Circles reshaping the RNA world: from waste to treasure

Abstract

A new type of RNAs was identified from genes traditionally thought to express messenger or linear ncRNA (noncoding RNA) only. They were subsequently named as circRNAs (circular RNAs) due to the covalently closed structure. Accumulating studies were performed to explore the expression profile of circRNAs in different cell types and diseases, the outcomes totally changed our view of ncRNAs, which was thought to be junk by-products in the process of gene transcription, and enriched our poor understanding of its underlying functions. The expression profile of circRNAs is tissue-specific and alters across various stages of cell differentiation. The biological function of circRNAs is multi-faceted, involving five main features (sponge effect, post-transcriptional regulation, rolling circle translation, circRNA-derived pseudogenes and splicing interference) and varying differently from the locations, binding sites and acting modes of circRNAs. The regulating role of circRNAs is not isolated but through an enormous complicated network involving mRNAs, miRNAs and proteins. Although most of the potential functions still remain unclear, circRNAs have been proved to be ubiquitous and critical in regulating cellular processes and diseases, especially in cancers, from the laboratory to the clinic. Herein, we review circRNAs' classification, biogenesis and metabolism, their well-studied and anticipated functions, the current understanding of the potential implications of circRNAs in tumorigenesis and cancer targeted therapy.

Keywords: Biomarker; Cancer; Circular RNA; Post-transcription regulation; miRNA.

Fig. 1

Three paths of circRNAs formation. Legend: There are four commonly acknowledged paths in the formation of circRNAs. a Spliceosome-Dependent Circulation Path: the processing of the back-splicing reaction requires the sequential assembly of snRNPs on the pre-mRNA to catalyse circulation. b Intron-Pairing-Driven Circularization Path: circRNA are formed depend on an intronic reverse complementary motif containing a GU-rich element and a C-rich element in two sides to promote circularization. c Lariat-Driven Circularization Path: formation of circRNA is promoted by a lariat structure; the ALU complementary flanking elements repeated in intronic regions compete with canonical linear-RNA splicing and accelerate the circularization by reverse complementary matches. d Protein Factors Associated Circulation Path: some RBPs can bind to specific targets in introns and bring the donor-acceptor sequences in proximity to each other thus trigger several circularization processes. At the mean time, RBPs also stabilize the splicing motifs and inhibit canonical linear splicing

Fig. 2

Composition of three types circRNAs. Legend: CircRNAs are generated in the process of the skip splicing of pre-mRNA and compete with the linear transcription, they are generally classified into three types focusing on their components. (1) EcircRNAs comprise exons and are the most common circRNAs. (2) CiRNAs are composed by two or more connected introns and are detected rare in eukaryocyte. (3) EIciRNAs are circularized with introns ‘retained’ between the exons and play a part in gene regulation

Fig. 3

The new five subsets classification of circRNAs. Legend: CircRNAs can be divided into five groups according to their location relationship with coding RNA. “exonic” and “intronic” represent circRNA composed by exons and intros respectively, “antisense” represents circRNA whose gene locus overlap with the linear RNA, but transcribed from the opposite strand; “sense overlapping” represents circRNA transcribed from same gene locus as the linear transcript, but not classified into “exonic” and “intronic”; “intergenic” represents circRNA located outside known gene locus

Fig. 4

Five main functions of circRNA. Legend: CircRNAs possess five main functions which have been validated in some related researches. 1. MiRNA sponge: circRNAs serve as the platform to bind miRNAs and affect their biological function, regulating the activity of miRNA-target gene. 2. Post-transcription regulation: the stable ciRNA and EIciRNA locate in nucleus, binding to elongating RNA Pol II and promoting transcription. 3. Rolling Circle Translation: some circRNAs can translate into proteins via a rolling circle amplification mechanism, while only the vitro circRNA till date has been verified to encode proteins in eukaryotic cells. 4. Generating the circRNA-derived pseudogenes: some circRNAs may be reversely transcribed to cDNA and integrated into the genome based on an unknown way. 5. Affects alternative splicing: circRNA biogenesis can compete with pre-mRNA splicing, resulting in lower levels of linear mRNAs and changing the composition of processed mRNA by excluding specific exons from the pre-mRNA