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Circular RNAs are abundant, conserved, and associated with ALU repeats
Open accessAbstract
Circular RNAs composed of exonic sequence have been described in a small number of genes. Thought to result from splicing errors, circular RNA species possess no known function. To delineate the universe of endogenous circular RNAs, we performed high-throughput sequencing (RNA-seq) of libraries prepared from ribosome-depleted RNA with or without digestion with the RNA exonuclease, RNase R. We identified >25,000 distinct RNA species in human fibroblasts that contained non-colinear exons (a "backsplice") and were reproducibly enriched by exonuclease degradation of linear RNA. These RNAs were validated as circular RNA (ecircRNA), rather than linear RNA, and were more stable than associated linear mRNAs in vivo. In some cases, the abundance of circular molecules exceeded that of associated linear mRNA by >10-fold. By conservative estimate, we identified ecircRNAs from 14.4% of actively transcribed genes in human fibroblasts. Application of this method to murine testis RNA identified 69 ecircRNAs in precisely orthologous locations to human circular RNAs. Of note, paralogous kinases HIPK2 and HIPK3 produce abundant ecircRNA from their second exon in both humans and mice. Though HIPK3 circular RNAs contain an AUG translation start, it and other ecircRNAs were not bound to ribosomes. Circular RNAs could be degraded by siRNAs and, therefore, may act as competing endogenous RNAs. Bioinformatic analysis revealed shared features of circularized exons, including long bordering introns that contained complementary ALU repeats. These data show that ecircRNAs are abundant, stable, conserved and nonrandom products of RNA splicing that could be involved in control of gene expression.
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“Two different models of circRNA formation have been proposed: an exon-skipping process known as “Lariat-Driven Circularization” and a nonsequential donor-acceptor pairing process called “Intron-Pairing-Driven Circularization” or “direct back splicing” [28].”
From Circular RNAs in depression: Biogenesis, function, expression, and therapeutic potential (2021) · cites this paper as [28]
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RETRACTED ARTICLE: CircHIPK3 promotes colorectal cancer growth and metastasis by sponging miR-7
Zeng, K., Chen, X., Xu, M., Liu, X., Hu, X., Xu, T., Sun, H., Pan, Y., He, B., & Wang, S. (2018) · Cell Death and Disease · doi:10.1038/s41419-018-0454-8 · Cited by 626
RetractedSzabo, L. A., Morey, R. E., Palpant, N. J., Wang, P., Afari, N., Chuan, J., Parast, M. M., Murry, C. E., Laurent, L. C., & Salzman, J. (2015) · Genome biology · doi:10.1186/s13059-015-0690-5 · Cited by 610
DHX9 suppresses RNA processing defects originating from the Alu invasion of the human genome
Aktaş, T., Ilik, İ., Maticzka, D., Bhardwaj, V., Rodrigues, C. P., Mittler, G., Manke, T., Backofen, R., & Akhtar, A. (2017) · Nature · doi:10.1038/nature21715 · Cited by 601
Circular RNAs: Identification, biogenesis and function
Ebbesen, K. K., Kjems, J., & Hansen, T. B. (2015) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2015.07.007 · Cited by 563
CircHIPK3 sponges miR‐558 to suppress heparanase expression in bladder cancer cells
Li, Y., Zheng, F., Xiao, X., Xie, F., Tao, D., Huang, C., Liu, D., Wang, M., Wang, L., Zeng, F., et al. (2017) · EMBO Reports · doi:10.15252/embr.201643581 · Cited by 562
Targeting circular RNAs as a therapeutic approach: current strategies and challenges
He, A. T., Liu, J., Li, F., & Yang, B. B. (2021) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-021-00569-5 · Cited by 567
Self-citationCircular RNAs: Biogenesis, Function and Role in Human Diseases
Greene, J. P., Baird, A., Brady, L., Lim, M. C. J., Gray, S. G., McDermott, R., & Finn, S. P. (2017) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2017.00038 · Cited by 563
The novel roles of circRNAs in human cancer
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Widespread and Functional RNA Circularization in Localized Prostate Cancer
Chen, S., Huang, V., Xu, X., Livingstone, J., Soares, F., Jeon, J., Zeng, Y., Hua, J. T., Petricca, J., Guo, H., et al. (2019) · Cell · doi:10.1016/j.cell.2019.01.025 · Cited by 544
FUS affects circular RNA expression in murine embryonic stem cell-derived motor neurons
Errichelli, L., Modigliani, S. D., Laneve, P., Colantoni, A., Legnini, I., Capauto, D., Rosa, A., Santis, R. D., Scarfò, R., Peruzzi, G., et al. (2017) · Nature Communications · doi:10.1038/ncomms14741 · Cited by 548
CircRNA in cancer: Fundamental mechanism and clinical potential
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[Retracted] Global Increase in Breast Cancer Incidence: Risk Factors and Preventive Measures
Kashyap, D., Pal, D., Sharma, R., Garg, V. K., Goel, N., Koundal, D., Zaguia, A., Koundal, S., & Belay, A. (2022) · BioMed Research International · doi:10.1155/2022/9605439 · Cited by 604
Retracted
Metadata
- Authors
- Jeck, W. R., Sorrentino, J. A., Wang, K., Slevin, M. K., Burd, C. E., Liu, J., Marzluff, W. F., & Sharpless, N. E.
- Affiliations
- University of North Carolina at Chapel Hill (US)
- University of Kentucky (US)
- ORCID
- Venue
- RNA
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2012-12-18
- Volume
- 19
- Issue
- 2
- Pages
- 141-157
- ISSN
- 1355-8382 (ISSN-L)
- 1469-9001
- PMC
- PMC3543092
- OpenAlex
- W2147806662
- Cited by
- 4,388
- References
- 41
- Citations by year
- 2026: 165 · 2025: 251 · 2024: 369 · 2023: 409 · 2022: 566 · 2021: 655 · 2020: 612 · 2019: 467 · 2018: 369 · 2017: 227 · 2016: 121 · 2015: 92 · 2014: 47 · 2013: 31 · 2012: 1
- FWCI
- 22.00
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- RNA (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Carolina Digital Repository (University of North Carolina at Chapel Hill) (submittedVersion)
- HighWire Press Open Archive (submittedVersion)
- UNC Libraries
- Funders
- Glenn Foundation for Medical Research
- National Institutes of Health (5r01ag024379-15)
- National Institute on Aging (AG024379, AG041567, R01-AG024379, F30AG041567)
- National Human Genome Research Institute (R01HG006272)
- National Institute of General Medical Sciences (F32GM087059, T32GM007092)
- National Institute of Environmental Health Sciences (T32ES007126)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Circular RNAs in diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
- Keywords
- circular RNA, back-splicing, Alu elements, RNase R, human fibroblasts, mouse testis, HIPK2, HIPK3, competing endogenous RNA, RNA stability, gene expression regulation
- MeSH terms
- RNA, Circular, Animals, Base Sequence, Cells, Cultured, Exons, Exoribonucleases, Gene Expression Regulation, Humans, Male, Molecular Sequence Data, Phosphotransferases, RNA, RNA Splicing, Conserved Sequence, Sequence Analysis, RNA, Evolution, Molecular, Computational Biology, Trans-Splicing, Alu Elements, RNA Stability, RNA, Small Interfering, Mice, High-Throughput Nucleotide Sequencing, Nucleotide Motifs
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