Thrown for a (stem) loop: How RNA structure impacts circular RNA regulation and function

• Published in: Methods (San Diego, Calif.) Vol. 196; pp. 56 - 67
• Main Authors: Busa, Veronica F., Leung, Anthony K.L.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.12.2021
• Subjects: Base Sequence; Circular RNA; Exons; RNA - genetics; RNA - metabolism; RNA secondary structure; RNA Splicing - genetics; RNA, Circular - genetics; circRNA; SRD; RNA secondary structure; RPAD; ASOs; siRNAs; SHAPE-MaP; TSEN; tricRNAs; AAV; LDN; Circular RNA; m6A; Tornado; shRNAs; EJC
• ISSN: 1046-2023; 1095-9130
• DOI: 10.1016/j.ymeth.2021.02.019

•circRNA secondary structure affects its regulation and function.•circRNA and cognate linear transcripts adopt different structures.•Identification and measurement methods may bias against structured circRNAs.•Generated circRNAs may not recapitulate endogenous secondary structures. Exonic circular RNAs (circRNAs) are RNA molecules that are covalently closed by back-splicing via canonical splicing machinery. Despite overlapping sequences, exon circularization generates RNA secondary structures through intramolecular base-pairing that are different from the linear transcript. Here we review factors that may affect circRNA structure and how structure affects circRNA function and regulation. We highlight considerations for RNA sequencing and expression measurement to ensure highly structured circRNAs are accurately represented by the data and discuss issues that need to be addressed in generating circRNAs to recapitulate their endogenous structures. We conclude our review by discussing experimental strategies on revealing the varied roles of RNA structure in circRNA biogenesis, function and decay.