Circular RNAs in immune responses and immune diseases

Abstract

Circular RNAs (circRNAs) are novel clusters of endogenous noncoding RNAs (ncRNAs) that are widely expressed in eukaryotic cells. In contrast to the generation of linear RNA transcripts, circRNAs undergo a "back-splicing" process to form a continuous, covalently closed, stable loop structure without 5' or 3' polarities and poly (A) tails during posttranscriptional modification. Due to the widespread availability of several technologies, especially high-throughput RNA sequencing, numerous circRNAs have been discovered not only in mammals but also in plants and insects. Notably, due to their abilities to serve as microRNA (miRNA) "sponges", miRNA "reservoirs", regulate gene expression and encode proteins, circRNAs participate in the development and progression of different immune responses and immune diseases by enriching various forms of epigenetic modification. CircRNAs have been demonstrated to be expressed in a tissue-specific and pathogenesis-related manner during the occurrence of multiple immune diseases. Additionally, because of their circular configurations, expression in blood and peripheral tissues and coexistence with exosomes, circRNAs show inherent conservation along with environmental resistance stability and may be regarded as potential biomarkers or therapeutic targets for some immune diseases. In this review, we summarize the characteristics, functions and mechanisms of circRNAs and their involvement in immune responses and diseases. Although our knowledge of circRNAs remains preliminary, this field is worthy of deeper exploration and greater research efforts.

Keywords: biogenesis; circRNAs; function; immune diseases; immune responses.

Figure 1

Biogenesis models of circular RNAs (circRNAs). Due to the emergence of differentially located breakpoints, primary RNA transcripts undergo “back-splicing” to produce the 5ʹ splicing donor site and 3ʹ splicing acceptor site. Subsequently, the 5ʹ splicing donor site is combined with the 3ʹ splicing acceptor site in reverse order to form a covalently closed loop without 5ʹ or 3ʹ polarities and poly (A) tails. (A) Exonic circRNAs (ecircRNAs) are composed exclusively of exons without flanking introns. The number of exons ranges from one to two or more depending on the breakpoints. Over 80% of circRNAs arise from ecircRNAs. (B) Exons (at least one) accompanied by flanking introns that have not been degraded during “back-splicing” compose exon-intron circRNAs (eiciRNAs). (C) Intron-derived circRNAs (ciRNAs) are produced through a lariat-derived mechanism depending on a consensus GU-rich domain near the 5ʹ splicing site and a C-rich domain near the breakpoint. The remaining noncircularized introns are sequestered. (D) tRNA intronic circRNAs (tricRNAs) originate from the exons and introns of pre-tRNAs cleaved by the tRNA splicing endonuclease complex. Abbreviations: ciRNA: circular intronic RNA; ecircRNA: exonic circRNA; eiciRNA: exon-intron circRNA; tricRNA: tRNA intronic circular RNA.

Figure 2

CircRNAs perform a series of biological functions. (A) Since primary RNA transcripts are generated by transcription, these immature products undergo “back-splicing”, which competitively suppresses linear splicing, producing circRNAs, including eiciRNAs, ciRNAs and ecircRNAs, at the cost of losing their linear equivalents. EiciRNAs and ciRNAs can conversely activate their parental genes by forming transcription complexes and binding the 300-nt region upstream of the transcription start site (TSS). Both eiciRNA and ciRNA transcription complexes require RNA polymerase II, but U1 snRNAs are also needed to complete the eiciRNA transcription complex. Notably, eiciRNAs and ciRNAs are primarily located in the nucleus, whereas ecircRNAs dominantly translocate to the cytoplasm to perform other tasks. (B) EcircRNAs contain a certain number of miRNA response elements (MREs) that create fundamental structures to interact with target miRNAs as specific miRNA “sponges”, which significantly interrupt the expression and behaviors of downstream miRNAs. In contrast, by using MREs, ecircRNAs can also store miRNAs to stabilize their expression and release under certain conditions, serving as miRNA “reservoirs”. Additionally, ecircRNAs harbor some internal ribosome entry sites (IRESs) to launch the cap-independent translation, open reading frames (ORFs) and start codons to initiate the “protein coding” in polymerases. Various translation initiation factors, such as N⁶-methyladenosine (m6A), eukaryotic initiation factor 3 (eIF3), eIF4G2, YTH N6-methyladenosine RNA binding protein 3 (YTHDF3) and methyltransferase like 14 (METTL14), are involved in this process. Moreover, many ecircRNAs can combine with RNA binding proteins (RBPs) via complimentary sequences, blocking the binding between RBPs and mRNAs/miRNAs as protein “sponges” and cooperatively regulating the procedures of translation. In conclusion, circRNAs broadly participate as critical links in intracellular events and form an intricate regulatory network. Abbreviations: ciRNA: circular intronic RNA; ecircRNA: exonic circRNA; eiciRNA: exon-intron circRNA; IRES: internal ribosome entry site; miRNA: microRNA; MRE: miRNA response element; ORF: open reading frame; RBP: RNA binding protein; snRNA: small nuclear RNA.