid Conformation*
  • RNA / chemistry*
  • RNA / genetics
  • RNA Folding*
  • RNA, Circular / chemistry*
  • RNA, Circular / genetics
  • Structure-Activity Relationship
  • Thermodynamics


  • MicroRNAs
  • RNA, Circular
  • RNA