What happens at or after transcription: Insights into circRNA biogenesis and function

References

• 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; PMID:22319583; http://dx.doi.org/10.1371/journal.pone.0030733
   PubMed Web of Science ®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; 495:333-8; PMID:23446348; http://dx.doi.org/10.1038/nature11928
   PubMed Web of Science ®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; 495:384-8; PMID:23446346; http://dx.doi.org/10.1038/nature11993
   PubMed Web of Science ®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:e90859; PMID:24609083; http://dx.doi.org/10.1371/journal.pone.0090859
   PubMed Web of Science ®Google Scholar
• 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; 9:1966-80; PMID:25544350; http://dx.doi.org/10.1016/j.celrep.2014.10.062
   PubMed Web of Science ®Google Scholar
• 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; 10:170-7; PMID:25558066; http://dx.doi.org/10.1016/j.celrep.2014.12.019
   PubMed Web of Science ®Google Scholar
• Chen L, Shan G. Circular RNAs remain peculiarly unclear in biogenesis and function. Sci China Life Sci 2015; 58(6):616-8; http://dx.doi.org/10.1007/s11427-015-4855-y
   PubMed Web of Science ®Google Scholar
• Chen L, Huang C, Wang X, Shan G. Circular RNAs in eukaryotic cells. Curr Genom 2015; 16(5): 312-8.
   Web of Science ®Google Scholar
• Moore MJ, Proudfoot NJ. Pre-mRNA processing reaches back to transcription and ahead to translation. Cell 2009; 136:688-700; PMID:19239889; http://dx.doi.org/10.1016/j.cell.2009.02.001
   PubMed Web of Science ®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; 56:55-66; PMID:25242144; http://dx.doi.org/10.1016/j.molcel.2014.08.019
   PubMed Web of Science ®Google Scholar
• Liang D, Wilusz JE. Short intronic repeat sequences facilitate circular RNA production. Genes Dev 2014; 28:2233-47; PMID:25281217; http://dx.doi.org/10.1101/gad.251926.114
   PubMed Web of Science ®Google Scholar
• Bentley DL. Rules of engagement: co-transcriptional recruitment of pre-mRNA processing factors. Curr Opin Cell Biol 2005; 17:251-6; PMID:15901493; http://dx.doi.org/10.1016/j.ceb.2005.04.006
   PubMed Web of Science ®Google Scholar
• Khodor YL, Menet JS, Tolan M, Rosbash M. Cotranscriptional splicing efficiency differs dramatically between Drosophila and mouse. RNA 2012; 18:2174-86; PMID:23097425; http://dx.doi.org/10.1261/rna.034090.112
   PubMed Web of Science ®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; 19:141-57; PMID:23249747; http://dx.doi.org/10.1261/rna.035667.112
   PubMed Web of Science ®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; 22:256-64; PMID:25664725; http://dx.doi.org/10.1038/nsmb.2959
   PubMed Web of Science ®Google Scholar
• Starke S, Jost I, Rossbach O, Schneider T, Schreiner S, Hung LH, Bindereif A. Exon circularization requires canonical splice signals. Cell Rep 2015; 10:103-11; PMID:25543144; http://dx.doi.org/10.1016/j.celrep.2014.12.002
   PubMed Web of Science ®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; 160:1125-34; PMID:25768908; http://dx.doi.org/10.1016/j.cell.2015.02.014
   PubMed Web of Science ®Google Scholar
• Guo JU, Agarwal V, Guo H, Bartel DP. Expanded identification and characterization of mammalian circular RNAs. Genome Biol 2014; 15:409; PMID:25070500; http://dx.doi.org/10.1186/s13059-014-0409-z
   PubMed Web of Science ®Google Scholar
• You X, Vlatkovic I, Babic A, Will T, Epstein I, Tushev G, Akbalik G, Wang M, Glock C, Quedenau C, et al. Neural circular RNAs are derived from synaptic genes and regulated by development and plasticity. Nat Neurosci 2015; 18:603-10; PMID:25714049; http://dx.doi.org/10.1038/nn.3975
   PubMed Web of Science ®Google Scholar
• Rybak-Wolf A, Stottmeister C, Glažar 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; S1097-2765: 00218-X; PMID:25921068
   PubMedGoogle Scholar
• Seraphin B, Rosbash M. Identification of functional U1 snRNA-pre-mRNA complexes committed to spliceosome assembly and splicing. Cell 1989; 59:349-358; PMID:2529976; http://dx.doi.org/10.1016/0092-8674(89)90296-1
   PubMed Web of Science ®Google Scholar
• Kwek KY, Murphy S, Furger A, Thomas B, O'Gorman W, Kimura H, Proudfoot NJ, Akoulitchev A. U1 snRNA associates with TFIIH and regulates transcriptional initiation. Nat Struct Biol 2002; 9:800-5; PMID:12389039
   PubMedGoogle Scholar
• Almada AE, Wu X, Kriz AJ, Burge CB, Sharp PA. Promoter directionality is controlled by U1 snRNP and polyadenylation signals. Nature 2013; 499:360-3; PMID:23792564; http://dx.doi.org/10.1038/nature12349
   PubMed Web of Science ®Google Scholar
• Berg MG, Singh LN, Younis I, Liu Q, Pinto AM, Kaida D, Zhang Z, Cho S, Sherrill-Mix S, Wan L, et al. U1 snRNP determines mRNA length and regulates isoform expression. Cell 2012; 150:53-64; PMID: 22770214; http://dx.doi.org/10.1016/j.cell.2012.05.029
   PubMed Web of Science ®Google Scholar
• Kaida D, Berg MG, Younis I, Kasim M, Singh LN, Wan L, Dreyfuss G. U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation. Nature 2010; 468:664-8; PMID:20881964; http://dx.doi.org/10.1038/nature09479
   PubMed Web of Science ®Google Scholar
• Goodrich JA, Kugel JF. Non-coding-RNA regulators of RNA polymerase II transcription. Nat Rev Mol Cell Biol 2006; 7:612-6; PMID:16723972; http://dx.doi.org/10.1038/nrm1946
   PubMed Web of Science ®Google Scholar
• Espinoza CA, Allen TA, Hieb AR, Kugel JF, Goodrich JA. B2 RNA binds directly to RNA polymerase II to repress transcript synthesis. Nat Struct Mol Biol 2004; 11:822-9; PMID:15300239; http://dx.doi.org/10.1038/nsmb812
   PubMed Web of Science ®Google Scholar
• Allen TA, Von Kaenel S, Goodrich JA, Kugel JF. The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock. Nat Struct Mol Biol 2004; 11:816-21; PMID:15300240; http://dx.doi.org/10.1038/nsmb813
   PubMed Web of Science ®Google Scholar
• Lee N, Moss WN, Yario TA, Steitz JA. EBV Noncoding RNA Binds Nascent RNA to Drive Host PAX5 to Viral DNA. Cell 2015; 160: 607-18; PMID:25662012; http://dx.doi.org/10.1016/j.cell.2015.01.015
   PubMed Web of Science ®Google Scholar
• Yang L, Lin C, Liu W, Zhang J, Ohgi KA, Grinstein JD, Dorrestein PC, Rosenfeld MG. ncRNA- and Pc2 methylation-dependent gene relocation between nuclear structures mediates gene activation programs. Cell 2011; 147: 773-88; PMID:22078878; http://dx.doi.org/10.1016/j.cell.2011.08.054
   PubMed Web of Science ®Google Scholar
• Kuwabara T, Hsieh J, Nakashima K, Taira K, Gage FH. A small modulatory dsRNA specifies the fate of adult neural stem cells. Cell 2004; 116:779-93; PMID:15035981; http://dx.doi.org/10.1016/S0092-8674(04)00248-X
   PubMed Web of Science ®Google Scholar
• Yang Z, Zhu Q, Luo K, Zhou Q. The 7SK small nuclear RNA inhibits the CDK9/cyclin T1 kinase to control transcription. Nature 2001; 414:317-22; PMID: 11713532; http://dx.doi.org/10.1038/35104575
   PubMed Web of Science ®Google Scholar
• Cech TR, Steitz JA.The noncoding RNA revolution-trashing old rules to forge new ones.Cell 2014; 157:77-94; PMID:24679528; http://dx.doi.org/10.1016/j.cell.2014.03.008
   PubMed Web of Science ®Google Scholar
• Guil S, Esteller M. RNA-RNA interactions in gene regulation: the coding and noncoding players. Trends Biochem Sci 2015; 40:248-56; PMID:25818326; http://dx.doi.org/10.1016/j.tibs.2015.03.001
   PubMed Web of Science ®Google Scholar
• Vincent HA, Deutscher MP. Substrate recognition and catalysis by the exoribonuclease RNase R. J Biol Chem 2006; 281: 29769-75; PMID:16893880; http://dx.doi.org/10.1074/jbc.M606744200
   PubMed Web of Science ®Google Scholar
• Suzuki H, Zuo Y, Wang J, Zhang MQ, Malhotra A, Mayeda A. Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing. Nucleic Acids Res 2006; 34:e63; PMID:16682442; http://dx.doi.org/10.1093/nar/gkl151
   PubMed Web of Science ®Google Scholar