Amara SG, Jonas V, Rosenfeld MG, Ong ES, Evans RM. Alternative RNA processing in calcitonin gene expression generates MRNAs encoding different polypeptide products. Nature. 1982;298(5871):240–4. https://doi.org/10.1038/298240a0.
Article
CAS
PubMed
Google Scholar
Bass AJ, Thorsson V, Shmulevich I, Reynolds SM, Miller M, Bernard B, Hinoue T, et al. Comprehensive molecular characterization of gastric adenocarcinoma. Nature. 2014;513(7517):202–9. https://doi.org/10.1038/nature13480.
Article
PubMed Central
Google Scholar
Bentley DL. Coupling MRNA processing with transcription in time and space. Nat Rev Genet. 2014;15(3):163–75 https://doi.org/10.1038/nrg3662.
Article
CAS
PubMed
PubMed Central
Google Scholar
Boise LH, González-García M, Postema CE, Ding L, Lindsten T, Turka LA, Mao X, Nuñez G, Thompson CB. Bcl-x, a Bcl-2-related gene that functions as a dominant regulator of apoptotic cell death. Cell. 1993;74(4):597–608. https://doi.org/10.1016/0092-8674(93)90508-N.
Article
CAS
PubMed
Google Scholar
Cartegni L, Wang J, Zhu Z, Zhang MQ, Krainer AR. ESEfinder: a web resource to identify Exonic splicing enhancers. Nucleic Acids Res. 2003;31(13):3568–71. https://doi.org/10.1093/nar/gkg616.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen S, Huang V, Xu X, Livingstone J, Soares F, Jeon J, Zeng Y, et al. Widespread and functional RNA circularization in localized prostate Cancer. Cell. 2019;176(4):831–843.e22 https://doi.org/10.1016/j.cell.2019.01.025.
Article
CAS
PubMed
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. https://doi.org/10.1093/bioinformatics/bts635.
CAS
PubMed
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. https://doi.org/10.1186/s13059-014-0571-3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Grossman RL, Heath AP, Ferretti V, Varmus HE, Lowy DR, Kibbe WA, Staudt LM. Toward a shared vision for Cancer genomic data. N Engl J Med. 2016;375(12):1109–12 https://doi.org/10.1056/NEJMp1607591.
Article
PubMed
PubMed Central
Google Scholar
Hammes A, Guo J-K, Lutsch G, Leheste J-R, Landrock D, Ziegler U, Gubler M-C, Schedl A. Two splice variants of the Wilms’ tumor 1 gene have distinct functions during sex determination and nephron formation. Cell. 2001;106(3):319–29 https://doi.org/10.1016/S0092-8674(01)00453-6.
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 https://doi.org/10.1038/nature11993.
Article
CAS
PubMed
Google Scholar
Ivanov A, Memczak S, Wyler E, Francesca Torti HT, Porath MR, Orejuela MP, et al. Analysis of intron sequences reveals hallmarks of circular RNA biogenesis in animals. Cell Rep. 2015;10(2):170–7. https://doi.org/10.1016/J.CELREP.2014.12.019.
Article
CAS
PubMed
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 (New York, NY). 2013;19(2):141–57. https://doi.org/10.1261/rna.035667.112.
Article
CAS
Google Scholar
Krainer AR, Conway GC, Kozak D. The essential pre-MRNA splicing factor SF2 influences 5′ splice site selection by activating proximal sites. Cell. 1990;62(1):35–42 https://doi.org/10.1016/0092-8674(90)90237-9.
Article
CAS
PubMed
Google Scholar
Lasda, Erika, and Roy Parker. 2016. “Circular RNAs co-precipitate with extracellular vesicles: a possible mechanism for CircRNA clearance.” edited by Pierre Busson. PLoS One 11 (2): e0148407. https://doi.org/10.1371/journal.pone.0148407.
Legnini I, Di Timoteo G, Rossi F, Morlando M, Briganti F, Sthandier O, Fatica A, et al. Circ-ZNF609 is a circular RNA that can be translated and functions in Myogenesis. Mol Cell. 2017;66(1):22–37.e9. https://doi.org/10.1016/j.molcel.2017.02.017.
Article
CAS
PubMed
PubMed Central
Google Scholar
Levine AJ, Momand J, Finlay CA. The P53 tumour suppressor gene. Nature. 1991;351(6326):453–6 https://doi.org/10.1038/351453a0.
Article
CAS
PubMed
Google Scholar
Li Y, Bor Y-c, Misawa Y, Xue Y, Rekosh D, Hammarskjöld M-L. An intron with a constitutive transport element is retained in a tap messenger RNA. Nature. 2006;443(7108):234–7 https://doi.org/10.1038/nature05107.
Article
CAS
PubMed
Google Scholar
Li Z, Huang C, Bao C, Chen L, Lin M, Wang X, Zhong G, et al. Exon-intron circular RNAs regulate transcription in the nucleus. Nat Struct Mol Biol. 2015;22(3):256–64 https://doi.org/10.1038/nsmb.2959.
Article
PubMed
Google Scholar
Marchionni MA, Goodearl ADJ, Chen MS, Bermingham-McDonogh O, Kirk C, Hendricks M, Danehy F, et al. Glial growth factors are alternatively spliced ErbB2 ligands expressed in the nervous system. Nature. 1993;362(6418):312–8 https://doi.org/10.1038/362312a0.
Article
CAS
PubMed
Google Scholar
Mayr C, Bartel DP. Widespread shortening of 3′UTRs by alternative cleavage and polyadenylation activates oncogenes in Cancer cells. Cell. 2009;138(4):673–84 https://doi.org/10.1016/J.CELL.2009.06.016.
Article
CAS
PubMed
PubMed Central
Google Scholar
Memczak S, Jens M, Elefsinioti A, Torti F, Krueger J, Rybak A, Maier L, et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 2013;495(7441):333–8 https://doi.org/10.1038/nature11928.
Article
CAS
PubMed
Google Scholar
O’Grady T, Cao S, Strong MJ, Concha M, Wang X, Splinter S, BonDurant MA, et al. Global bidirectional transcription of the Epstein-Barr virus genome during reactivation. J Virol. 2014;88(3):1604–16. https://doi.org/10.1128/JVI.02989-13.
Article
PubMed
PubMed Central
Google Scholar
Pamudurti NR, Bartok O, Jens M, Ashwal-Fluss R, Stottmeister C, Ruhe L, Hanan M, et al. Translation of CircRNAs. Mol Cell. 2017;66(1):9–21.e7. https://doi.org/10.1016/j.molcel.2017.02.021.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet. 2008;40(12):1413–5 https://doi.org/10.1038/ng.259.
Article
CAS
PubMed
Google Scholar
Rauscher F, Morris J, Tournay O, Cook D, Curran T, Hastie ND. Binding of the Wilms’ tumor locus zinc finger protein to the EGR-1 consensus sequence. Science. 1990;250(4985):1259–62 https://doi.org/10.1126/science.2244209.
Article
CAS
PubMed
Google Scholar
Ray D, Hilal Kazan KB, Cook MT, Weirauch HS, Najafabadi XL, Gueroussov S, et al. A compendium of RNA-binding motifs for decoding gene regulation. Nature. 2013;499(7457):172–7 https://doi.org/10.1038/nature12311.
Article
CAS
PubMed
PubMed Central
Google Scholar
Reed R, Maniatis T. A role for exon sequences and splice-site proximity in splice-site selection. Cell. 1986;46(5):681–90. https://doi.org/10.1016/0092-8674(86)90343-0.
Article
CAS
PubMed
Google Scholar
Rosenfeld MG, Mermod J-J, Amara SG, Swanson LW, Sawchenko PE, Rivier J, Vale WW, Evans RM. Production of a novel neuropeptide encoded by the calcitonin gene via tissue-specific RNA processing. Nature. 1983;304(5922):129–35 https://doi.org/10.1038/304129a0.
Article
CAS
PubMed
Google Scholar
Rybak-Wolf A, Stottmeister C, Glažar P, Jens M, Pino N, Giusti S, Hanan M, et al. Circular RNAs in the mammalian brain are highly abundant, conserved, and dynamically expressed. Mol Cell. 2015;58(5):870–85. https://doi.org/10.1016/j.molcel.2015.03.027.
Article
CAS
PubMed
Google Scholar
Salzman, Julia, Charles Gawad, Peter Lincoln Wang, Norman Lacayo, and Patrick O Brown. 2012. “Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types.” edited by Thomas Preiss. PLoS One 7 (2): e30733. https://doi.org/10.1371/journal.pone.0030733.
Singh R, Valcárcel J, Green MR. Distinct binding specificities and functions of higher eukaryotic Polypyrimidine tract-binding proteins. Science (New York, NY). 1995;268(5214):1173–6 https://doi.org/10.1126/SCIENCE.7761834.
Article
CAS
Google Scholar
Solnick D. Alternative splicing caused by RNA secondary structure. Cell. 1985;43(3):667–76 https://doi.org/10.1016/0092-8674(85)90239-9.
Article
CAS
PubMed
Google Scholar
Starke S, Jost I, Rossbach O, Schneider T, Schreiner S, Hung L-H, Bindereif A. Exon circularization requires canonical splice signals. Cell Rep. 2015;10(1):103–11 https://doi.org/10.1016/J.CELREP.2014.12.002.
Article
CAS
PubMed
Google Scholar
Ungerleider, Nathan, Monica Concha, Zhen Lin, Claire Roberts, Xia Wang, Subing Cao, Melody Baddoo, et al. 2018. “The Epstein Barr virus CircRNAome.” edited by Bryan R. Cullen. PLoS Pathog 14 (8): e1007206. https://doi.org/10.1371/journal.ppat.1007206.
van der Walt S, Chris Colbert S, Varoquaux G. The NumPy Array: a structure for efficient numerical computation. Computing in Science & Engineering. 2011;13(2):22–30 https://doi.org/10.1109/MCSE.2011.37.
Article
Google Scholar
Wahl MC, Will CL, Lührmann R. The spliceosome: design principles of a dynamic RNP machine. Cell. 2009;136(4):701–18 https://doi.org/10.1016/J.CELL.2009.02.009.
Article
CAS
PubMed
Google Scholar
Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB. Alternative isoform regulation in human tissue transcriptomes. Nature. 2008;456(7221):470–6. https://doi.org/10.1038/nature07509.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang Peter L, Yun Bao, Muh-Ching Yee, Steven P. Barrett, Gregory J. Hogan, Mari N. Olsen, José R. Dinneny, Patrick O. Brown, and Julia Salzman. 2014. “Circular RNA is expressed across the eukaryotic tree of life.” edited by Thomas Preiss. PLoS One 9 (3): e90859. https://doi.org/10.1371/journal.pone.0090859.
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(5):1966–80. https://doi.org/10.1016/J.CELREP.2014.10.062.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang X-O, Wang H-B, Zhang Y, Lu X, Chen L-L, Yang L. Complementary sequence-mediated exon circularization. Cell. 2014;159(1):134–47. https://doi.org/10.1016/J.CELL.2014.09.001.
Article
CAS
PubMed
Google Scholar
Zhang Y, Xue W, Li X, Zhang J, Chen S, Zhang J-L, Yang L, Chen L-L. The biogenesis of nascent circular RNAs. Cell Rep. 2016;15(3):611–24. https://doi.org/10.1016/j.celrep.2016.03.058.
Article
CAS
PubMed
Google Scholar
Zhuang Y, Weiner AM. A Compensatory Base change in human U2 SnRNA can suppress a branch site mutation. Genes Dev. 1989;3(10):1545–52. https://doi.org/10.1101/GAD.3.10.1545.
Article
CAS
PubMed
Google Scholar