Translation of CircRNAs

Abstract

Circular RNAs (circRNAs) are abundant and evolutionarily conserved RNAs of largely unknown function. Here, we show that a subset of circRNAs is translated in vivo. By performing ribosome footprinting from fly heads, we demonstrate that a group of circRNAs is associated with translating ribosomes. Many of these ribo-circRNAs use the start codon of the hosting mRNA, are bound by membrane-associated ribosomes, and have evolutionarily conserved termination codons. In addition, we found that a circRNA generated from the muscleblind locus encodes a protein, which we detected in fly head extracts by mass spectrometry. Next, by performing in vivo and in vitro translation assays, we show that UTRs of ribo-circRNAs (cUTRs) allow cap-independent translation. Moreover, we found that starvation and FOXO likely regulate the translation of a circMbl isoform. Altogether, our study provides strong evidence for translation of circRNAs, revealing the existence of an unexplored layer of gene activity.

Keywords: cap-independent; circRNA; muscleblind; translation.

Graphical abstract

Figure 1

A Subset of CircRNAs Is Associated with Translating Ribosomes (A) Approach used to detect circRNA reads in RFP data. (B) Datasets utilized and ribo-circRNAs detected. (C) circRNA expression was plotted against their ranking in these datasets. Red dots indicate ribo-circRNAs. (D and E) Integrated genome browser (IGV) snapshots of small and large RFP datasets for tai (D) and ct (E) show that more RFP reads are in the circularized exons, mainly in the lighter polysomes (red). See Table S1.

Figure 2

CircRNAs Can Produce Proteins as Tagged Minigenes (A) Ribo-circRNA tagging strategy. MT, metallothionein promoter. (B) circMbl V5, Pde8 V5, and Cdi V5 minigenes produce proteins of their expected size (red arrows). GFP was co-transfected. (C) circMbl minigenes produce both circMbl and linear concatemers when transfected into Drosophila S2 cells. Left: EtBr staining. Right: northern blot using a probe directed against the circMbl backsplice junction. (D) Top: scheme of the minigene expressing a split Cherry molecule under the control of the circMbl cUTR. Bottom: representative picture of Drosophila S2 cells transfected with this minigene. (E) Western blot from Drosophila S2 cells transfected with the specified circMbl V5 minigenes. (F) Northern blot using a probe directed against the circMbl backsplice junction. Samples were prepared from heads of control (actin-gal4/+) or circMbl overexpression (OE) flies (actin-gal4; UAS-circMbl). Left: EtBr staining. Right: northern blot. The asterisk indicates an unknown RNA species that is detected by the probe, and it is resistant to RNaseR. (G) RT-PCR analysis of control and circMbl OE flies. Gene expression was normalized to rp49 and 28S RNAs. Mean ± SD (n = 2 for control and n = 3 for circMbl samples). (H) Western blot of control or circMbl OE flies utilizing the anti-MBL or anti-tubulin antibodies. See Figures S1 and S2.

Figure 3

Genome-wide Analysis of Translation in Fly Heads by RFP (A) Meta-analysis of the RFP reads. (B) “Pile ups” of the RFP reads at two different resolutions in the Arr2 locus. (C) Meta-analysis of the RFP reads in the proximity of the start and stop codons of all annotated genes. The total frequency of RFP read 5′ end positions plotted against the relative distance (in nucleotides) to the start/stop codon (left). The same information, but subdivided into reads of different length, is shown, with frequency represented by color (middle). Relative enrichment of RFP reads around real start/stop codons over the background frequency for reads of such length in the vicinity of start/stop codons, expressed as log ratio of these frequencies (right). Positive scores (red) indicate consistency with the signature of start/stop codons, and negative scores (blue) consistency with the uniform background distribution. (D) Main over-represented GO terms for the mRNAs significantly higher in the normal detergent library. (E) Venn diagrams displaying the number of circRNAs found in the different libraries (number of backspliced reads). The detergent libraries were sequenced 3.4 times deeper. (F) The x axis presents the number of backspliced reads, and the y axis presents the number of linear reads from the downstream junction of the circ-hosting gene. The asterisks (^∗) indicate the position of the three circRNAs with higher number of RFP reads. We also indicated the number of RFP reads within the parentheses. (G) Stop codon RFP pattern observed around the putative stop codon of circMbl. Top: considering genome-aligned as well as backspliced reads, the pattern is not consistent with a stop codon because of superimposed reads from mbl mRNA. Bottom: when extracting only backspliced reads, the RFP pattern is consistent with a stop codon at the inferred position in the circRNA. See Figure S3 and Table S2.

Figure 4

A Subset of CircRNAs Is Associated with Translating Ribosomes (A) Results of the translating ribosome affinity purification (TRAP) assay. Ribo-GFP strains: Actin-Gal4; UAS-EGFPL10a. Control strain: UAS-EGFPL10a. The number indicates the difference in the normalized ratio between the Ribo-GFP and control strains. n = 4. (B). RNaseR validation of the ribosome-bound circRNAs. RNA from the input and IP TRAP samples was subjected to RNaseR treatment. Mouse RNA was added and quantified as spike-in for the normalization. The RNaseR resistance was assessed and normalized to the one observed in the input sample. n = 3. (C) RNaseR validation of the ribosome-bound RNAs. Normalization was performed using the internal spike-in. n = 3. (D) RNA expression in the mbl locus. Red track represents the expression of the different exons in fly heads. Hemi-circles indicate the most abundant circRNAs. Top inset: comparison of the expression levels in the mock and RNase-treated samples corroborates the high expression of circMbl3 and circMbl4. Right boxes indicate the size of the proteins produced by the annotated mbl mRNAs or circRNAs. (E) Top: schematics of the circMbl3-encoded protein and the peptides generated by proteolysis. (F) Northern blot assay showing the presence of circMbl3 in fly heads of yw and CS flies. In both strains this circRNA is resistant to RNaseR. Blotting was done using probes for the relevant circRNA junction. In (A)–(C), error bars indicate SEM. See also Figure S4.

Figure 5

Features of Fly Ribo-CircRNAs (A) Ribo-circRNAs are strongly enriched for 5′ UTR and CDS overlap (p < 0.0055, Fisher’s exact test). (B) Percentage of control, utc-circRNAs, and ribo-circRNAs ORFs, which share their putative start codon with their hosting linear mRNA. The differences between ribo-circRNAs and control or utc-circRNAs are statistically significant (p < 2 × 10⁻⁹ and p < 0.05, respectively, Fisher’s exact test). (C) Percentage of control, cORFs, and ribo-circRNAs that contain cUTR. The differences between ribo-circRNAs and control or utc-circRNAs are significant (p < 0.002 and p < 0.05, respectively, Fisher’s exact test). (D) Average length of cUTR for control groups as well as for ribo-circRNAs (p < 0.019, double-sided Mann-Whitney U test). (E) Excerpt of a multiple species alignment of circMbl. First codon position is in uppercase, and other codon positions are in lowercase. STP, stop codon. Arrows indicate the beginning (green) and end (red) of the exon. (F) Ratio between the linear and circular forms of the second exon of mbl in different Drosophila species. n = 2. (G) Boxplot showing the distribution of stop codon conservation scores for circRNAs composed of CDS and 5′ UTR exonic sequences. Negative controls are randomly selected stop codons inside the same 5′ UTR stretches. CDS denotes annotated stop codons from mRNAs sharing the circRNA exons. Red lines indicate the median, and blue dots indicate the mean. Boxes show interquartile range. Whiskers show 5th to 95th percentile range. Significantly different medians are indicated by asterisks: ^∗∗∗∗p < 0.0001, two-sided Mann-Whitney U test. ^∗p < 0.05; ^∗∗p < 0.01; ^∗∗∗p < 0.001; ^∗∗∗∗p < 0.0001. See also Figures S5 and S6 and Tables S3, S4, S5, and S6.

Figure 6

Characterization of CircRNAs Putative IRESs (A) Proteins expressed by the circMbl and circCdi minigenes are resistant to the activity of 4E-BP. (B) Quantification of the fluorescent signal from cells transfected with the Cherry minigene and GFP in the presence or absence of 4E-BP, detected by high-throughput microscopy. n = 3. In each experiment more than 3,000 cells were measured. (C) Relative firefly luciferase levels of the indicated bicistronic reporters. To normalize between experiments, we divided the luciferase reads to the ones obtained with the HCV IRES construct. n = 6. Error bars represent SEM. (D) Drosophila S2 cells were transfected with a bicistronic IRES reporter and with or without a plasmid expressing 4E-BP. The results show the ratio between the firefly/Renilla coefficients in presence or absence of 4E-BP. Error bars indicate SEM. n = 6. (E) Expression of the G-capped RLuc reporter bearing mbl 5′ UTR (m⁷Gppp-circMbl-RLuc) was compared with the analogous A-capped reporter (Appp-circMbl-RLuc) and bicistronic reporter (m⁷Gppp-FLuc-circMbl-RLuc) in a cell-free Drosophila translation system. RLuc activity was normalized to FLuc activity; expression of m⁷Gppp-circMbl-RLuc was taken for 100%, and the rest was expressed accordingly. (F) Linear reporter containing the A-capped CrPV IRES (CrPV-RL) was used as a positive control, and circular reporters with mbl 5′ UTR in a reverse orientation (circMblRevcUTR-RLuc) or deleted mbl 5′ UTR (circMblcUTR-RLuc) were used as negative controls in a cell-free Drosophila translation system. Each reaction was assembled in the presence or absence of m⁷GpppG. See Figure S7.

Figure 7

MBL Isoforms Are Expressed in Different Cellular Fractions, and Their Levels Are Modulated by Starvation and FOXO (A) Wild-type (CS) fly heads were subjected to centrifugation-based biochemical fractionation and western blot using antibodies against MBL and Brunchpilot (BRP). The fraction P2 contains synaptosomes, and the fraction LP1 contains the pre- and post-synaptic membranes. (B) RT-PCR analysis examining circular, linear, and precursor transcript levels in the synaptosomal fractions. The mbl (2–3) and mbl (1–2) primer pairs are used to quantify different mbl mRNA isoforms. The y axis indicates the ratio between the signal in the synaptosomal (P2) and predominantly nuclear (P1) fractions. Data were normalized to spike-in and to the volume of the fraction. Mean ± SD. n = 2. (C) Western blot analysis of Drosophila S2 cells stably transfected with copper-induced Foxo. Cells were harvested at the indicated time after copper induction. (D) Adult flies were starved (or not) for 12 hr, harvested, and their head extracts were subjected to western blot analysis. The arrow indicates the position of the putative circMbl-1-encoded protein. (E) RT-PCR analysis examining circular and mbl mRNA levels in response to starvation. Mean ± SD (n = 2). Data were normalized to rp49 and 28S rRNA. Actin-gal4 flies were used for the experiment. (F) Western blot analysis showing the MBL 10 kDa isoform expression upon induction of FOXO expression (elav-GS; UAS-Foxo fly line). The experiment was performed by triplicate. See Table S7.