Circular RNAs in Cancer - Lessons Learned From microRNAs

Abstract

Circular RNAs (circRNA) are RNA molecules built from fragments of linear pre-messenger RNAs and other linear RNA species through a process termed "back-splicing" in which the 3' and 5' ends are joined together giving rise to a covalently uninterrupted loop. circRNAs are not new members of the RNA world; they were first discovered in the early 1990s. The novelty is their abundance in the mammalian cells, as recently thousands of circRNAs were discovered and annotated. The biogenesis of circRNAs is a partially characterized process, regulated by three different mechanisms: exon skipping, intron pairing, and RNA-binding proteins. On the other hand, the function of circRNAs remains largely unknown and only a handful of singular reports describe in detail the biological roles of some circular transcripts. In a very short period of time, numerous circRNAs were associated with various cancer types and were also identified in bodily fluids with the potential of being disease-specific biomarkers. In this review, we briefly describe the biogenesis and function of circRNAs and present the circular transcripts that were more than once reported in literature to be associated with cancer. Finally, we point out some of the difficulties encountered in the study of circRNAs in cancer, as we consider that taking these into account could accelerate and improve our understanding of the biologic and translational use of circRNAs in human diseases.

Keywords: biomarker; cancer; circular RNA; microRNA; non-coding RNA.

Figure 1

From the same linear pre-mRNA, multiple types of circular RNA (circRNAs) can be generated via back-splicing, a form of alternative splicing. CircRNAs can be composed by one or more exons and some circular transcripts are containing also intronic segments. As a generalization: circRNAs contain two or three exons, exceeding the average length, and the flanking introns are likewise longer. The relationship between the expression level of a mature messenger RNA (mRNA) and circRNA originating from the same pre-mRNA is not always correlated and is not predictable.

Figure 2

The biogenesis of circular RNAs (circRNAs) is summarized by the term “back-splicing.” Until now, three different mechanisms that promote this process were described. The first mechanism is characterized by exon skipping and intron lariat formation. In order to bring distant exons together (jumping exons), the introns build a circular lariat. The lariat formation makes the circularization of the “skipped” exons possible. This process leads to the formation of three different types of RNA molecules: circRNA, intron lariat, and mRNA with skipping exons. In the second mechanism, the circularization of the exon/exons is promoted by the complementary pairing of the flanking introns. A common hallmark of the introns that are prone to pair is the inverted ALU repeats. The third mechanism is controlled by RNA-binding proteins, which bind the neighboring introns of the future circular exon and dimerize, creating an RNA loop. The most studied proteins able to induce circularization are Quaking (QKI) and Muscleblind (MBL).

Figure 3

Data about the function of circular RNAs (circRNAs) is limited; until now, only four roles of circRNAs were studied in detail, and the observations regarding the function cannot be generalized to all circular transcripts. (A) The most studied function of circRNAs is microRNA (miRNA) sponging. By sequestering miRNA molecules that downregulate mRNAs, circRNAs indirectly increase the expression of mRNAs. Initially proposed as potent miRNA sponges which are able to bind to dozens of short RNAs, circRNAs are considered now to have the same number of interaction sites with miRNAs as other molecules. (B) Recently, two papers reported that circRNAs can associate with ribosomes and be translated into short proteins, long enough to contain a functional domain. (C) Similar to miRNA sponging, circRNAs also bind to proteins. The exact function of this interaction is not clear and numerous speculations exist: circRNA are a transport vehicle for proteins; circRNAs are sequestering proteins; circRNAs are a platform for protein interactions; or circRNAs bind to proteins and induce allosteric changes, regulating their function. (D) Finally, simply the formation of circRNAs can be perceived as a function of circular transcripts. It was reported that synthesis of a circRNA from a pre-mRNA competes with the formation of a linear, functional mRNA. Therefore, circRNA formation is another form of post-translational regulation.