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Volumn 6, Issue 5, 2015, Pages 563-579

Biogenesis, identification, and function of exonic circular RNAs

Author keywords

[No Author keywords available]

Indexed keywords

CIRCULAR RNA; NONCO LINEAR RNA; RNA; RNA BINDING PROTEIN; UNCLASSIFIED DRUG;

EID: 84939463369     PISSN: 17577004     EISSN: 17577012     Source Type: Journal    
DOI: 10.1002/wrna.1294     Document Type: Review
Times cited : (340)

References (79)
  • 1
    • 84939470194 scopus 로고    scopus 로고
    • a database for circular RNAs
    • CircBase, a database for circular RNAs, http://circbase.org/.
  • 2
    • 84939465271 scopus 로고    scopus 로고
    • a database of human circular RNAs associated with disease or traits
    • circ2Traits, a database of human circular RNAs associated with disease or traits, http://gyanxet-beta.com/circdb/.
  • 3
    • 84939473547 scopus 로고    scopus 로고
    • (version 2.0.13), an algorithm for detecting both intergenic and intragenic NCL events,.
    • TopHat-Fusion (version 2.0.13), an algorithm for detecting both intergenic and intragenic NCL events, http://ccb.jhu.edu/software/tophat/fusion_index.html.
  • 4
    • 84939467091 scopus 로고    scopus 로고
    • (version 2.17), an algorithm for detecting both intergenic and intragenic NCL events,.
    • MapSplice (version 2.17), an algorithm for detecting both intergenic and intragenic NCL events, http://www.netlab.uky.edu/p/bioinfo/MapSplice2.
  • 5
    • 84939464248 scopus 로고    scopus 로고
    • segemenhl (version 0.2.0), an algorithm for detecting both intergenic and intragenic NCL events (filterjunctions.py was applied to extracting circRNA candidates),.
    • segemenhl (version 0.2.0), an algorithm for detecting both intergenic and intragenic NCL events (filterjunctions.py was applied to extracting circRNA candidates), http://www.bioinf.uni-leipzig.de/Software/segemehl/.
  • 6
    • 84939468148 scopus 로고    scopus 로고
    • (version 1.0), an algorithm for detecting circRNAs,.
    • find_circ (version 1.0), an algorithm for detecting circRNAs, https://github.com/bioxfu/circRNAFinder/blob/master/src/find_circ.py.
  • 7
    • 84939469415 scopus 로고    scopus 로고
    • (version 1.1), an algorithm for detecting circRNAs,.
    • CIRI (version 1.1), an algorithm for detecting circRNAs, http://sourceforge.net/projects/ciri/.
  • 8
    • 84939466112 scopus 로고    scopus 로고
    • the simulated datasets that were generated in this study for evaluation of the sensitivity and precision of the circRNA-detecting tools examined
    • Simulated datasets, the simulated datasets that were generated in this study for evaluation of the sensitivity and precision of the circRNA-detecting tools examined, ftp://treeslab1.genomics.sinica.edu.tw/simulated_expression/.
  • 9
    • 0017180370 scopus 로고
    • Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures
    • Sanger HL, Klotz G, Riesner D, Gross HJ, Kleinschmidt AK. Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures. Proc Natl Acad Sci USA 1976, 73:3852-3856.
    • (1976) Proc Natl Acad Sci USA , vol.73 , pp. 3852-3856
    • Sanger, H.L.1    Klotz, G.2    Riesner, D.3    Gross, H.J.4    Kleinschmidt, A.K.5
  • 10
    • 77949421377 scopus 로고    scopus 로고
    • Origin of hepatitis delta virus
    • Taylor J, Pelchat M. Origin of hepatitis delta virus. Future Microbiol 2010, 5:393-402.
    • (2010) Future Microbiol , vol.5 , pp. 393-402
    • Taylor, J.1    Pelchat, M.2
  • 11
    • 0019430645 scopus 로고
    • The intervening sequence of the ribosomal RNA precursor is converted to a circular RNA in isolated nuclei of Tetrahymena
    • Grabowski PJ, Zaug AJ, Cech TR. The intervening sequence of the ribosomal RNA precursor is converted to a circular RNA in isolated nuclei of Tetrahymena. Cell 1981, 23:467-476.
    • (1981) Cell , vol.23 , pp. 467-476
    • Grabowski, P.J.1    Zaug, A.J.2    Cech, T.R.3
  • 12
    • 0038049910 scopus 로고    scopus 로고
    • Group II introns: structure and catalytic versatility of large natural ribozymes
    • Lehmann K, Schmidt U. Group II introns: structure and catalytic versatility of large natural ribozymes. Crit Rev Biochem Mol Biol 2003, 38:249-303.
    • (2003) Crit Rev Biochem Mol Biol , vol.38 , pp. 249-303
    • Lehmann, K.1    Schmidt, U.2
  • 13
    • 0026438985 scopus 로고
    • Protein-coding introns from the 23S rRNA-encoding gene form stable circles in the hyperthermophilic archaeon Pyrobaculum organotrophum
    • Dalgaard JZ, Garrett RA. Protein-coding introns from the 23S rRNA-encoding gene form stable circles in the hyperthermophilic archaeon Pyrobaculum organotrophum. Gene 1992, 121:103-110.
    • (1992) Gene , vol.121 , pp. 103-110
    • Dalgaard, J.Z.1    Garrett, R.A.2
  • 14
    • 84860171056 scopus 로고    scopus 로고
    • Transcriptome-wide discovery of circular RNAs in Archaea
    • Danan M, Schwartz S, Edelheit S, Sorek R. Transcriptome-wide discovery of circular RNAs in Archaea. Nucleic Acids Res 2012, 40:3131-3142.
    • (2012) Nucleic Acids Res , vol.40 , pp. 3131-3142
    • Danan, M.1    Schwartz, S.2    Edelheit, S.3    Sorek, R.4
  • 18
    • 84863045982 scopus 로고    scopus 로고
    • Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types
    • Salzman J, Gawad C, Wang PL, Lacayo N, Brown PO. Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS One 2012, 7:e30733.
    • (2012) PLoS One , vol.7 , pp. e30733
    • Salzman, J.1    Gawad, C.2    Wang, P.L.3    Lacayo, N.4    Brown, P.O.5
  • 23
  • 26
    • 84920511291 scopus 로고    scopus 로고
    • The Landscape of microRNA, Piwi-Interacting RNA, and circular RNA in human saliva
    • Bahn JH, Zhang Q, Li F, Chan TM, Lin X, Kim Y, Wong DT, Xiao X. The Landscape of microRNA, Piwi-Interacting RNA, and circular RNA in human saliva. Clin Chem 2015, 61:221-230.
    • (2015) Clin Chem , vol.61 , pp. 221-230
    • Bahn, J.H.1    Zhang, Q.2    Li, F.3    Chan, T.M.4    Lin, X.5    Kim, Y.6    Wong, D.T.7    Xiao, X.8
  • 31
    • 84956906428 scopus 로고    scopus 로고
    • Expanded identification and characterization of mammalian circular RNAs
    • Guo JU, Agarwal V, Guo H, Bartel DP. Expanded identification and characterization of mammalian circular RNAs. Genome Biol 2014, 15:409.
    • (2014) Genome Biol , vol.15 , pp. 409
    • Guo, J.U.1    Agarwal, V.2    Guo, H.3    Bartel, D.P.4
  • 34
    • 84937578024 scopus 로고    scopus 로고
    • CIRI: an efficient and unbiased algorithm for de novo circular RNA identification
    • Gao Y, Wang J, Zhao F. CIRI: an efficient and unbiased algorithm for de novo circular RNA identification. Genome Biol 2015, 16:4.
    • (2015) Genome Biol , vol.16 , pp. 4
    • Gao, Y.1    Wang, J.2    Zhao, F.3
  • 35
    • 80051507403 scopus 로고    scopus 로고
    • TopHat-Fusion: an algorithm for discovery of novel fusion transcripts
    • Kim D, Salzberg SL. TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. Genome Biol 2011, 12:R72.
    • (2011) Genome Biol , vol.12 , pp. R72
    • Kim, D.1    Salzberg, S.L.2
  • 37
    • 84894582458 scopus 로고    scopus 로고
    • A day in the life of the spliceosome
    • Matera AG, Wang Z. A day in the life of the spliceosome. Nat Rev Mol Cell Biol 2014, 15:108-121.
    • (2014) Nat Rev Mol Cell Biol , vol.15 , pp. 108-121
    • Matera, A.G.1    Wang, Z.2
  • 39
    • 84921368391 scopus 로고    scopus 로고
    • Efficient backsplicing produces translatable circular mRNAs
    • Wang Y, Wang Z. Efficient backsplicing produces translatable circular mRNAs. RNA 2015, 21:172-179.
    • (2015) RNA , vol.21 , pp. 172-179
    • Wang, Y.1    Wang, Z.2
  • 40
    • 84908093894 scopus 로고    scopus 로고
    • Short intronic repeat sequences facilitate circular RNA production
    • Liang D, Wilusz JE. Short intronic repeat sequences facilitate circular RNA production. Genes Dev 2014, 28:2233-2247.
    • (2014) Genes Dev , vol.28 , pp. 2233-2247
    • Liang, D.1    Wilusz, J.E.2
  • 41
    • 0029900081 scopus 로고    scopus 로고
    • Circular RNAs from transcripts of the rat cytochrome P450 2C24 gene: correlation with exon skipping
    • Zaphiropoulos PG. Circular RNAs from transcripts of the rat cytochrome P450 2C24 gene: correlation with exon skipping. Proc Natl Acad Sci USA 1996, 93:6536-6541.
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 6536-6541
    • Zaphiropoulos, P.G.1
  • 42
    • 0032976697 scopus 로고    scopus 로고
    • Circular dystrophin RNAs consisting of exons that were skipped by alternative splicing
    • 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, 8:493-500.
    • (1999) Hum Mol Genet , vol.8 , pp. 493-500
    • Surono, A.1    Takeshima, Y.2    Wibawa, T.3    Ikezawa, M.4    Nonaka, I.5    Matsuo, M.6
  • 43
    • 84870561895 scopus 로고    scopus 로고
    • Re-splicing of mature mRNA in cancer cells promotes activation of distant weak alternative splice sites
    • Kameyama T, Suzuki H, Mayeda A. Re-splicing of mature mRNA in cancer cells promotes activation of distant weak alternative splice sites. Nucleic Acids Res 2012, 40:7896-7906.
    • (2012) Nucleic Acids Res , vol.40 , pp. 7896-7906
    • Kameyama, T.1    Suzuki, H.2    Mayeda, A.3
  • 44
    • 0029585914 scopus 로고
    • Inverted repeats are necessary for circularization of the mouse testis Sry transcript
    • Dubin RA, Kazmi MA, Ostrer H. Inverted repeats are necessary for circularization of the mouse testis Sry transcript. Gene 1995, 167:245-248.
    • (1995) Gene , vol.167 , pp. 245-248
    • Dubin, R.A.1    Kazmi, M.A.2    Ostrer, H.3
  • 48
    • 84891681158 scopus 로고    scopus 로고
    • Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency
    • Wu CS, Yu CY, Chuang CY, Hsiao M, Kao CF, Kuo HC, Chuang TJ. Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency. Genome Res 2014, 24:25-36.
    • (2014) Genome Res , vol.24 , pp. 25-36
    • Wu, C.S.1    Yu, C.Y.2    Chuang, C.Y.3    Hsiao, M.4    Kao, C.F.5    Kuo, H.C.6    Chuang, T.J.7
  • 49
    • 84906275961 scopus 로고    scopus 로고
    • Is an observed non-co-linear RNA product spliced in trans, in cis or just in vitro?
    • Yu CY, Liu HJ, Hung LY, Kuo HC, Chuang TJ. Is an observed non-co-linear RNA product spliced in trans, in cis or just in vitro? Nucleic Acids Res 2014, 42:9410-9423.
    • (2014) Nucleic Acids Res , vol.42 , pp. 9410-9423
    • Yu, C.Y.1    Liu, H.J.2    Hung, L.Y.3    Kuo, H.C.4    Chuang, T.J.5
  • 51
    • 84901423529 scopus 로고    scopus 로고
    • A view of pre-mRNA splicing from RNase R resistant RNAs
    • Suzuki H, Tsukahara T. A view of pre-mRNA splicing from RNase R resistant RNAs. Int J Mol Sci 2014, 15:9331-9342.
    • (2014) Int J Mol Sci , vol.15 , pp. 9331-9342
    • Suzuki, H.1    Tsukahara, T.2
  • 52
    • 54149091257 scopus 로고    scopus 로고
    • Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail
    • Marzluff WF, Wagner EJ, Duronio RJ. Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail. Nat Rev Genet 2008, 9:843-854.
    • (2008) Nat Rev Genet , vol.9 , pp. 843-854
    • Marzluff, W.F.1    Wagner, E.J.2    Duronio, R.J.3
  • 54
    • 84900322651 scopus 로고    scopus 로고
    • Detecting and characterizing circular RNAs
    • Jeck WR, Sharpless NE. Detecting and characterizing circular RNAs. Nat Biotechnol 2014, 32:453-461.
    • (2014) Nat Biotechnol , vol.32 , pp. 453-461
    • Jeck, W.R.1    Sharpless, N.E.2
  • 56
    • 84889000676 scopus 로고    scopus 로고
    • Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives
    • Wang Q, Xia J, Jia P, Pao W, Zhao Z. Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives. Brief Bioinform 2013, 14:506-519.
    • (2013) Brief Bioinform , vol.14 , pp. 506-519
    • Wang, Q.1    Xia, J.2    Jia, P.3    Pao, W.4    Zhao, Z.5
  • 57
    • 84868332770 scopus 로고    scopus 로고
    • nFuse: discovery of complex genomic rearrangements in cancer using high-throughput sequencing
    • McPherson A, Wu C, Wyatt AW, Shah S, Collins C, Sahinalp SC. nFuse: discovery of complex genomic rearrangements in cancer using high-throughput sequencing. Genome Res 2012, 22:2250-2261.
    • (2012) Genome Res , vol.22 , pp. 2250-2261
    • McPherson, A.1    Wu, C.2    Wyatt, A.W.3    Shah, S.4    Collins, C.5    Sahinalp, S.C.6
  • 58
    • 84887612694 scopus 로고    scopus 로고
    • Fusion genes and their discovery using high throughput sequencing
    • Annala MJ, Parker BC, Zhang W, Nykter M. Fusion genes and their discovery using high throughput sequencing. Cancer Lett 2013, 340:192-200.
    • (2013) Cancer Lett , vol.340 , pp. 192-200
    • Annala, M.J.1    Parker, B.C.2    Zhang, W.3    Nykter, M.4
  • 59
    • 77957893329 scopus 로고    scopus 로고
    • Apparent non-canonical trans-splicing is generated by reverse transcriptase in vitro
    • Houseley J, Tollervey D. Apparent non-canonical trans-splicing is generated by reverse transcriptase in vitro. PLoS One 2010, 5:e12271.
    • (2010) PLoS One , vol.5 , pp. e12271
    • Houseley, J.1    Tollervey, D.2
  • 61
    • 33746683274 scopus 로고    scopus 로고
    • Reverse transcriptase template switching and false alternative transcripts
    • Cocquet J, Chong A, Zhang G, Veitia RA. Reverse transcriptase template switching and false alternative transcripts. Genomics 2006, 88:127-131.
    • (2006) Genomics , vol.88 , pp. 127-131
    • Cocquet, J.1    Chong, A.2    Zhang, G.3    Veitia, R.A.4
  • 62
    • 0026665434 scopus 로고
    • Temperature-dependent template switching during in vitro cDNA synthesis by the AMV-reverse transcriptase
    • Ouhammouch M, Brody EN. Temperature-dependent template switching during in vitro cDNA synthesis by the AMV-reverse transcriptase. Nucleic Acids Res 1992, 20:5443-5450.
    • (1992) Nucleic Acids Res , vol.20 , pp. 5443-5450
    • Ouhammouch, M.1    Brody, E.N.2
  • 64
    • 84911491114 scopus 로고    scopus 로고
    • Circular RNAs: diversity of form and function
    • Lasda E, Parker R. Circular RNAs: diversity of form and function. RNA 2014, 20:1829-1842.
    • (2014) RNA , vol.20 , pp. 1829-1842
    • Lasda, E.1    Parker, R.2
  • 65
    • 79957460169 scopus 로고    scopus 로고
    • A novel and well-defined benchmarking method for second generation read mapping
    • Holtgrewe M, Emde AK, Weese D, Reinert K. A novel and well-defined benchmarking method for second generation read mapping. BMC Bioinformatics 2011, 12:210.
    • (2011) BMC Bioinformatics , vol.12 , pp. 210
    • Holtgrewe, M.1    Emde, A.K.2    Weese, D.3    Reinert, K.4
  • 66
    • 79960126958 scopus 로고    scopus 로고
    • FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution
    • Ge H, Liu K, Juan T, Fang F, Newman M, Hoeck W. FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution. Bioinformatics 2011, 27:1922-1928.
    • (2011) Bioinformatics , vol.27 , pp. 1922-1928
    • Ge, H.1    Liu, K.2    Juan, T.3    Fang, F.4    Newman, M.5    Hoeck, W.6
  • 67
    • 84908128765 scopus 로고    scopus 로고
    • circBase: a database for circular RNAs
    • Glazar P, Papavasileiou P, Rajewsky N. circBase: a database for circular RNAs. RNA 2014, 20:1666-1670.
    • (2014) RNA , vol.20 , pp. 1666-1670
    • Glazar, P.1    Papavasileiou, P.2    Rajewsky, N.3
  • 70
    • 0029053190 scopus 로고
    • Initiation of protein synthesis by the eukaryotic translational apparatus on circular RNAs
    • Chen CY, Sarnow P. Initiation of protein synthesis by the eukaryotic translational apparatus on circular RNAs. Science 1995, 268:415-417.
    • (1995) Science , vol.268 , pp. 415-417
    • Chen, C.Y.1    Sarnow, P.2
  • 71
    • 0031718582 scopus 로고    scopus 로고
    • Circular mRNA can direct translation of extremely long repeating-sequence proteins in vivo
    • Perriman R, Ares M Jr. Circular mRNA can direct translation of extremely long repeating-sequence proteins in vivo. RNA 1998, 4:1047-1054.
    • (1998) RNA , vol.4 , pp. 1047-1054
    • Perriman, R.1    Ares, M.2
  • 74
    • 84906251756 scopus 로고    scopus 로고
    • Circular RNAs are depleted of polymorphisms at microRNA binding sites
    • Thomas LF, Saetrom P. Circular RNAs are depleted of polymorphisms at microRNA binding sites. Bioinformatics 2014, 30:2243-2246.
    • (2014) Bioinformatics , vol.30 , pp. 2243-2246
    • Thomas, L.F.1    Saetrom, P.2
  • 76
    • 84875962753 scopus 로고    scopus 로고
    • Circular RNAs: splicing's enigma variations
    • Hentze MW, Preiss T. Circular RNAs: splicing's enigma variations. EMBO J 2013, 32:923-925.
    • (2013) EMBO J , vol.32 , pp. 923-925
    • Hentze, M.W.1    Preiss, T.2
  • 77
    • 0026661135 scopus 로고
    • A spliced intron accumulates as a lariat in the nucleus of T cells
    • Qian L, Vu MN, Carter M, Wilkinson MF. A spliced intron accumulates as a lariat in the nucleus of T cells. Nucleic Acids Res 1992, 20:5345-5350.
    • (1992) Nucleic Acids Res , vol.20 , pp. 5345-5350
    • Qian, L.1    Vu, M.N.2    Carter, M.3    Wilkinson, M.F.4
  • 78
    • 0026655632 scopus 로고
    • Introns excised from the delta primary transcript are localized near sites of Delta transcription
    • Kopczynski CC, Muskavitch MA. Introns excised from the delta primary transcript are localized near sites of Delta transcription. J Cell Biol 1992, 119:503-512.
    • (1992) J Cell Biol , vol.119 , pp. 503-512
    • Kopczynski, C.C.1    Muskavitch, M.A.2
  • 79
    • 84919454027 scopus 로고    scopus 로고
    • MBNL proteins and their target RNAs, interaction and splicing regulation
    • Konieczny P, Stepniak-Konieczna E, Sobczak K. MBNL proteins and their target RNAs, interaction and splicing regulation. Nucleic Acids Res 2014, 42:10873-10887.
    • (2014) Nucleic Acids Res , vol.42 , pp. 10873-10887
    • Konieczny, P.1    Stepniak-Konieczna, E.2    Sobczak, K.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.