Emerging roles and context of circular RNAs

Wiley Interdisciplinary Reviews: RNA

Volumn 8, Issue 2, 2017, Pages

  Panda, Amaresh C ^a   Grammatikakis, Ioannis ^a   Munk, Rachel ^a   Gorospe, Myriam ^a   Abdelmohsen, Kotb ^a  

^a NATIONAL INSTITUTE ON AGING   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CIRCULAR RNA; UNCLASSIFIED DRUG; UNTRANSLATED RNA; RNA; RNA, CIRCULAR;

BIOGENESIS; CELL DIFFERENTIATION; CELL PROLIFERATION; CELL SURVIVAL; CELLULAR DISTRIBUTION; DNA BINDING; GENE EXPRESSION REGULATION; PROTEIN RNA BINDING; REVIEW; RNA ANALYSIS; RNA METABOLISM; RNA TRANSCRIPTION; RNA TRANSLATION; TURNOVER TIME; ANIMAL; GENETIC TRANSCRIPTION; GENETICS; HUMAN; PHYSIOLOGICAL STRESS; RNA SPLICING;

ANIMALS; GENE EXPRESSION REGULATION; HUMANS; RNA; RNA SPLICING; STRESS, PHYSIOLOGICAL; TRANSCRIPTION, GENETIC;

EID: 84987704700     PISSN: 17577004     EISSN: 17577012     Source Type: Journal    
DOI: 10.1002/wrna.1386     Document Type: Review

References (61)

1. Hsu MT, Coca-Prados M. Electron microscopic evidence for the circular form of RNA in the cytoplasm of eukaryotic cells. Nature 1979, 280:339–340.
2. Nigro JM, Cho KR, Fearon ER, Kern SE, Ruppert JM, Oliner JD, Kinzler KW, Vogelstein B. Scrambled exons. Cell 1991, 64:607–613.
3. Salzman J, Chen RE, Olsen MN, Wang PL, Brown PO. Cell-type specific features of circular RNA expression. PLoS Genet 2013, 9:e1003777.
4. Rybak-Wolf A, Stottmeister C, Glazar P, Jens M, Pino N, Giusti S, Hanan M, Behm M, Bartok O, Ashwal-Fluss R, et al. Circular RNAs in the mammalian brain are highly abundant, conserved, and dynamically expressed. Mol Cell 2015, 58:870–885.
5. Jeck WR, Sorrentino JA, Wang K, Slevin MK, Burd CE, Liu J, Marzluff WF, Sharpless NE. Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA 2013, 19:141–157.
6. Glazar P, Papavasileiou P, Rajewsky N. circBase: a database for circular RNAs. RNA 2014, 20:1666–1670.
7. Abdelmohsen K, Panda AC, De S, Grammatikakis I, Kim J, Ding J, Noh JH, Kim KM, Mattison JA, de Cabo R, et al. Circular RNAs in monkey muscle: age-dependent changes. Aging 2015, 7:903–910.
8. Guo JU, Agarwal V, Guo H, Bartel DP. Expanded identification and characterization of mammalian circular RNAs. Genome Biol 2014, 15:409.
9. Hansen TB, Jensen TI, Clausen BH, Bramsen JB, Finsen B, Damgaard CK, Kjems J. Natural RNA circles function as efficient microRNA sponges. Nature 2013, 495:384–388.
10. Memczak S, Jens M, Elefsinioti A, Torti F, Krueger J, Rybak A, Maier L, Mackowiak SD, Gregersen LH, Munschauer M, et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 2013, 495:333–338.
11. Wilusz JE, Sharp PA. Molecular biology. A circuitous route to noncoding RNA. Science 2013, 340:440–441.
12. Jeck WR, Sharpless NE. Detecting and characterizing circular RNAs. Nat Biotechnol 2014, 32:453–461.
13. Zhang Y, Xue W, Li X, Zhang J, Chen S, Zhang JL, Yang L, Chen LL. The biogenesis of nascent circular RNAs. Cell Rep 2016, 15:611–624.
14. Salzman J, Circular RNA. Expression: its potential regulation and function. Trends Genet 2016, 32:309–316.
15. Chen LL. The biogenesis and emerging roles of circular RNAs. Nat Rev Mol Cell Biol 2016, 17:205–211.
16. Vicens Q, Westhof E. Biogenesis of circular RNAs. Cell 2014, 159:13–14.
17. Li J, Yang J, Zhou P, Le Y, Zhou C, Wang S, Xu D, Lin HK, Gong Z. Circular RNAs in cancer: novel insights into origins, properties, functions and implications. Am J Cancer Res 2015, 5:472–480.
18. Shao Y, Chen Y. Roles of circular RNAs in neurologic disease. Front Mol Neurosci 2016, 9:25.
19. Barrett SP, Wang PL, Salzman J. Circular RNA biogenesis can proceed through an exon-containing lariat precursor. eLife 2015, 4:e07540.
20. Ashwal-Fluss R, Meyer M, Pamudurti NR, Ivanov A, Bartok O, Hanan M, Evantal N, Memczak S, Rajewsky N, Kadener S. circRNA biogenesis competes with pre-mRNA splicing. Mol Cell 2014, 56:55–66.
21. Liang D, Wilusz JE. Short intronic repeat sequences facilitate circular RNA production. Genes Dev 2014, 28:2233–2247.
22. Zhang XO, Wang HB, Zhang Y, Lu X, Chen LL, Yang L. Complementary sequence-mediated exon circularization. Cell 2014, 159:134–147.
23. Ivanov A, Memczak S, Wyler E, Torti F, Porath HT, Orejuela MR, Piechotta M, Levanon EY, Landthaler M, Dieterich C, et al. Analysis of intron sequences reveals hallmarks of circular RNA biogenesis in animals. Cell Rep 2015, 10:170–177.
24. Chen T, Xiang JF, Zhu S, Chen S, Yin QF, Zhang XO, Zhang J, Feng H, Dong R, Li XJ, et al. ADAR1 is required for differentiation and neural induction by regulating microRNA processing in a catalytically independent manner. Cell Res 2015, 25:459–476.
25. Conn SJ, Pillman KA, Toubia J, Conn VM, Salmanidis M, Phillips CA, Roslan S, Schreiber AW, Gregory PA, Goodall GJ. The RNA binding protein quaking regulates formation of circRNAs. Cell 2015, 160:1125–1134.
26. Kramer MC, Liang D, Tatomer DC, Gold B, March ZM, Cherry S, Wilusz JE. Combinatorial control of Drosophila circular RNA expression by intronic repeats, hnRNPs, and SR proteins. Genes Dev 2015, 29:2168–2182.
27. Capel B, Swain A, Nicolis S, Hacker A, Walter M, Koopman P, Goodfellow P, Lovell-Badge R. Circular transcripts of the testis-determining gene Sry in adult mouse testis. Cell 1993, 73:1019–1030.
28. Westholm JO, Miura P, Olson S, Shenker S, Joseph B, Sanfilippo P, Celniker SE, Graveley BR, Lai EC. Genome-wide analysis of drosophila circular RNAs reveals their structural and sequence properties and age-dependent neural accumulation. Cell Rep 2014, 9:1966–1980.
29. Li Z, Huang C, Bao C, Chen L, Lin M, Wang X, Zhong G, Yu B, Hu W, Dai L, et al. Exon-intron circular RNAs regulate transcription in the nucleus. Nat Struct Mol Biol 2015, 22:256–264.
30. Wilusz JE. Repetitive elements regulate circular RNA biogenesis. Mob Genet Elements 2015, 5:1–7.
31. Hansen TB, Veno MT, Damgaard CK, Kjems J. Comparison of circular RNA prediction tools. Nucleic Acids Res 2016, 44:e58.
32. Dudekula DB, Panda AC, Grammatikakis I, De S, Abdelmohsen K, Gorospe M. CircInteractome: a web tool for exploring circular RNAs and their interacting proteins and microRNAs. RNA Biol 2016, 13:34–42.
33. Valinezhad Orang A, Safaralizadeh R, Kazemzadeh-Bavili M. Mechanisms of miRNA-mediated gene regulation from common downregulation to mRNA-specific upregulation. Int J Genomics 2014, 2014:970607.
34. Geng HH, Li R, Su YM, Xiao J, Pan M, Cai XX, Ji XP. The circular RNA Cdr1as promotes myocardial infarction by mediating the regulation of miR-7a on its target genes expression. PLoS One 2016, 11:e0151753.
35. Han L, Zhang G, Zhang N, Li H, Liu Y, Fu A, Zheng Y. Prognostic potential of microRNA-138 and its target mRNA PDK1 in sera for patients with non-small cell lung cancer. Med Oncol 2014, 31:129.
36. 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/beta-catenin pathway. Oncotarget 2015, 6:6001–6013.
37. Zheng Q, Bao C, Guo W, Li S, Chen J, Chen B, Luo Y, Lyu D, Li Y, Shi G, et al. Circular RNA profiling reveals an abundant circHIPK3 that regulates cell growth by sponging multiple miRNAs. Nat Commun 2016, 7:11215.
38. Zhang C, Wu H, Wang Y, Zhu S, Liu J, Fang X, Chen H. Circular RNA of cattle casein genes are highly expressed in bovine mammary gland. J Dairy Sci 2016, 99:4750–4760.
39. Xu H, Guo S, Li W, Yu P. The circular RNA Cdr1as, via miR-7 and its targets, regulates insulin transcription and secretion in islet cells. Sci Rep 2015, 5:12453.
40. Du WW, Yang W, Liu E, Yang Z, Dhaliwal P, Yang BB. Foxo3 circular RNA retards cell cycle progression via forming ternary complexes with p21 and CDK2. Nucleic Acids Res 2016, 44:2846–2858.
41. Du WW, Yang W, Chen Y, Wu ZK, Foster FS, Yang Z, Li X, Yang BB. Foxo3 circular RNA promotes cardiac senescence by modulating multiple factors associated with stress and senescence responses. Eur Heart J 2016.
42. Enuka Y, Lauriola M, Feldman ME, Sas-Chen A, Ulitsky I, Yarden Y. Circular RNAs are long-lived and display only minimal early alterations in response to a growth factor. Nucleic Acids Res 2016, 44:1370–1383.
43. Bachmayr-Heyda A, Reiner AT, Auer K, Sukhbaatar N, Aust S, Bachleitner-Hofmann T, Mesteri I, Grunt TW, Zeillinger R, Pils D. Correlation of circular RNA abundance with proliferation – exemplified with colorectal and ovarian cancer, idiopathic lung fibrosis, and normal human tissues. Sci Rep 2015, 5:8057.
44. Lukiw WJ. Circular RNA (circRNA) in Alzheimer's disease (AD). Front Genet 2013, 4:307.
45. Kahvejian A, Roy G, Sonenberg N. The mRNA closed-loop model: the function of PABP and PABP-interacting proteins in mRNA translation. Cold Spring Harb Symp Quant Biol 2001, 66:293–300.
46. Abdelmohsen K, Gorospe M. Posttranscriptional regulation of cancer traits by HuR. WIREs RNA 2010, 1:214–229.
47. White EJ, Brewer G, Wilson GM. Post-transcriptional control of gene expression by AUF1: mechanisms, physiological targets, and regulation. Biochim Biophys Acta 1829, 2013:680–688.
48. Williams GT, Mourtada-Maarabouni M, Farzaneh F. A critical role for non-coding RNA GAS5 in growth arrest and rapamycin inhibition in human T-lymphocytes. Biochem Soc Trans 2011, 39:482–486.
49. Schmitz KM, Mayer C, Postepska A, Grummt I. Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes. Genes Dev 2010, 24:2264–2269.
50. Beckedorff FC, Ayupe AC, Crocci-Souza R, Amaral MS, Nakaya HI, Soltys DT, Menck CF, Reis EM, Verjovski-Almeida S. The intronic long noncoding RNA ANRASSF1 recruits PRC2 to the RASSF1A promoter, reducing the expression of RASSF1A and increasing cell proliferation. PLoS Genet 2013, 9:e1003705.
51. Chu C, Qu K, Zhong FL, Artandi SE, Chang HY. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol Cell 2011, 44:667–678.
52. Villegas VE, Zaphiropoulos PG. Neighboring gene regulation by antisense long non-coding RNAs. Int J Mol Sci 2015, 16:3251–3266.
53. Mercer TR, Mattick JS. Structure and function of long noncoding RNAs in epigenetic regulation. Nat Struct Mol Biol 2013, 20:300–307.
54. Hershey JW, Sonenberg N, Mathews MB. Principles of translational control: an overview. Cold Spring Harb Perspect Biol 2012, 4.
55. Pacheco A, Martinez-Salas E. Insights into the biology of IRES elements through riboproteomic approaches. J Biomed Biotechnol 2010, 2010:458927.
56. Perriman R, Ares M. Circular mRNA can direct translation of extremely long repeating-sequence proteins in vivo. RNA 1998, 4:1047–1054.
57. Anderson DM, Anderson KM, Chang CL, Makarewich CA, Nelson BR, McAnally JR, Kasaragod P, Shelton JM, Liou J, Bassel-Duby R, et al. A micropeptide encoded by a putative long noncoding RNA regulates muscle performance. Cell 2015, 160:595–606.
58. AbouHaidar MG, Venkataraman S, Golshani A, Liu BL, Ahmad T. Novel coding, translation, and gene expression of a replicating covalently closed circular RNA of 220 nt. Proc Natl Acad Sci U S A 2014, 111:14542–14547.
59. Chen CY, Sarnow P. Initiation of protein synthesis by the eukaryotic translational apparatus on circular RNAs. Science 1995, 268:415–417.
60. Meyer KD, Patil DP, Zhou J, Zinoviev A, Skabkin MA, Elemento O, Pestova TV, Qian SB, Jaffrey SR. 5′ UTR m(6)A promotes cap-independent translation. Cell 2015, 163:999–1010.
61. Zhou J, Wan J, Gao X, Zhang X, Jaffrey SR, Qian SB. Dynamic m(6)A mRNA methylation directs translational control of heat shock response. Nature 2015, 526:591–594.