The expanding regulatory mechanisms and cellular functions of circular RNAs

Last updated: 05-06-2020

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The expanding regulatory mechanisms and cellular functions of circular RNAs

nature reviews molecular cell biology
RNA splicing
Abstract
Many protein-coding genes in higher eukaryotes can produce circular RNAs (circRNAs) through back-splicing of exons. CircRNAs differ from mRNAs in their production, structure and turnover and thereby have unique cellular functions and potential biomedical applications. In this Review, I discuss recent progress in our understanding of the biogenesis of circRNAs and the regulation of their abundance and of their biological functions, including in transcription and splicing, sequestering or scaffolding of macromolecules to interfere with microRNA activities or signalling pathways, and serving as templates for translation. I further discuss the emerging roles of circRNAs in regulating immune responses and cell proliferation, and the possibilities of applying circRNA technologies in biomedical research.
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Fig. 1: Back-splicing and alternative (back-) splicing in the formation of circular RNAs.
Fig. 2: Regulation of back-splicing efficiency.
Fig. 3: Nuclear export and degradation of circular RNAs.
Fig. 4: Molecular mechanisms of circular RNA function.
Fig. 5: Cellular and physiological roles of circular RNAs.
References
1.
Google Scholar
2.
Nilsen, T. W. & Graveley, B. R. Expansion of the eukaryotic proteome by alternative splicing. Nature 463, 457–463 (2010).
Google Scholar
5.
Li, X., Yang, L. & Chen, L. L. The biogenesis, functions, and challenges of circular RNAs. Mol. Cell 71, 428–442 (2018).
Google Scholar
6.
Sanger, H. L., Klotz, G., Riesner, D., Gross, H. J. & Kleinschmidt, A. K. Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures. Proc. Natl Acad. Sci. USA 73, 3852–3856 (1976).
Google Scholar
7.
Capel, B. et al. Circular transcripts of the testis-determining gene Sry in adult mouse testis. Cell 73, 1019–1030 (1993).
Google Scholar
8.
Cocquerelle, C., Daubersies, P., Majerus, M. A., Kerckaert, J. P. & Bailleul, B. Splicing with inverted order of exons occurs proximal to large introns. EMBO J. 11, 1095–1098 (1992).
Google Scholar
9.
Cocquerelle, C., Mascrez, B., Hetuin, D. & Bailleul, B. Mis-splicing yields circular RNA molecules. FASEB J. 7, 155–160 (1993).
Google Scholar
11.
Pasman, Z., Been, M. D. & Garcia-Blanco, M. A. Exon circularization in mammalian nuclear extracts. RNA 2, 603–610 (1996).
Google Scholar
12.
Yang, L., Duff, M. O., Graveley, B. R., Carmichael, G. G. & Chen, L. L. Genomewide characterization of non-polyadenylated RNAs. Genome Biol. 12, R16 (2011).
Google Scholar
13.
Salzman, J., Gawad, C., Wang, P. L., Lacayo, N. & Brown, P. O. Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS One 7, e30733 (2012). This study suggests that circRNA production can be a general feature of gene expression in human cells.
Google Scholar
14.
Jeck, W. R. et al. Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA 19, 141–157 (2013). This study uncovers circRNAs as a large class of RNA molecules in human cells.
Google Scholar
15.
Ivanov, A. et al. Analysis of intron sequences reveals hallmarks of circular RNA biogenesis in animals. Cell Rep. 10, 170–177 (2015).
Google Scholar
16.
Shen, Y., Guo, X. & Wang, W. Identification and characterization of circular RNAs in zebrafish. FEBS Lett. 591, 213–220 (2017).
Google Scholar
17.
Westholm, J. O. et al. Genome-wide analysis of Drosophila circular RNAs reveals their structural and sequence properties and age-dependent neural accumulation. Cell Rep. 9, 1966–1980 (2014).
Google Scholar
18.
Guo, J. U., Agarwal, V., Guo, H. & Bartel, D. P. Expanded identification and characterization of mammalian circular RNAs. Genome Biol. 15, 409 (2014).
Google Scholar
19.
Memczak, S. et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495, 333–338 (2013). This study reports that circRNAs are a large class of RNA molecules with functional potential.
Google Scholar
20.
Fan, X. et al. Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos. Genome Biol. 16, 148 (2015).
Google Scholar
21.
Dong, R., Ma, X. K., Chen, L. L. & Yang, L. Increased complexity of circRNA expression during species evolution. RNA Biol. 14, 1064–1074 (2017).
Google Scholar
22.
Zhang, X. O. et al. Complementary sequence-mediated exon circularization. Cell 159, 134–147 (2014). This study reports that exon circularization often requires flanking ICSs and also uncovers alternative circularization.
Google Scholar
23.
Veno, M. T. et al. Spatio-temporal regulation of circular RNA expression during porcine embryonic brain development. Genome Biol. 16, 245 (2015).
Google Scholar
24.
Barrett, S. P., Wang, P. L. & Salzman, J. Circular RNA biogenesis can proceed through an exon-containing lariat precursor. eLife 4, e07540 (2015).
Google Scholar
25.
Broadbent, K. M. et al. Strand-specific RNA sequencing in Plasmodium falciparum malaria identifies developmentally regulated long non-coding RNA and circular RNA. BMC Genomics 16, 454 (2015).
Google Scholar
27.
Wang, P. L. et al. Circular RNA is expressed across the eukaryotic tree of life. PLoS One 9, e90859 (2014).
Google Scholar
28.
Dong, R., Ma, X. K., Li, G. W. & Yang, L. CIRCpedia v2: an updated database for comprehensive circular RNA annotation and expression comparison. Genomics Proteomics Bioinformatics 16, 226–233 (2018).
Google Scholar
29.
Zheng, Y., Ji, P., Chen, S., Hou, L. & Zhao, F. Reconstruction of full-length circular RNAs enables isoform-level quantification. Genome Med. 11, 2 (2019).
Google Scholar
30.
Ji, P. et al. Expanded expression landscape and prioritization of circular RNAs in mammals. Cell Rep. 26, 3444–3460 (2019).
Google Scholar
31.
Rybak-Wolf, A. et al. Circular RNAs in the mammalian brain are highly abundant, conserved, and dynamically expressed. Mol. Cell 58, 870–885 (2015). This study reports enrichment of circRNA expression in brains and provides an atlas of circRNA expression in mammalian brains.
Google Scholar
32.
You, X. et al. Neural circular RNAs are derived from synaptic genes and regulated by development and plasticity. Nat. Neurosci. 18, 603–610 (2015). This study shows enrichment of circRNA expression in brains and suggests circRNAs have a potential to regulate synaptic function.
Google Scholar
33.
Preusser, C. et al. Selective release of circRNAs in platelet-derived extracellular vesicles. J. Extracell. Vesicles 7, 1424473 (2018).
Google Scholar
34.
Conn, S. J. et al. The RNA binding protein quaking regulates formation of circRNAs. Cell 160, 1125–1134 (2015).
Google Scholar
35.
Nicolet, B. P. et al. Circular RNA expression in human hematopoietic cells is widespread and cell-type specific. Nucleic Acids Res. 46, 8168–8180 (2018).
Google Scholar
36.
Salzman, J., Chen, R. E., Olsen, M. N., Wang, P. L. & Brown, P. O. Cell-type specific features of circular RNA expression. PLoS Genet. 9, e1003777 (2013).
Google Scholar
37.
Zhang, X. O. et al. Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Res. 26, 1277–1287 (2016). This study defines the diversity of alternative back-splicing and alternative splicing in circRNAs.
Google Scholar
38.
Errichelli, L. et al. FUS affects circular RNA expression in murine embryonic stem cell-derived motor neurons. Nat. Commun. 8, 14741 (2017).
Google Scholar
39.
Xia, P. et al. A circular RNA protects dormant hematopoietic stem cells from DNA sensor cGAS-mediated exhaustion. Immunity 48, 688–701 (2018). This study generates a circRNA-knockout mouse model that can exhibit phenotypes related to hematopoietic stem cell homeostasis.
Google Scholar
40.
Li, Q. et al. CircACC1 regulates assembly and activation of AMPK complex under metabolic stress. Cell Metab. 30, 157–173 e157 (2019).
Google Scholar
41.
Moore, M. J. & Proudfoot, N. J. Pre-mRNA processing reaches back to transcription and ahead to translation. Cell 136, 688–700 (2009).
Google Scholar
42.
Vo, J. N. et al. The landscape of circular RNA in cancer. Cell 176, 869–881 e813 (2019).
Google Scholar
46.
Li, X. et al. A unified mechanism for intron and exon definition and back-splicing. Nature 573, 375–380 (2019). This study provides cryo-electron microscopy structures of the yeast spliceosomal E complex and demonstrates back-splicing is catalysed by the spliceosome.
Google Scholar
48.
Liang, D. & Wilusz, J. E. Short intronic repeat sequences facilitate circular RNA production. Genes Dev. 28, 2233–2247 (2014).
Google Scholar
49.
Liang, D. et al. The output of protein-coding genes shifts to circular RNAs when the pre-mRNA processing machinery is limiting. Mol. Cell 68, 940–954 e943 (2017). This study suggests differential use of spliceosome components between back-splicing and canonical splicing.
Google Scholar
50.
Zaphiropoulos, P. G. Circular RNAs from transcripts of the rat cytochrome P450 2C24 gene: correlation with exon skipping. Proc. Natl Acad. Sci. USA 93, 6536–6541 (1996).
Google Scholar
51.
Kelly, S., Greenman, C., Cook, P. R. & Papantonis, A. Exon skipping is correlated with exon circularization. J. Mol. Biol. 427, 2414–2417 (2015).
53.
Jeck, W. R. & Sharpless, N. E. Detecting and characterizing circular RNAs. Nat. Biotechnol. 32, 453–461 (2014).
Google Scholar
54.
Gao, Y. et al. Comprehensive identification of internal structure and alternative splicing events in circular RNAs. Nat. Commun. 7, 12060 (2016).
Google Scholar
55.
Ottesen, E. W., Luo, D., Seo, J., Singh, N. N. & Singh, R. N. Human survival motor neuron genes generate a vast repertoire of circular RNAs. Nucleic Acids Res. 47, 2884–2905 (2019).
Google Scholar
56.
Braunschweig, U., Gueroussov, S., Plocik, A. M., Graveley, B. R. & Blencowe, B. J. Dynamic integration of splicing within gene regulatory pathways. Cell 152, 1252–1269 (2013).
Google Scholar
57.
Fong, N. et al. Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate. Genes Dev. 28, 2663–2676 (2014).
Google Scholar
58.
Dubin, R. A., Kazmi, M. A. & Ostrer, H. Inverted repeats are necessary for circularization of the mouse testis Sry transcript. Gene 167, 245–248 (1995).
Google Scholar
59.
Kramer, M. C. et al. Combinatorial control of Drosophila circular RNA expression by intronic repeats, hnRNPs, and SR proteins. Genes Dev. 29, 2168–2182 (2015).
Google Scholar
60.
Guarnerio, J. et al. Oncogenic role of fusion-circRNAs derived from cancer-associated chromosomal translocations. Cell 165, 289–302 (2016).
Google Scholar
61.
Wang, M., Hou, J., Muller-McNicoll, M., Chen, W. & Schuman, E. M. Long and repeat-rich intronic sequences favor circular RNA formation under conditions of reduced spliceosome activity. iScience 20, 237–247 (2019).
Google Scholar
62.
Khan, M. A. et al. RBM20 regulates circular RNA production from the titin gene. Circ. Res. 119, 996–1003 (2016).
Google Scholar
63.
Fei, T. et al. Genome-wide CRISPR screen identifies HNRNPL as a prostate cancer dependency regulating RNA splicing. Proc. Natl Acad. Sci. USA 114, E5207–E5215 (2017).
Google Scholar
64.
Patino, C., Haenni, A. L. & Urcuqui-Inchima, S. NF90 isoforms, a new family of cellular proteins involved in viral replication? Biochimie 108, 20–24 (2015).
Google Scholar
65.
Li, X. et al. Coordinated circRNA biogenesis and function with NF90/NF110 in viral infection. Mol. Cell 67, 214–227 (2017).
Google Scholar
66.
Aktas, T. et al. DHX9 suppresses RNA processing defects originating from the Alu invasion of the human genome. Nature 544, 115–119 (2017).
Google Scholar
67.
Braunschweig, U. et al. Widespread intron retention in mammals functionally tunes transcriptomes. Genome Res. 24, 1774–1786 (2014).
Google Scholar
68.
Li, Z. et al. Exon-intron circular RNAs regulate transcription in the nucleus. Nat. Struct. Mol. Biol. 22, 256–264 (2015).
Google Scholar
69.
Conn, V. M. et al. A circRNA from SEPALLATA3 regulates splicing of its cognate mRNA through R-loop formation. Nat. Plants 3, 17053 (2017).
Google Scholar
70.
Huang, C., Liang, D., Tatomer, D. C. & Wilusz, J. E. A length-dependent evolutionarily conserved pathway controls nuclear export of circular RNAs. Genes Dev. 32, 639–644 (2018). This study reveals that circRNA nuclear export occurs in a length-dependent manner.
Google Scholar
71.
Gatfield, D. et al. The DExH/D box protein HEL/UAP56 is essential for mRNA nuclear export in Drosophila. Curr. Biol. 11, 1716–1721 (2001).
Google Scholar
72.
Liu, C. X. et al. Structure and degradation of circular RNAs regulate PKR activation in innate immunity. Cell 177, 865–880 e821 (2019). This study shows that circRNAs can form unique structures and regulate PKR activity, and reports that circRNA misregulation is related to an autoimmune disease.
Google Scholar
73.
Zhou, C. et al. Genome-wide maps of m6A circRNAs identify widespread and cell-type-specific methylation patterns that are distinct from mRNAs. Cell Rep. 20, 2262–2276 (2017).
74.
Roundtree, I. A. et al. YTHDC1 mediates nuclear export of N6-methyladenosine methylated mRNAs. Elife 6, e31311 (2017).
Google Scholar
75.
Enuka, Y. et al. Circular RNAs are long-lived and display only minimal early alterations in response to a growth factor. Nucleic Acids Res. 44, 1370–1383 (2016).
Google Scholar
76.
Hansen, T. B. et al. miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA. EMBO J. 30, 4414–4422 (2011).
Google Scholar
77.
Kleaveland, B., Shi, C. Y., Stefano, J. & Bartel, D. P. A network of noncoding regulatory RNAs acts in the mammalian brain. Cell 174, 350–362 (2018).
Google Scholar
78.
Hansen, T. B. et al. Natural RNA circles function as efficient microRNA sponges. Nature 495, 384–388 (2013). This study functionally characterizes naturally expressed circRNAs by their acting as miRNA sponges.
Google Scholar
79.
Piwecka, M. et al. Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function. Science 357, eaam8526 (2017). This study generates a circRNA-knockout mouse model that can exhibit neuronal phenotypes.
Google Scholar
80.
Han, Y. et al. Structure of human RNase L reveals the basis for regulated RNA decay in the IFN response. Science 343, 1244–1248 (2014).
Google Scholar
81.
Park, O. H. et al. Endoribonucleolytic cleavage of m6A-containing RNAs by RNase P/MRP complex. Mol. Cell 74, 494–507 (2019).
Google Scholar
83.
Fischer, J. W., Busa, V. F., Shao, Y. & Leung, A. K. L. Structure-mediated RNA decay by UPF1 and G3BP1. Mol. Cell 78, 70–84 (2020).
Google Scholar
84.
Kim, Y. K. & Maquat, L. E. UPFront and center in RNA decay: UPF1 in nonsense-mediated mRNA decay and beyond. RNA 25, 407–422 (2019).
Google Scholar
86.
Guarnerio, J. et al. Intragenic antagonistic roles of protein and circRNA in tumorigenesis. Cell Res. 29, 628–640 (2019).
Google Scholar
87.
Liu, Y. et al. Back-spliced RNA from retrotransposon binds to centromere and regulates centromeric chromatin loops in maize. PLoS Biol. 18, e3000582 (2020).
Google Scholar
88.
Salmena, L., Poliseno, L., Tay, Y., Kats, L. & Pandolfi, P. P. A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell 146, 353–358 (2011).
Google Scholar
89.
Poliseno, L. et al. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 465, 1033–1038 (2010).
Google Scholar
90.
Bosson, A. D., Zamudio, J. R. & Sharp, P. A. Endogenous miRNA and target concentrations determine susceptibility to potential ceRNA competition. Mol. Cell 56, 347–359 (2014).
Google Scholar
91.
Denzler, R., Agarwal, V., Stefano, J., Bartel, D. P. & Stoffel, M. Assessing the ceRNA hypothesis with quantitative measurements of miRNA and target abundance. Mol. Cell 54, 766–776 (2014).
Google Scholar
92.
Huang, R. et al. Circular RNA HIPK2 regulates astrocyte activation via cooperation of autophagy and ER stress by targeting MIR124–2HG. Autophagy 13, 1722–1741 (2017).
Google Scholar
93.
Zheng, Q. et al. Circular RNA profiling reveals an abundant circHIPK3 that regulates cell growth by sponging multiple miRNAs. Nat. Commun. 7, 11215 (2016).
Google Scholar
94.
Stoll, L. et al. Circular RNAs as novel regulators of beta-cell functions in normal and disease conditions. Mol. Metab. 9, 69–83 (2018).
Google Scholar
95.
Kristensen, L. S., Okholm, T. L. H., Veno, M. T. & Kjems, J. Circular RNAs are abundantly expressed and upregulated during human epidermal stem cell differentiation. RNA Biol. 15, 280–291 (2018).
Google Scholar
96.
Yu, C. Y. et al. The circular RNA circBIRC6 participates in the molecular circuitry controlling human pluripotency. Nat. Commun. 8, 1149 (2017).
Google Scholar
97.
Li, Q. et al. Circular RNA MAT2B promotes glycolysis and malignancy of hepatocellular carcinoma through the miR-338-3p/PKM2 Axis under hypoxic stress. Hepatology 70, 1298–1316 (2019).
Google Scholar
98.
Hu, Z. Q. et al. Circular RNA sequencing identifies CircASAP1 as a key regulator in hepatocellular carcinoma metastasis. Hepatology https://doi.org/10.1002/hep.31068 (2019).
Google Scholar
99.
Li, Y. et al. Circular RNA is enriched and stable in exosomes: a promising biomarker for cancer diagnosis. Cell Res. 25, 981–984 (2015).
Google Scholar
100.
Du, W. W. et al. Foxo3 circular RNA retards cell cycle progression via forming ternary complexes with p21 and CDK2. Nucleic Acids Res. 44, 2846–2858 (2016).
Google Scholar
101.
Du, W. W. et al. Foxo3 circular RNA promotes cardiac senescence by modulating multiple factors associated with stress and senescence responses. Eur. Heart J. 38, 1402–1412 (2017).
Google Scholar
102.
Zeng, Y. et al. A circular RNA binds to and activates AKT phosphorylation and nuclear localization reducing apoptosis and enhancing cardiac repair. Theranostics 7, 3842–3855 (2017).
Google Scholar
103.
Huang, S. et al. Loss of super-enhancer-regulated circRNA Nfix induces cardiac regeneration after myocardial infarction in adult mice. Circulation 139, 2857–2876 (2019).
Google Scholar
104.
Burd, C. E. et al. Expression of linear and novel circular forms of an INK4/ARF-associated non-coding RNA correlates with atherosclerosis risk. PLoS Genet. 6, e1001233 (2010).
Google Scholar
105.
Holdt, L. M. et al. Circular non-coding RNA ANRIL modulates ribosomal RNA maturation and atherosclerosis in humans. Nat. Commun. 7, 12429 (2016).
Google Scholar
106.
Abdelmohsen, K. et al. Identification of HuR target circular RNAs uncovers suppression of PABPN1 translation by CircPABPN1. RNA Biol. 14, 361–369 (2017).
Google Scholar
107.
Grammatikakis, I., Abdelmohsen, K. & Gorospe, M. Posttranslational control of HuR function. Wiley Interdiscip. Rev. RNA 8, e1372 (2017).
Google Scholar
108.
Hein, M. Y. et al. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell 163, 712–723 (2015).
Google Scholar
109.
Armakola, M. et al. Inhibition of RNA lariat debranching enzyme suppresses TDP-43 toxicity in ALS disease models. Nat. Genet. 44, 1302–1309 (2012).
Google Scholar
110.
Zhang, S. Y. et al. Inborn errors of RNA lariat metabolism in humans with brainstem viral infection. Cell 172, 952–965 (2018).
Google Scholar
111.
Harashima, A., Guettouche, T. & Barber, G. N. Phosphorylation of the NFAR proteins by the dsRNA-dependent protein kinase PKR constitutes a novel mechanism of translational regulation and cellular defense. Genes Dev. 24, 2640–2653 (2010).
Google Scholar
112.
Isken, O. et al. Members of the NF90/NFAR protein group are involved in the life cycle of a positive-strand RNA virus. EMBO J. 22, 5655–5665 (2003).
Google Scholar
113.
Smola, M. J., Rice, G. M., Busan, S., Siegfried, N. A. & Weeks, K. M. Selective 2’-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis. Nat. Protoc. 10, 1643–1669 (2015).
Google Scholar
114.
Moldovan, L. I. et al. High-throughput RNA sequencing from paired lesional- and non-lesional skin reveals major alterations in the psoriasis circRNAome. BMC Med. Genomics 12, 174 (2019).
Google Scholar
115.
Zhu, P. et al. IL-13 secreted by ILC2s promotes the self-renewal of intestinal stem cells through circular RNA circPan3. Nat. Immunol. 20, 183–194 (2019).
Google Scholar
116.
Chen, Y. G. et al. Sensing self and foreign circular RNAs by intron identity. Mol. Cell 67, 228–238 e225 (2017).
Google Scholar
117.
Wesselhoeft, R. A. et al. RNA circularization diminishes immunogenicity and can extend translation duration in vivo. Mol. Cell 74, 508–520 e504 (2019).
118.
Chen, Y. G. et al. N6-methyladenosine modification controls circular RNA immunity. Mol. Cell 76, 96–109 (2019).
Google Scholar
119.
Toptan, T. et al. Circular DNA tumor viruses make circular RNAs. Proc. Natl Acad. Sci. USA 115, E8737–E8745 (2018).
Google Scholar
121.
Tagawa, T. et al. Discovery of Kaposi’s sarcoma herpesvirus-encoded circular RNAs and a human antiviral circular RNA. Proc. Natl Acad. Sci. USA 115, 12805–12810 (2018).
Google Scholar
123.
Zhao, J. et al. Transforming activity of an oncoprotein-encoding circular RNA from human papillomavirus. Nat. Commun. 10, 2300 (2019).
Google Scholar
124.
Chen, S. et al. Widespread and functional RNA circularization in localized prostate cancer. Cell 176, 831–843 (2019).
Google Scholar
125.
Bachmayr-Heyda, A. et al. Correlation of circular RNA abundance with proliferation — exemplified with colorectal and ovarian cancer, idiopathic lung fibrosis, and normal human tissues. Sci. Rep. 5, 8057 (2015).
Google Scholar
126.
Panda, A. C. et al. Identification of senescence-associated circular RNAs (SAC-RNAs) reveals senescence suppressor CircPVT1. Nucleic Acids Res. 45, 4021–4035 (2017).
Google Scholar
127.
Yu, J. et al. Circular RNA cSMARCA5 inhibits growth and metastasis in hepatocellular carcinoma. J. Hepatol. 68, 1214–1227 (2018).
Google Scholar
128.
Yang, W., Du, W. W., Li, X., Yee, A. J. & Yang, B. B. Foxo3 activity promoted by non-coding effects of circular RNA and Foxo3 pseudogene in the inhibition of tumor growth and angiogenesis. Oncogene 35, 3919–3931 (2016).
Google Scholar
130.
Dube, U. et al. An atlas of cortical circular RNA expression in Alzheimer disease brains demonstrates clinical and pathological associations. Nat. Neurosci. 22, 1903–1912 (2019).
Google Scholar
131.
Chen, Y. J. et al. Genome-wide, integrative analysis of circular RNA dysregulation and the corresponding circular RNA-microRNA-mRNA regulatory axes in autism. Genome Res. 30, 375–391 (2020).
Google Scholar
132.
Litke, J. L. & Jaffrey, S. R. Highly efficient expression of circular RNA aptamers in cells using autocatalytic transcripts. Nat. Biotechnol. 37, 667–675 (2019).
Google Scholar
133.
Jost, I. et al. Functional sequestration of microRNA-122 from hepatitis C virus by circular RNA sponges. RNA Biol. 15, 1032–1039 (2018).
Google Scholar
134.
Memczak, S., Papavasileiou, P., Peters, O. & Rajewsky, N. Identification and characterization of circular RNAs as a new class of putative biomarkers in human blood. PLoS One 10, e0141214 (2015).
Google Scholar
135.
Li, H. et al. Comprehensive circular RNA profiles in plasma reveals that circular RNAs can be used as novel biomarkers for systemic lupus erythematosus. Clin. Chim. Acta 480, 17–25 (2018).
Google Scholar
136.
Bahn, J. H. et al. The landscape of microRNA, Piwi-interacting RNA, and circular RNA in human saliva. Clin. Chem. 61, 221–230 (2015).
Google Scholar
137.
Rees, H. A. & Liu, D. R. Base editing: precision chemistry on the genome and transcriptome of living cells. Nat. Rev. Genet. 19, 770–788 (2018).
Google Scholar
139.
Konermann, S. et al. Transcriptome engineering with RNA-targeting type VI-D CRISPR effectors. Cell 173, 665–676 e614 (2018).
Google Scholar
140.
Yang, L. Z. et al. Dynamic imaging of RNA in living cells by CRISPR-Cas13 systems. Mol. Cell 76, 981–997 e987 (2019).
Google Scholar
141.
Zhang, Y., Yang, L. & Chen, L. L. Characterization of circular RNAs. Methods Mol. Biol. 1402, 215–227 (2016).
Google Scholar
142.
Xiao, M. S. & Wilusz, J. E. An improved method for circular RNA purification using RNase R that efficiently removes linear RNAs containing G-quadruplexes or structured 3’ ends. Nucleic Acids Res. 47, 8755–8769 (2019).
Google Scholar
143.
Ma, X. K. et al. CIRCexplorer3: a CLEAR pipeline for direct comparison of circular and linear RNA expression. Genomics Proteomics Bioinformatics 17, 511–521 (2019).
Google Scholar
144.
Jakobi, T., Uvarovskii, A. & Dieterich, C. Circtools-a one-stop software solution for circular RNA research. Bioinformatics 35, 2326–2328 (2019).
Google Scholar
145.
Chuang, T. J. et al. Integrative transcriptome sequencing reveals extensive alternative trans-splicing and cis-backsplicing in human cells. Nucleic Acids Res. 46, 3671–3691 (2018).
Google Scholar
146.
Dahl, M. et al. Enzyme-free digital counting of endogenous circular RNA molecules in B-cell malignancies. Lab. Invest. 98, 1657–1669 (2018).
Google Scholar
147.
Li, T. et al. Plasma circular RNA profiling of patients with gastric cancer and their droplet digital RT-PCR detection. J. Mol. Med. 96, 85–96 (2018).
Google Scholar
148.
Legnini, I. et al. Circ-ZNF609 is a circular RNA that can be translated and functions in myogenesis. Mol Cell 66, 22–37 e29 (2017).
Google Scholar
150.
Yang, Y. et al. Extensive translation of circular RNAs driven by N6-methyladenosine. Cell Res. 27, 626–641 (2017).
Google Scholar
151.
Schneider, T. et al. CircRNA-protein complexes: IMP3 protein component defines subfamily of circRNPs. Sci. Rep. 6, 31313 (2016).
Google Scholar
152.
Wang, K. et al. A circular RNA protects the heart from pathological hypertrophy and heart failure by targeting miR-223. Eur. Heart J. 37, 2602–2611 (2016).
Google Scholar
153.
Chen, C. Y. & Sarnow, P. Initiation of protein synthesis by the eukaryotic translational apparatus on circular RNAs. Science 268, 415–417 (1995).
Google Scholar
154.
Wesselhoeft, R. A., Kowalski, P. S. & Anderson, D. G. Engineering circular RNA for potent and stable translation in eukaryotic cells. Nat. Commun. 9, 2629 (2018).
155.
van Heesch, S. et al. The translational landscape of the human heart. Cell 178, 242–260 (2019).
156.
Fan, X. et al. Pervasive translation of circular RNAs driven by short IRES-like elements. bioRxiv https://doi.org/10.1101/473207 (2019).
Google Scholar
157.
Tang, C. et al. m6A-dependent biogenesis of circular RNAs in male germ cells. Cell Res. 30, 211–228 (2020).
Google Scholar
158.
Mankan, A. K. et al. Cytosolic RNA:DNA hybrids activate the cGAS-STING axis. EMBO J. 33, 2937–2946 (2014).
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Acknowledgements
The author apologizes to colleagues whose work is not discussed here owing to space limitations. The author thanks L. Yang, C.-X. Liu, X. Li and S.-K. Guo for discussions. This work was supported by grants from the Chinese Academy of Sciences (XDB19020104), the National Natural Science Foundation of China (91940303, 31725009, 31821004, 31861143025) and the HHMI International Research Scholar Program (55008728).
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Affiliations
State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
Ling-Ling Chen
School of Life Science and Technology, ShanghaiTech University, Shanghai, China
Ling-Ling Chen
The author declares no competing interests.
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Nature Reviews Molecular Cell Biology thanks Albrecht Bindereif, Howard Chang and Jeremy Wilusz for their contribution to the peer review of this work.
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Supplementary Box 1
Glossary
RNase R
A 3′-to-5′ exonuclease that preferentially digests linear RNAs, thereby allowing the enrichment of circular RNAs.
Internal ribosome entry site
(IRES). A structural RNA element that makes possible the initiation of cap-independent translation.
Spliceosomal E complex
Formation of this complex initiates the splicing cycle and is crucial for the accurate definition of introns and exons by the splicing machinery.
Cassette exons
Exons present in one RNA transcript but absent in an isoform of the transcript.
Alu elements
Primate-specific retrotransposons that constitute almost 11% of the human genome.
Exon definition complexes
Protein complexes that initially recognize splice sites and direct prespliceosome assembly on exons. They further interact across long introns to form the catalytic spliceosome.
A-to-I editing
In higher eukaryotes, the predominant form of RNA modification, in which adenosine is modified to inosine within imperfect double-stranded RNAs.
Nonsense-mediated mRNA decay
A mechanism of selective degradation of mRNAs; a means of post-transcriptional gene regulation in mammals.
R-loops
Triple-stranded nucleic acid structures that form during transcription; they consist of a DNA–RNA hybrid and the single-stranded non-template DNA.
Group I introns


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