Circular RNAs in eukaryotic cells

Current Genomics

Volumn 16, Issue 5, 2015, Pages 312-318

  Chen, Liang ^a   Huang, Chuan ^a   Wang, Xiaolin ^a   Shan, Ge ^a  

^a UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

Author keywords

Biogenesis; CircRNA; EIciRNA; MicroRNA; MicroRNA sponge; NcRNA; Transcription

Indexed keywords

CIRCULAR RNA; MICRORNA; MICRORNA 7; RNA; SMALL NUCLEAR RIBONUCLEOPROTEIN; UNCLASSIFIED DRUG;

ARABIDOPSIS THALIANA; ARTICLE; BIOINFORMATICS; CAENORHABDITIS ELEGANS; CELLULAR DISTRIBUTION; DEGENERATIVE DISEASE; DISEASE ASSOCIATION; DROSOPHILA; EUKARYOTIC CELL; EXON; GENE EXPRESSION; GENOME ANALYSIS; HUMAN; INTRON; MAMMAL; NONHUMAN; PROKARYOTE; PROTIST; RNA SPLICING; RNA STABILITY; RNA SYNTHESIS; SINGLE NUCLEOTIDE POLYMORPHISM; YEAST;

CAENORHABDITIS ELEGANS; EUKARYOTA; MUS;

EID: 84938605127     PISSN: 13892029     EISSN: 18755488     Source Type: Journal    
DOI: 10.2174/1389202916666150707161554     Document Type: Article

References (66)

1. Crick, F.H. On Protein Synthesis. Symp. Soc. Exp. Biol., 1956, 12, 139-163.
2. Geiduschek, E.P.; Haselkorn, R. Messenger RNA. Annu. Rev. Biochem., 1969, 38, 647-76.
3. 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. U.S.A. 1976, 73(11), 3852-3856.
4. Gould, A.R. Studies on encapsidated viroid-like RNA. II. Purification and characterization of a viroid-like RNA associated with velvet tobacco mottle virus (VTMoV). Virology 1981, 708(1), 123-33.
5. Kos, A.; Dijkema, R.; Arnberg, A.C.; van der Meide, P.H.; Schellekens, H. The hepatitis delta (delta) virus possesses a circular RNA. Nature, 1986, 323(6088), 558-60.
6. Hsu, M.T.; Coca-Prados, M-THaM. Electron microscopic evidence for the circular form of RNA in the cytoplasm of eukaryotic cells. Nature, 1979, 280, 339-340.
7. Arnberg, A.C.; Van Ommen GJ; Grivell LA; Van Bruggen EF; Borst P. Some Yeast Mitochondrial Rnas Are Circular. Cell, 1980, 19(2), 313-319.
8. Cech, T.R. RNA splicing: three themes with variations. Cell, 1983, 34(3), 713-6.
9. Vincent, H.A.; Deutscher, M.P. Substrate recognition and catalysis by the exoribonuclease RNase R. J. Biol. Chem., 2006, 281(40), 29769-29775.
10. Suzuki, H.; Zuo, Y.; Wang, J.; Zhang, M.Q.; Malhotra, A.; May-eda, A. Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing. Nucleic Acids Res., 2006, 34, e63.
11. Zhang, Y.; Zhang, X.O.; Chen, T.; Xiang, J.F.; Yin, Q.F.; Xing, Y.H.; Zhu, S.; Yang, L.; Chen, L.L. Circular intronic long noncod-ing RNAs. Mol. Cell. 2013, 5l(6), 792-806.
12. Nigro, J.M.; Cho, K.R.; Fearon, E.R.; Kern, S.E.; Ruppert, J.M.; Oliner, J.D.; Kinzler, K.W.; Vogelstein, B. Scrambled exons. Cell, 1991, 64(3), 607-613.
13. Cocquerelle, C.; Daubersies, P.; Majerus, M.A.; Kerckaert, J.P.; Bailleul, B. Splicing with inverted order of exons occurs proximal to large introns. EMBOJ., 1992,11, 1095-1098.
14. Cocquerelle, C.; Mascrez, B.; Hetuin, D.; Bailleul, B. Mis-splicing yields circular RNA molecules. FASEB J., 1993, 7(1), 155-60.
15. Capel, B.; Swain, A.; Nicolis, S.; Hacker, A.; Walter, M.; Koop-man, P.; Goodfellow, P.; Lovell-Badge, R. Circular transcripts of the testis-determining gene Sry in adult mouse testis. Cell, 1993, 73, 1019-1030.
16. Zaphiropoulos, P.G. Circular RNAs from transcripts of the rat cytochrome P450 2C24 gene: correlation with exon skipping. Proc. Natl. Acad. Sci. U.S.A., 1996, 93(13), 6536-6541.
17. Zaphiropoulos, P.G. Exon skipping and circular RNA formation in transcripts of the human cytochrome P-450 2C18 gene in epidermis and of the rat androgen binding protein gene in testis. Mol. Cell. Biol., 1997, 17(6), 2985-2993.
18. Bailleul, B. During in vivo maturation of eukaryotic nuclear mRNA, splicing yields excised exon circles. Nucleic Acids Res., 1996, 24, 1015-1019.
19. Caldas, C.; So, C W, MacGregor, A, Ford, A M, McDonald, B, Chan, L C, Wiedemann, L M.; Exon scrambling of MLL transcripts occur commonly and mimic partial genomic duplication of the gene. Gene, 1998, 208, 167-176.
20. Chao, C.W.; Chan, D.C.; Kuo, A.; Leder, P. The mouse formin (Fmn) gene: abundant circular RNA transcripts and gene-targeted deletion analysis. Mol. Med., 1998, 4(9), 614-28.
21. Surono, A.; Takeshima, Y.; Wibawa, T.; Ikezawa, M.; Nonaka, I.; Matsuo, M. Circular dystrophin RNAs consisting of exons that were skipped by alternative splicing Hum. Mol. Genet. 1999, 8(3), 493-500.
22. Li, X.F.; Lytton, J. A circularized sodium-calcium exchanger exon 2 transcript. J. Biol. Chem., 1999, 274(12), 8153-8160.
23. Gualandi, F.; Trabanelli, C.; Rimessi, P.; Calzolari, E.; Toffolatti, L.; Patarnello, T.; Kunz, G.; Muntoni, F.; Ferlini, A.; Multiple exon skipping and RNA circularisation contribute to the severe pheno-typic expression of exon 5 dystrophin deletion. J. Med. Genet, 2003, 40(8), e100.
24. Houseley, J.M.; Garcia-Casado, Z.; Pascual, M.; Paricio, N.; O'Dell, K.M.; Monckton, D.G.; Artero, R.D. Noncanonical RNAs from transcripts of the Drosophila muscleblind gene. J Hered, 2006, 97(3), 253-60.
25. Burd, C E, Jeck, W R, Liu, Y, Sanoff, H K, Wang, Z, Sharpless, N.E.; Expression of linear and novel circular forms of an INK4/ARF-associated non-coding RNA correlates with atherosclerosis risk. PLoS Genetics, 2010, 6(12), e1001233.
26. Hansen, T.B.; Wiklund, E.D.; Bramsen, J.B.; Villadsen, S.B.; Statham, A.L.; Clark, S.J.; Kjems, J. miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA. EMBO J., 2011, 30(21), 4414-4422.
27. 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, 2012, 7(2), e30733.
28. Jeck, W.R.; Sorrentino, J.A.; Wang, K.; Slevin, M.K.; Burd, C.E.; Liu, J.; Marzluff, W.F.; Sharpless, N.E. Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA, 2013, 19(2),141-157.
29. Memczak, S.; Jens, M.; Elefsinioti, A.; Torti, F; Krueger, J.; Ry-bak, A; Maier, L, Mackowiak, S.D.; Gregersen, L.H.; Munschauer, M.; Loewer, A.; Ziebold, U.; Landthaler, M.; Kocks, C.; le Noble, F. Rajewsky N. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature, 2013, 495(7441), 333-338.
30. Soma, A.; Onodera, A.; Sugahara, J.; Kanai, A.; Yachie, N.; To-mita, M.; Kawamura, F.; Sekine, Y. Permuted tRNA genes expressed via a circular RNA intermediate in Cyanidioschyzon mero-lae. Science, 2007, 318(5849), 450-453.
31. Guo, J.U.; Agarwal, V.; Guo, H.; Bartel, D.P.; Expanded identification and characterization of mammalian circular RNAs. Genome Biol., 2014, 15(7), 409.
32. You, X.; Vlatkovic, I.; Babic, A.; Will, T.; Epstein, I.; Tushev, G.; Akbalik, G.; Wang, M.; Glock, C.; Quedenau, C.; Wang, X.; Hou, J.; Liu, H.; Sun, W.; Sambandan, S.; Chen, T.; Schuman, E.M.; Chen, W. Neural circular RNAs are derived from synaptic genes and regulated by development and plasticity. Nat. Neurosci., 2015, 18(4), 603-610.
33. Westholm, J.O.; Miura, P.; Olson, S.; Shenker, S.; Joseph, B.; Sanfilippo, P.; Celniker, S.E.; Graveley, B.R.; Lai, E.C. Genome-wide analysis of drosophila circular RNAs reveals their structural and sequence properties and age-dependent neural accumulation. Cell Rep., 2014, 9(5):1966-80.
34. Ivanov, A.; Memczak, S.; Wyler, E.; Torti, F.; Porath, H.T.; Ore-juela, M.R.; Piechotta, M.; Levanon, E.Y.; Landthaler, M.; Dieterich, C.; Rajewsky, N. Analysis of intron sequences reveals hallmarks of circular RNA biogenesis in animals. Cell Rep., 2015, 10(2):170-177.
35. Wang, P.L.; Bao, Y.; Yee, M.C.; Barrett, S.P.; Hogan, G.J.; Olsen, M.N.; Dinneny, J.R.; Brown, P.O.; Salzman, J. Circular RNA is expressed across the eukaryotic tree of life. PLoS One, 2014, 9(6), e90859.
36. Danan, M.; Schwartz, S.; Edelheit, S.; Sorek, R. Transcriptome-wide discovery of circular RNAs in Archaea. Nucleic Acids Res., 2012, 40(7), 3131-3142.
37. Doose, G.; Alexis, M.; Kirsch, R.; Findeiᵝ, S, Langenberger, D, Machne, R, Morl, M, Hoffmann, S, Stadler, P F.; Mapping the RNA-Seq trash bin: unusual transcripts in prokaryotic transcrip-tome sequencing data. RNA Biol., 2013,10(7), 1204-1210.
38. Hoffmann, S.; Otto, C.; Doose, G.; Tanzer, A.; Langenberger, D.; Christ, S.; Kunz, M.; Holdt, L.M.; Teupser, D.; Hackermuller, J.; Stadler, P.F. A multi-split mapping algorithm for circular RNA, splicing, trans-splicing, and fusion detection. Genome Biol., 2014, 15(2), R34.
39. Zhang, X.O.; Wang, H.B.; Zhang, Y.; Lu, X.; Chen, L.L.; Yang, L. Complementary sequence-mediated exon circularization. Cell, 2014,159(1), 134-147.
40. Gao, Y.; Wang, J.; Zhao, F. CIRI: an efficient and unbiased algorithm for de novo circular RNA identification. Genome Biol., 2015, 16(1), 4.
41. Wu, Q.F.; Wang, Y.; Cao, M.; Pantaleo, V.; Burgyan, J.; Li, W.X.; Ding, S W.; Homology-independent discovery of replicating pathogenic circular RNAs by deep sequencing and a new computational algorithm. Proc. Natl. Acad. Sci. U.S.A., 2012,109(10), 3938-3943.
42. Zhang, Z, Qi, S, Tang, N, Zhang, X, Chen, S, Zhu, P, Ma, L, Cheng, J, Xu, Y, Lu, M, Wang, H, Ding, S W, Li, S, Wu, Q.; Discovery of replicating circular RNAs by RNA-seq and computational algorithms. PLoS Pathog., 2014,10(12), e1004553.
43. Dubin, R.A.; Kazmi, M.A.; Ostrer, H. Inverted repeats are necessary for circularization of the mouse testis Sry transcript. Gene, 1995,167(1-2), 245-248.
44. Liang, D.; Wilusz, J.E. Short intronic repeat sequences facilitate circular RNA production. Genes Dev., 2014, 28(20), 2233-2247.
45. Li, Z.Y.; Huang, C.; Bao, C.; Chen, L.; Lin, M.; Wang, X.L.; Zhong, G.L.; Yu, B.; Hu, W.C.; Dai, L.M.; Zhu, P.F.; Chang, Z.; Wu, Q.F.; Zhao, Y.; Jia, Y.; Xu, P.; Liu, H.J.; Shan, G. Exon-intron circular RNAs regulate transcription in the nucleus. Nat. Struct. Mol. Biol., 2015, 22(3): 256-264.
46. Starke, S.; Jost, I.; Rossbach, O.; Schneider, T.; Schreiner, S.; Hung, L.H.; Bindereif, A. Exon circularization requires canonical splice signals. Cell Reports, 2015,10(1), 103-111.
47. Conn, S.J.; Pillman, K.A.; Toubia, J.; Conn, V.M.; Salmanidis, M, Phillips, C.A.; Roslan, S.; Schreiber, A.W.; Gregory, P.A.; Goodall, G.J. The RNA Binding Protein Quaking Regulates Formation of circRNAs. Cell, 2015,160(6), 1125-1134.
48. Ashwal-Fluss, R.; Meyer, M.; Pamudurti, N.R.; Ivanov, A.; Bartok, O.; Hanan, M.; Evantal, N.; Memczak, S.; Rajewsky, N.; Kadener, S.; circRNA Biogenesis Competes with Pre-mRNA Splicing. Mol. Cell, 2014, 56(1), 55-66.
49. Chen, L.; Shan, G.; Circular RNAs remain peculiarly unclear in biogenesis and function. Sci. China Life Sci 2015, 2015 Apr 23.[Epub ahead of print].
50. Salzman, J, Chen, R E, Olsen, M N, Wang, P L, Brown, P O.; Cell-type specific features of circular RNA expression. PLoS Genet, 2013, 9(9), e1003777.
51. Hansen, T.B.; Jensen, T.I.; Clausen, B.H.; Bramsen, J.B.; Fin-sen, B.; Damgaard, C.K.; Kjems, J. Natural RNA circles function as efficient microRNA sponges. Nature, 2013, 495(7441), 384-388.
52. Junn, E, Lee, K W, Jeong, B S, Chan, T W, Im, J Y, Mouradian, M M.; Repression of alpha-synuclein expression and toxicity by mi-croRNA-7. Proc. Natl. Acad. Sci. U.S.A, 2009, 106(31), 13052-13057.
53. Lau, P.; de Strooper, B. Dysregulated microRNAs in neurodegen-erative disorders. Semin Cell Dev. Biol., 2010, 21(7), 768-773.
54. Lukiw, W.J. Circular RNA (circRNA) in Alzheimer's disease (AD). Front Genet., 2013, 4, 307.
55. Hill, J.M.; Lukiw, W.J.; Bhattacharjee S.; Zhao Y.H.; Alexandrov P.N.; Dua P.; Pogue A.I. Deficits in the natural circular RNA (cir-cRNA) 'sponge' for miRNA-7 (cirs7) in Alzheimer's Disease (AD): miRNA-7 up-regulation, and down-regulation of the key phagocytosis protein Ubiquitin Ligase A (UBE2A). Alzheimer's & Dementia, 2014, 10(4),785-786.
56. Hansen, T.B.; Kjems, J.; Damgaard, C.K. Circular RNA and miR-7 in cancer. Cancer Res., 2013, 73(18), 5609-5612.
57. Li, F, Zhang, L, Li, W, Deng, J, Zheng, J, An, M, Lu, J, Zhou, Y.; Circular RNA ITCH has inhibitory effect on ESCC by suppressing the Wnt/3 -catenin pathway. Oncotarget, 2015, 6(8), 6001-6013.
58. Li, P.; Chen, S.; Chen, H.; Mo, X.; Li, T.; Shao, Y.; Xiao, B.; Guo, J. Using circular RNA as a novel type of biomarker in the screening of gastric cancer. Clin. Chim. Acta, 2015, 444, 132-136.
59. Bachmayr-Heyda, A.; Reiner, A.T.; Auer, K.; Sukhbaatar, N.; Aust, S.; Bachleitner-Hofmann, T.; Mesteri, I.; Grunt, T.W.; Zeillinger, R.; Pils, D. Correlation of circular RNA abundance with proliferation--exemplified with colorectal and ovarian cancer, idio-pathic lung fibrosis, and normal human tissues. Sci. Rep, 2015, 5, 8057.
60. Ghosal, S.; Das, S.; Sen, R.; Basak, P.; Chakrabarti, J. Circ2Traits: a comprehensive database for circular RNA potentially associated with disease and traits. Front Genet., 2013, 4, 283.
61. Wutz, A. Gene silencing in X-chromosome inactivation: advances in understanding facultative heterochromatin formation. Nat. Rev. Genet, 2011, 12(8), 542-553.
62. Fu, X. Non-coding RNA: a new frontier in regulatory biology. Natl. Sci. Rev., 2014, 1(2), 190-204.
63. Liu, H.; Wang, X.; Wang, H.D.; Wu, J.; Ren, J.; Meng, L.; Wu, Q.; Dong, H.S.; Wu, J.; Kao, T.Y.; Ge, Q.; Wu, Z.X.; Yuh, C.H.; Shan, G.; Escherichia coli noncoding RNAs can affect gene expression and physiology of Caenorhabditis elegans. Nat. Com-mun., 2012, 3, 1073.
64. Hu, S.; Wu, J.; Chen, L.; Shan, G. Signals from noncoding RNAs: Unconventional roles for conventional pol III transcripts. Int. J. Biochem. Cell Biol., 2012, 44(11), 1847-1851.
65. Ulitsky, I.; Bartel, D P.; lincRNAs: genomics, evolution, and mechanisms. Cell, 2013,154(1), 26-46.
66. Cech, T R, Steitz, J A.; The noncoding RNA revolution-trashing old rules to forge new ones. Cell, 2014,157(1), 77-94.