Chuang TJ, Wu CS, Chen CY, Hung LY, Chiang TW, Yang MY. NCLscan: accurate identification of non-co-linear transcripts (fusion, trans-splicing and circular RNA) with a good balance between sensitivity and precision. Nucleic Acids Res. 2016;44(3):e29.
Article
PubMed
Google Scholar
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(14):9410–23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gingeras TR. Implications of chimaeric non-co-linear transcripts. Nature. 2009;461(7261):206–11.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen I, Chen CY, Chuang TJ. Biogenesis, identification, and function of exonic circular RNAs. Wiley Interdiscip Rev RNA. 2015;6(5):563–79.
Article
CAS
PubMed
PubMed Central
Google Scholar
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(2):141–57.
Article
CAS
PubMed
PubMed Central
Google Scholar
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(7441):333–8.
Article
CAS
PubMed
Google Scholar
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(1):25–36.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen LL. The biogenesis and emerging roles of circular RNAs. Nat Rev Mol Cell Biol. 2016;17(4):205–11.
Article
CAS
PubMed
Google Scholar
Chwalenia K, Facemire L, Li H. Chimeric RNAs in cancer and normal physiology. Wiley Interdiscip Rev RNA. 2017;8(6):e1427.
Shtivelman E, Lifshitz B, Gale RP, Canaani E. Fused transcript of abl and bcr genes in chronic myelogenous leukaemia. Nature. 1985;315(6020):550–4.
Article
CAS
PubMed
Google Scholar
Mitelman F, Johansson B, Mertens F. Fusion genes and rearranged genes as a linear function of chromosome aberrations in cancer. Nat Genet. 2004;36(4):331–4.
Article
CAS
PubMed
Google Scholar
Mitelman F, Johansson B, Mertens F. The impact of translocations and gene fusions on cancer causation. Nat Rev Cancer. 2007;7(4):233–45.
Article
CAS
PubMed
Google Scholar
Frohling S, Dohner H. Chromosomal abnormalities in cancer. N Engl J Med. 2008;359(7):722–34.
Article
CAS
PubMed
Google Scholar
O'Brien SG, Guilhot F, Larson RA, Gathmann I, Baccarani M, Cervantes F, Cornelissen JJ, Fischer T, Hochhaus A, Hughes T, et al. Imatinib compared with interferon and low-dose cytarabine for newly diagnosed chronic-phase chronic myeloid leukemia. N Engl J Med. 2003;348(11):994–1004.
Article
CAS
PubMed
Google Scholar
Druker BJ, Guilhot F, O'Brien SG, Gathmann I, Kantarjian H, Gattermann N, Deininger MW, Silver RT, Goldman JM, Stone RM, et al. Five-year follow-up of patients receiving imatinib for chronic myeloid leukemia. N Engl J Med. 2006;355(23):2408–17.
Article
CAS
PubMed
Google Scholar
Tkachuk DC, Westbrook CA, Andreeff M, Donlon TA, Cleary ML, Suryanarayan K, Homge M, Redner A, Gray J, Pinkel D. Detection of bcr-abl fusion in chronic myelogeneous leukemia by in situ hybridization. Science. 1990;250(4980):559–62.
Article
CAS
PubMed
Google Scholar
Westbrook CA, Hooberman AL, Spino C, Dodge RK, Larson RA, Davey F, Wurster-Hill DH, Sobol RE, Schiffer C, Bloomfield CD. Clinical significance of the BCR-ABL fusion gene in adult acute lymphoblastic leukemia: a Cancer and leukemia group B study (8762). Blood. 1992;80(12):2983–90.
CAS
PubMed
Google Scholar
Li H, Wang J, Mor G, Sklar J. A neoplastic gene fusion mimics trans-splicing of RNAs in normal human cells. Science. 2008;321(5894):1357–61.
Article
CAS
PubMed
Google Scholar
Schoenfelder S, Clay I, Fraser P. The transcriptional interactome: gene expression in 3D. Curr Opin Genet Dev. 2010;20(2):127–33.
Article
CAS
PubMed
Google Scholar
Rickman DS, Pflueger D, Moss B, VanDoren VE, Chen CX, de la Taille A, Kuefer R, Tewari AK, Setlur SR, Demichelis F, et al. SLC45A3-ELK4 is a novel and frequent erythroblast transformation-specific fusion transcript in prostate cancer. Cancer Res. 2009;69(7):2734–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yu CY, Kuo HC. The trans-spliced long noncoding RNA tsRMST impedes human embryonic stem cell differentiation through WNT5A-mediated inhibition of the epithelial-to-mesenchymal transition. Stem Cells. 2016;34(8):2052–62.
Article
CAS
PubMed
Google Scholar
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(2):e30733.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang PL, Bao Y, Yee MC, Barrett SP, Hogan GJ, Olsen MN, Dinneny JR, Brown PO, Salzman J. Circular RNA is expressed across the eukaryotic tree of life. PLoS One. 2014;9(3):e90859.
Article
PubMed
PubMed Central
Google Scholar
Guo JU, Agarwal V, Guo H, Bartel DP. Expanded identification and characterization of mammalian circular RNAs. Genome Biol. 2014;15(7):409.
Article
PubMed
PubMed Central
Google Scholar
Gao Y, Wang J, Zhao F. CIRI: an efficient and unbiased algorithm for de novo circular RNA identification. Genome Biol. 2015;16(1):4.
Article
CAS
PubMed
PubMed Central
Google Scholar
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(5):870–85.
Article
CAS
PubMed
Google Scholar
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(3):1370–83.
Article
CAS
PubMed
Google Scholar
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(7441):384–8.
Article
CAS
PubMed
Google Scholar
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.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zheng J, Liu X, Xue Y, Gong W, Ma J, Xi Z, Que Z, Liu Y. TTBK2 circular RNA promotes glioma malignancy by regulating miR-217/HNF1beta/Derlin-1 pathway. J Hematol Oncol. 2017;10(1):52.
Article
PubMed
PubMed Central
Google Scholar
Yang W, Du WW, Li X, Yee AJ, Yang BB. Foxo3 activity promoted by non-coding effects of circular RNA and Foxo3 pseudogene in the inhibition of tumor growth and angiogenesis. Oncogene. 2016;35(30):3919–31.
Article
CAS
PubMed
Google Scholar
Hsiao KY, Lin YC, Gupta SK, Chang N, Yen L, Sun HS, Tsai SJ. Non-coding effects of circular RNA CCDC66 promote colon cancer growth and metastasis. Cancer Res. 2017;77:2339–50.
Article
CAS
PubMed
PubMed Central
Google Scholar
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(1):55–66.
Article
CAS
PubMed
Google Scholar
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(3):256–64.
Article
PubMed
Google Scholar
Zhang Y, Zhang XO, Chen T, Xiang JF, Yin QF, Xing YH, Zhu S, Yang L, Chen LL. Circular intronic long noncoding RNAs. Mol Cell. 2013;51(6):792–806.
Article
CAS
PubMed
Google Scholar
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(6):1125–34.
Article
CAS
PubMed
Google Scholar
Szabo L, Morey R, Palpant NJ, Wang PL, Afari N, Jiang C, Parast MM, Murry CE, Laurent LC, Salzman J. Statistically based splicing detection reveals neural enrichment and tissue-specific induction of circular RNA during human fetal development. Genome Biol. 2015;16:126.
Article
PubMed
PubMed Central
Google Scholar
Gruner H, Cortes-Lopez M, Cooper DA, Bauer M, Miura P. CircRNA accumulation in the aging mouse brain. Sci Rep. 2016;6:38907.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhu M, Xu Y, Chen Y, Yan F, Circular BANP. An upregulated circular RNA that modulates cell proliferation in colorectal cancer. Biomed Pharmacother. 2017;88:138–44.
Article
CAS
PubMed
Google Scholar
Kim P, Yoon S, Kim N, Lee S, Ko M, Lee H, Kang H, Kim J. ChimerDB 2.0--a knowledgebase for fusion genes updated. Nucleic Acids Res. 2010;38(Database issue):D81–5.
Article
CAS
PubMed
Google Scholar
Ha KC, Lalonde E, Li L, Cavallone L, Natrajan R, Lambros MB, Mitsopoulos C, Hakas J, Kozarewa I, Fenwick K, et al. Identification of gene fusion transcripts by transcriptome sequencing in BRCA1-mutated breast cancers and cell lines. BMC Med Genet. 2011;4:75.
CAS
Google Scholar
McManus CJ, Duff MO, Eipper-Mains J, Graveley BR. Global analysis of trans-splicing in Drosophila. Proc Natl Acad Sci U S A. 2010;107(29):12975–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang G, Guo G, Hu X, Zhang Y, Li Q, Li R, Zhuang R, Lu Z, He Z, Fang X, et al. Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Res. 2010;20(5):646–54.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhao Q, Caballero OL, Levy S, Stevenson BJ, Iseli C, de Souza SJ, Galante PA, Busam D, Leversha MA, Chadalavada K, et al. Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line. Proc Natl Acad Sci U S A. 2009;106(6):1886–91.
Article
CAS
PubMed
PubMed Central
Google Scholar
Maher CA, Kumar-Sinha C, Cao X, Kalyana-Sundaram S, Han B, Jing X, Sam L, Barrette T, Palanisamy N, Chinnaiyan AM. Transcriptome sequencing to detect gene fusions in cancer. Nature. 2009;458(7234):97–101.
Article
CAS
PubMed
PubMed Central
Google Scholar
Maher CA, Palanisamy N, Brenner JC, Cao X, Kalyana-Sundaram S, Luo S, Khrebtukova I, Barrette TR, Grasso C, Yu J, et al. Chimeric transcript discovery by paired-end transcriptome sequencing. Proc Natl Acad Sci U S A. 2009;106(30):12353–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ma L, Yang S, Zhao W, Tang Z, Zhang T, Li K. Identification and analysis of pig chimeric mRNAs using RNA sequencing data. BMC Genomics. 2012;13:429.
Article
CAS
PubMed
PubMed Central
Google Scholar
Inaki K, Hillmer AM, Ukil L, Yao F, Woo XY, Vardy LA, Zawack KF, Lee CW, Ariyaratne PN, Chan YS, et al. Transcriptional consequences of genomic structural aberrations in breast cancer. Genome Res. 2011;21(5):676–87.
Article
CAS
PubMed
PubMed Central
Google Scholar
Al-Balool HH, Weber D, Liu Y, Wade M, Guleria K, Nam PL, Clayton J, Rowe W, Coxhead J, Irving J, et al. Post-transcriptional exon shuffling events in humans can be evolutionarily conserved and abundant. Genome Res. 2011;21(11):1788–99.
Article
CAS
PubMed
PubMed Central
Google Scholar
Glazar P, Papavasileiou P, Rajewsky N. circBase: a database for circular RNAs. RNA. 2014;20(11):1666–70.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zeng X, Lin W, Guo M, Zou Q. A comprehensive overview and evaluation of circular RNA detection tools. PLoS Comput Biol. 2017;13(6):e1005420.
Article
PubMed
PubMed Central
Google Scholar
Abate F, Acquaviva A, Paciello G, Foti C, Ficarra E, Ferrarini A, Delledonne M, Iacobucci I, Soverini S, Martinelli G, et al. Bellerophontes: an RNA-Seq data analysis framework for chimeric transcripts discovery based on accurate fusion model. Bioinformatics. 2012;28(16):2114–21.
Article
CAS
PubMed
Google Scholar
Carrara M, Beccuti M, Cavallo F, Donatelli S, Lazzarato F, Cordero F, Calogero RA. State of art fusion-finder algorithms are suitable to detect transcription-induced chimeras in normal tissues? BMC Bioinformatics. 2013;14(Suppl 7):S2.
Article
PubMed
PubMed Central
Google Scholar
Cocquerelle C, Mascrez B, Hetuin D, Bailleul B. Mis-splicing yields circular RNA molecules. FASEB Journal. 1993;7(1):155–60.
Article
CAS
PubMed
Google Scholar
Hansen TB, Veno MT, Damgaard CK, Kjems J. Comparison of circular RNA prediction tools. Nucleic Acids Res. 2016;44(6):e58.
Article
PubMed
Google Scholar
Kumar S, Vo AD, Qin F, Li H. Comparative assessment of methods for the fusion transcripts detection from RNA-Seq data. Sci Rep. 2016;6:21597.
Article
CAS
PubMed
PubMed Central
Google Scholar
Song X, Zhang N, Han P, Moon BS, Lai RK, Wang K, Lu W. Circular RNA profile in gliomas revealed by identification tool UROBORUS. Nucleic Acids Res. 2016;44(9):e87.
Article
PubMed
PubMed Central
Google Scholar
Jia W, Qiu K, He M, Song P, Zhou Q, Zhou F, Yu Y, Zhu D, Nickerson ML, Wan S, et al. SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data. Genome Biol. 2013;14(2):R12.
Article
PubMed
PubMed Central
Google Scholar
Chuang TJ, Chen YJ, Chen CY, Mai TL, Wang YD, Yeh CS, Yang MY, Hsiao YT, Chang TH, Kuo TC, et al. Integrative transcriptome sequencing reveals extensive alternative trans-splicing and cis-backsplicing in human cells. Nucleic Acids Res. 2018;46(7):3671–91.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen C-Y, Chuang T-J. Comment on A comprehensive overview and evaluation of circular RNA detection tools. PLoS Comp Biol. 2018; in press.
Kent WJ. BLAT--the BLAST-like alignment tool. Genome Res. 2002;12(4):656–64.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15–21.
Article
CAS
PubMed
Google Scholar
Chuang TJ, Chen FC, Chen YZ. Position-dependent correlations between DNA methylation and the evolutionary rates of mammalian coding exons. Proc Natl Acad Sci U S A. 2012;109(39):15841–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Veno MT, Hansen TB, Veno ST, Clausen BH, Grebing M, Finsen B, Holm IE, Kjems J. Spatio-temporal regulation of circular RNA expression during porcine embryonic brain development. Genome Biol. 2015;16:245.
Article
PubMed
PubMed Central
Google Scholar
Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011;12:323.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011;478(7370):476–82.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lin MF, Kheradpour P, Washietl S, Parker BJ, Pedersen JS, Kellis M. Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes. Genome Res. 2011;21(11):1916–28.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hoffmann S, Otto C, Doose G, Tanzer A, Langenberger D, Christ S, Kunz M, Holdt LM, Teupser D, Hackermuller J, et al. A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection. Genome Biol. 2014;15(2):R34.
Article
PubMed
PubMed Central
Google Scholar
Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, Savich GL, He X, Mieczkowski P, Grimm SA, Perou CM, et al. MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res. 2010;38(18):e178.
Article
PubMed
PubMed Central
Google Scholar
Shao X, Shepelev V, Fedorov A. Bioinformatic analysis of exon repetition, exon scrambling and trans-splicing in humans. Bioinformatics. 2006;22(6):692–8.
Article
CAS
PubMed
Google Scholar
Ozsolak F, Milos PM. RNA sequencing: advances, challenges and opportunities. Nat Rev. 2011;12(2):87–98.
Article
CAS
Google Scholar
Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM, Howald C, Foissac S, Ucla C, Chrast J, et al. Evidence for transcript networks composed of chimeric RNAs in human cells. PLoS One. 2012;7(1):e28213.
Article
CAS
PubMed
PubMed Central
Google Scholar
Houseley J, Tollervey D. Apparent non-canonical trans-splicing is generated by reverse transcriptase in vitro. PLoS One. 2010;5(8):e12271.
Article
PubMed
PubMed Central
Google Scholar
Kong Y, Zhou H, Yu Y, Chen L, Hao P, Li X. The evolutionary landscape of intergenic trans-splicing events in insects. Nat Commun. 2015;6:8734.
Article
CAS
PubMed
Google Scholar
McPherson A, Wu C, Hajirasouliha I, Hormozdiari F, Hach F, Lapuk A, Volik S, Shah S, Collins C, Sahinalp SC. Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data. Bioinformatics. 2011;27(11):1481–8.
Article
CAS
PubMed
Google Scholar
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(4):506–19.
Article
CAS
PubMed
Google Scholar
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(11):2250–61.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen K, Navin NE, Wang Y, Schmidt HK, Wallis JW, Niu B, Fan X, Zhao H, McLellan MD, Hoadley KA, et al. BreakTrans: uncovering the genomic architecture of gene fusions. Genome Biol. 2013;14(8):R87.
Article
PubMed
PubMed Central
Google Scholar
Zhang J, White NM, Schmidt HK, Fulton RS, Tomlinson C, Warren WC, Wilson RK, Maher CA. INTEGRATE: gene fusion discovery using whole genome and transcriptome data. Genome Res. 2016;26(1):108–18.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ma C, Shao M, Kingsford C. SQUID: transcriptomic structural variation detection from RNA-seq. Genome Biol. 2018;19(1):52.
Article
PubMed
PubMed Central
Google Scholar