Emerging roles and context of circular RNAs

Abstract

Circular RNAs (circRNAs) represent a large class of noncoding RNAs (ncRNAs) that have recently emerged as regulators of gene expression. They have been shown to suppress microRNAs, thereby increasing the translation and stability of the targets of such microRNAs. In this review, we discuss the emerging functions of circRNAs, including RNA transcription, splicing, turnover, and translation. We also discuss other possible facets of circRNAs that can influence their function depending on the cell context, such as circRNA abundance, subcellular localization, interacting partners (RNA, DNA, and proteins), dynamic changes in interactions following stimulation, and potential circRNA translation. The ensuing changes in gene expression patterns elicited by circRNAs are proposed to drive key cellular processes, such as cell proliferation, differentiation, and survival, that govern health and disease. WIREs RNA 2017, 8:e1386. doi: 10.1002/wrna.1386 For further resources related to this article, please visit the WIREs website.

Figure 1. Schematic representation of splicing events leading to the generation of circRNA

(A) The canonical splicing machinery conventionally generates normal mRNA. (B) Exonic circular RNA (circRNA) is generated through noncanonical splicing (backsplicing) through the unique ‘head-to tail’ joining of the 5′ spice site (5’ss, donor site) to an 3′ splice site (3’ss, acceptor site). RNA-binding proteins (RBP) or trans-acting factors can bridge two flanking introns close together. The introns are then are removed to form a circRNA. (C) Reverse complementary sequences (purple arrows) in Intron1 and Intron3 can pair and bring the 5’ss of Exon3 close to 3’ss of Exon2, promote circularization of Exon2 and Exon3 with a retained intron, and form an Exon-Intron circRNA (EIciRNA). In addition, backsplicing in combination of canonical splicing may lead to the formation of circRNA with Exon2 and Exon3 only. (D) The circular intronic RNA (ciRNA) is derived from the lariat intron excised from pre-mRNA by canonical splicing machinery and depends on the presence of consensus RNA sequences (yellow bars) to avoid debranching of the lariat intron to form stable ciRNAs. The red and blue dotted lines indicate linear and head-to-tail backsplicing, respectively.

Figure 2. Emerging activities, proposed functions, and dynamic interactions of circRNAs

(From top clockwise) CircRNAs may influence transcription factor (TF) function by influencing TF localization and/or activity. CircRNAs may also may also associate with traditional RNA-binding proteins (RBPs) or multi-RBP complexes and influence the fate of the circRNAs themselves (e.g., localization, stability), impact upon the mRNAs that the RBPs interact with (e.g., mRNA stability or translation), or perhaps serve as a platform for the assembly of multi-protein complexes. Partial interaction of circRNAs with mRNAs can similarly lead to altered mRNA turnover and/or translation. CircRNAs may also interact with single-stranded (as in the schematic) or double-stranded DNA forming double or triple helices, respectively, with potential impact on DNA metabolism (e.g., transcription, replication). The interaction of circRNAs with linear lncRNAs could directly affect lncRNA functions (e.g., localization, folding, etc.) or impact upon the target molecules (e.g., RNAs or proteins) with which the lncRNA associates. The ability to sequester or ‘sponge’ microRNAs is another recognized function of circRNAs. As several circRNAs comprise exonic 5′UTR segments that bear internal ribosome entry sites (IRESs), circRNAs may also serve as templates for translation synthesis. Finally, circRNA interaction with splicing factors may affect splicing of pre-mRNAs. Shaded text boxes, additional considerations critical for the study of circRNAs, including the aforementioned interactions with DNA in the nucleus and with the translation machinery via IRESs in the cytosol. CircRNA levels change as a function of development, in disease states, and in response to stress, immune, hormonal or other stimuli (left). CircRNA interactions with RNA, protein, and DNA may change depending on the cell context, and these interactions may be competitive, cooperative, sequential, etc. The localization of circRNA intracellularly and possibly even outside should be examined, as it impacts directly on its function.