Role of circular RNAs in brain development and CNS diseases

Abstract

In mammals, many classes of noncoding RNAs (ncRNAs) are expressed at a much higher level in the brain than in other organs. Recent studies have identified a new class of ncRNAs called circular RNAs (circRNAs), which are produced by back-splicing and fusion of either exons, introns, or both exon-intron into covalently closed loops. The circRNAs are also highly enriched in the brain and increase continuously from the embryonic to the adult stage. Although the functional significance and mechanism of action of circRNAs are still being actively explored, they are thought to regulate the transcription of their host genes and sequestration of miRNAs and RNA binding proteins. Some circRNAs are also shown to have translation potential to form peptides. The expression and abundance of circRNAs seem to be spatiotemporally maintained in a normal brain. Altered expression of circRNAs is also thought to mediate several disorders, including brain-tumor growth, and acute and chronic neurodegenerative disorders by affecting mechanisms such as angiogenesis, neuronal plasticity, autophagy, apoptosis, and inflammation. This review discusses the involvement of various circRNAs in brain development and CNS diseases. A better understanding of the circRNA function will help to develop novel therapeutic strategies to treat CNS complications.

Keywords: Acute and chronic neurodegeneration; Brain; Cancer; CircRNAs; Development; miRNAs.

Fig. 1.. Biogenesis of circRNAs.

CircRNAs are formed from either exons, introns or both exon-intron by back-splicing events and spliceosomal machinery. On the contrary, canonical splicing forms a mature mRNA after removal of introns. Various processes that form circRNAs are conventional back-splicing driven, intron-pairing-driven circularization, and lariat-driven circularization. The downstream donor and upstream acceptor sites are brought into close proximity during circularization by exon-containing lariats, direct base pairing between cis-acting regulatory elements containing reverse complementary sequences (Alu repeats) and flanking introns, trans-acting factors, such as RNA-binding proteins (RBPs, QKI, MBL) and intron lariats that escape the usual intron debranching and degradation.

Fig. 2.. Methods to detect circRNAs.

Coupled with the bioinformatics algorithms, deep sequencing and longer reads of RNAs digested with RNase R and poly(A) depleted RNAs increases the specificity of circRNAs detection (A). PCR analysis with convergent and divergent primers in RNase R-treated RNA preparations can be used to detect circRNAs (B). Droplet digital PCR quantifies absolute circRNA levels based on the single droplet molecules (C). Northern blotting can accurately detect and confirm an exact circRNA in a gel using probes that are designed to target both the circular and the linear transcript or only the circRNA with backsplice junction probe (D). Finally, RNA fluorescence in situ hybridization (RNA-FISH) coupled with high-resolution microscopy using probes flanking the junction sites can determine the distribution and abundance of circRNAs (E).

Fig. 3.. Functions of circRNAs.

CircRNas plays diverse roles by regulating transcription (circEIF3J and circPAIP2) of their host genes, sponging miRNAs (CDR1as, SRY and HIPK3) and thereby derepressing miRNA-target mRNA translation, sponging RNA binding proteins (RBPs) such as CDK2 and P21, and some circRNAs also show translation potential (circMbl and circ-ZNF609) to form peptides.

Fig. 4.. Mechanisms regulated by circRNAs during brain development and disease conditions.

CircRNAs are not just abundant, but they continually increase from embryonic to adult stage in the brain to regulates functions related to neuronal plasticity. Additionally, their altered levels are engaged in brain diseases, and degeneration by various mechanisms, including angiogenesis, autophagy, apoptosis, tumorigenesis, and inflammation.