Complementary sequence-mediated exon circularization

Cell

Volumn 159, Issue 1, 2014, Pages 134-147

  Zhang, Xiao Ou ^a   Wang, Hai Bin ^b,c   Zhang, Yang ^b   Lu, Xuhua ^c   Chen, Ling Ling ^b   Yang, Li ^a  

^a Chinese Academy of Sciences   (China)

^b INSTITUTE OF BIOCHEMISTRY AND CELL BIOLOGY   (China)

^c SECOND MILITARY MEDICAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

RIBONUCLEASE; RNA;

ALTERNATIVE RNA SPLICING; ARTICLE; COMPETITION; CONTROLLED STUDY; EXON; EXON SKIPPING; EXPRESSION VECTOR; GENE EXPRESSION REGULATION; GENE LOCUS; HUMAN; INTRON; NUCLEOTIDE SEQUENCE; RNA SEQUENCE; RNA STRUCTURE; TRANSCRIPTION REGULATION; ALU SEQUENCE; ANIMAL; CONFORMATION; EMBRYONIC STEM CELL; GENETICS; HUMAN GENOME; MAMMAL; METABOLISM; MOLECULAR EVOLUTION; MOLECULAR GENETICS; SEQUENCE ALIGNMENT;

ALTERNATIVE SPLICING; ALU ELEMENTS; ANIMALS; BASE SEQUENCE; EMBRYONIC STEM CELLS; EVOLUTION, MOLECULAR; EXONS; GENOME, HUMAN; HUMANS; INTRONS; MAMMALS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; SEQUENCE ALIGNMENT;

EID: 84907509527     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2014.09.001     Document Type: Article

References (35)

1. A. Athanasiadis, A. Rich, and S. Maas Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome PLoS Biol. 2 2004 e391
2. D.L. Black Mechanisms of alternative pre-messenger RNA splicing Annu. Rev. Biochem. 72 2003 291 336
3. C.E. Burd, W.R. Jeck, Y. Liu, H.K. Sanoff, Z. Wang, and N.E. Sharpless Expression of linear and novel circular forms of an INK4/ARF-associated non-coding RNA correlates with atherosclerosis risk PLoS Genet. 6 2010 e1001233
4. B. Capel, A. Swain, S. Nicolis, A. Hacker, M. Walter, P. Koopman, P. Goodfellow, and R. Lovell-Badge Circular transcripts of the testis-determining gene Sry in adult mouse testis Cell 73 1993 1019 1030
5. L.L. Chen, and G.G. Carmichael Gene regulation by SINES and inosines: biological consequences of A-to-I editing of Alu element inverted repeats Cell Cycle 7 2008 3294 3301
6. L.L. Chen, J.N. DeCerbo, and G.G. Carmichael Alu element-mediated gene silencing EMBO J. 27 2008 1694 1705
7. C. Cocquerelle, P. Daubersies, M.A. Majérus, J.P. Kerckaert, and B. Bailleul Splicing with inverted order of exons occurs proximal to large introns EMBO J. 11 1992 1095 1098
8. C. Cocquerelle, B. Mascrez, D. Hétuin, and B. Bailleul Mis-splicing yields circular RNA molecules FASEB J. 7 1993 155 160
9. R.A. Dubin, M.A. Kazmi, and H. Ostrer Inverted repeats are necessary for circularization of the mouse testis Sry transcript Gene 167 1995 245 248
10. W.G. Fairbrother, R.F. Yeh, P.A. Sharp, and C.B. Burge Predictive identification of exonic splicing enhancers in human genes Science 297 2002 1007 1013
11. J.U. Guo, V. Agarwal, H. Guo, and D.P. Bartel Expanded identification and characterization of mammalian circular RNAs Genome Biol. 15 2014 409
12. T.B. Hansen, E.D. Wiklund, J.B. Bramsen, S.B. Villadsen, A.L. Statham, S.J. Clark, and J. Kjems miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA EMBO J. 30 2011 4414 4422
13. T.B. Hansen, T.I. Jensen, B.H. Clausen, J.B. Bramsen, B. Finsen, C.K. Damgaard, and J. Kjems Natural RNA circles function as efficient microRNA sponges Nature 495 2013 384 388
14. W.R. Jeck, and N.E. Sharpless Detecting and characterizing circular RNAs Nat. Biotechnol. 32 2014 453 461
15. W.R. Jeck, J.A. Sorrentino, K. Wang, M.K. Slevin, C.E. Burd, J. Liu, W.F. Marzluff, and N.E. Sharpless Circular RNAs are abundant, conserved, and associated with ALU repeats RNA 19 2013 141 157
16. D. Kim, and S.L. Salzberg TopHat-Fusion: an algorithm for discovery of novel fusion transcripts Genome Biol. 12 2011 R72
17. D. Kim, G. Pertea, C. Trapnell, H. Pimentel, R. Kelley, and S.L. Salzberg TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions Genome Biol. 14 2013 R36
18. A. Kos, R. Dijkema, A.C. Arnberg, P.H. van der Meide, and H. Schellekens The hepatitis delta (delta) virus possesses a circular RNA Nature 323 1986 558 560
19. M.T. Lovci, D. Ghanem, H. Marr, J. Arnold, S. Gee, M. Parra, T.Y. Liang, T.J. Stark, L.T. Gehman, and S. Hoon Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges Nat. Struct. Mol. Biol. 20 2013 1434 1442
20. S. Memczak, M. Jens, A. Elefsinioti, F. Torti, J. Krueger, A. Rybak, L. Maier, S.D. Mackowiak, L.H. Gregersen, and M. Munschauer Circular RNAs are a large class of animal RNAs with regulatory potency Nature 495 2013 333 338
21. M.M. Mukaka Statistics corner: A guide to appropriate use of correlation coefficient in medical research Malawi Med. J. 24 2012 69 71
22. J.M. Nigro, K.R. Cho, E.R. Fearon, S.E. Kern, J.M. Ruppert, J.D. Oliner, K.W. Kinzler, and B. Vogelstein Scrambled exons Cell 64 1991 607 613
23. T.W. Nilsen, and B.R. Graveley Expansion of the eukaryotic proteome by alternative splicing Nature 463 2010 457 463
24. Z. Pasman, M.D. Been, and M.A. Garcia-Blanco Exon circularization in mammalian nuclear extracts RNA 2 1996 603 610
25. J. Salzman, C. Gawad, P.L. Wang, N. Lacayo, and P.O. Brown Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types PLoS ONE 7 2012 e30733
26. J. Salzman, R.E. Chen, M.N. Olsen, P.L. Wang, and P.O. Brown Cell-type specific features of circular RNA expression PLoS Genet. 9 2013 e1003777
27. H.L. Sanger, G. Klotz, D. Riesner, H.J. Gross, and A.K. Kleinschmidt Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures Proc. Natl. Acad. Sci. USA 73 1976 3852 3856
28. H. Suzuki, Y. Zuo, J. Wang, M.Q. Zhang, A. Malhotra, and A. Mayeda Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing Nucleic Acids Res. 34 2006 e63 10.1093/nar/gkl151
29. Z. Wang, M.E. Rolish, G. Yeo, V. Tung, M. Mawson, and C.B. Burge Systematic identification and analysis of exonic splicing silencers Cell 119 2004 831 845
30. L. Yang, M.O. Duff, B.R. Graveley, G.G. Carmichael, and L.L. Chen Genomewide characterization of non-polyadenylated RNAs Genome Biol. 12 2011 R16
31. Y. Zhang, X.O. Zhang, T. Chen, J.F. Xiang, Q.F. Yin, Y.H. Xing, S. Zhu, L. Yang, and L.L. Chen Circular intronic long noncoding RNAs Mol. Cell 51 2013 792 806
32. S. Hoffmann, C. Otto, G. Doose, A. Tanzer, D. Langenberger, S. Christ, M. Kunz, L.M. Holdt, D. Teupser, J. Hackermüller, and P.F. Stadler A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection Genome Biol. 15 2014 R34
33. R. Lorenz, S.H. Bernhart, C. Höner Zu Siederdissen, H. Tafer, C. Flamm, P.F. Stadler, and I.L. Hofacker ViennaRNA Package 2.0 Algorithms Mol. Biol. 6 2011 26
34. C. Trapnell, D.G. Hendrickson, M. Sauvageau, L. Goff, J.L. Rinn, and L. Pachter Differential analysis of gene regulation at transcript resolution with RNA-seq Nat. Biotechnol. 31 2013 46 53
35. X.O. Zhang, Q.F. Yin, H.B. Wang, Y. Zhang, T. Chen, P. Zheng, X. Lu, L.L. Chen, and L. Yang Species-specific alternative splicing leads to unique expression of sno-lncRNAs BMC Genomics 15 2014 287