Engineering and expressing circular RNAs via tRNA splicing

References

• Jeck WR, Sharpless NE. Detecting and characterizing circular RNAs. Nat Biotechnol 2014; 32:453-61; PMID:24811520; https://doi.org/10.1038/nbt.2890
   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; https://doi.org/10.1261/rna.035667.112
   PubMed Web of Science ®Google Scholar
• Coqcuerelle C, Mascrez B, Hetuin D, Bailleul B. Mis-splicing yields circular RNA molecules. FASEB J 1993; 7:155-60; PMID:7678559; https://doi.org/10.1261/rna.047126.114
   PubMed Web of Science ®Google Scholar
• Lasda E, Parker R. Circular RNAs: Diversity of form and function. RNA 2014; 20:1829-42; PMID:25404635; https://doi.org/10.1261/rna.047126.114
   PubMed Web of Science ®Google Scholar
• Petkovic S, Müller S. RNA circularization strategies in vivo and in vitro. Nucleic Acids Res 2015; 43:2454-65; PMID:25662225; https://doi.org/10.1093/nar/gkv045
   PubMed Web of Science ®Google Scholar
• Ebbesen KK, Hansen TB, Kjems J. Insights into circular RNA biology. RNA Biol 2016; PMID:27982727; https://doi.org/10.1080/15476286.2016.1271524
   PubMedGoogle Scholar
• Fischer JW, Leung AKL. CircRNAs: A regulator of cellular stress. Crit Rev Biochem Mol Biol 2017; 9238:1-17; PMID:28095716; https://doi.org/10.1080/10409238.2016.1276882
   PubMed Web of Science ®Google Scholar
• Salzman J. Circular RNA expression: Its potential regulation and function. Trends Genet 2016; 32:309-16; PMID:27050930; https://doi.org/10.1016/j.tig.2016.03.002
   PubMed Web of Science ®Google Scholar
• Qu S, Zhong Y, Shang R, Zhang X, Song W, Kjems J, Li H. The emerging landscape of circular RNA in life processes. RNA Biol 2016; PMID:27617908; https://doi.org/10.1080/15476286.2016.1220473
   PubMedGoogle Scholar
• Lu Z, Filonov GS, Noto JJ, Schmidt CA, Hatkevich TL, Wen Y, Jaffrey SR, Matera AG. Metazoan tRNA introns generate stable circular RNAs in vivo. RNA 2015; 21:1554-65; PMID:26194134; https://doi.org/10.1261/rna.052944.115
   PubMed Web of Science ®Google Scholar
• Dalgaard JZ, Garrett RA. Protein-coding introns from the 23S rRNA-encoding gene form stable circles in the hyperthermophilic archaeon Pyrobaculum organotrophum. Gene 1992; 121:103-10; PMID:1427083; https://doi.org/10.1016/0378-1119(92)90167-N
   PubMed Web of Science ®Google Scholar
• Kjems J, Garrett RA. Novel splicing mechanism for the ribosomal RNA intron in the archaebacterium desulfurococcus mobilis. Cell 1988; 54:693-703; PMID:3136929; https://doi.org/10.1016/S0092-8674(88)80014-X
   PubMed Web of Science ®Google Scholar
• Chen L. The biogenesis and emerging roles of circular RNAs. Nat Rev Mol Cell Biol 2016; 17:205-11; PMID:26908011; https://doi.org/10.1038/nrm.2015.32
   PubMed Web of Science ®Google Scholar
• Salzman J, Chen RE, Olsen MN, Wang PL, Brown PO. Cell-Type specific features of circular RNA expression. PLoS Genet 2013; 9:pgen.1003777; PMID:24039610; https://doi.org/10.1371/journal.pgen.1003777
   PubMed Web of Science ®Google Scholar
• Rybak-Wolf A, Stottmeister C, Glažar P, Jens M, Pino N, Hanan M, Behm M, Bartok O, Ashwal-Fluss R, Herzog M, et al. Circular RNAs in the mammalian brain are highly abundant, conserved, and dynamically expressed. Mol Cell 2014; 58:870-85; PMID:25921068; https://doi.org/10.1016/j.molcel.2015.03.027
   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; https://doi.org/10.1016/j.celrep.2014.10.062
   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; https://doi.org/10.1038/nature11993
   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; https://doi.org/10.1038/nature11928
   PubMed Web of Science ®Google Scholar
• Burd CE, Jeck WR, Liu Y, Sanoff HK, Wang Z, Sharpless NE. Expression of linear and novel circular forms of an INK4/ARF-associated non-coding RNA correlates with atherosclerosis risk. PLoS Genet 2010; 6:1-15; PMID:21151960; https://doi.org/10.1371/journal.pgen.1001233
   PubMed Web of Science ®Google Scholar
• Seitz H. Redefining MicroRNA targets. Curr Biol 2009; 19:870-3; PMID:19375315; https://doi.org/10.1016/j.cub.2009.03.059
   PubMed Web of Science ®Google Scholar
• Salmena L, Poliseno L, Tay Y, Kats L, Pandolfi PP. A ceRNA hypothesis: The rosetta stone of a hidden RNA language? Cell 2011; 146:353-58; PMID:21802130; https://doi.org/10.1016/j.cell.2011.07.014
   PubMed Web of Science ®Google Scholar
• Tay Y, Kats L, Salmena L, Weiss D, Tan SM, Ala U, Karreth F, Poliseno L, Provero P, Di Cunto F, et al. Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs. Cell 2011; 147:344-57; PMID:22000013; https://doi.org/10.1016/j.cell.2011.09.029
   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; https://doi.org/10.1016/j.molcel.2014.08.019
   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; https://doi.org/10.1016/j.celrep.2014.12.002
   PubMed Web of Science ®Google Scholar
• Kramer MC, Liang D, Tatomer DC, Gold B, March ZM, Cherry S, Wilusz JE. Combinatorial control of Drosophila circular RNA expression by intronic repeats, hnRNPs, and SR proteins. Genes Dev 2015; 29:2168-82; PMID:26450910; https://doi.org/10.1101/gad.270421.115
   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; https://doi.org/10.1101/gad.251926.114
   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; https://doi.org/10.1016/j.cell.2015.02.014
   PubMed Web of Science ®Google Scholar
• Johnson PJ. Spliceosomal introns in a deep-branching eukaryote: The splice of life. Proc Natl Acad Sci USA 2002; 99:3359-61; PMID:11904397; https://doi.org/10.1073/pnas.072084199
   PubMed Web of Science ®Google Scholar
• Woodson SA. Ironing out the kinks: Splicing and translation in bacteria. Genes Dev 1998; 12:1243-7; PMID:9573040; https://doi.org/10.1101/gad.12.9.1243
   PubMed Web of Science ®Google Scholar
• Calvin K, Li H. RNA-splicing endonuclease structure and function. Cell Mol Life Sci 2008; 65:1176-85; PMID:18217203; https://doi.org/10.1007/s00018-008-7393-y
   PubMed Web of Science ®Google Scholar
• Tocchini-Valentini GD, Fruscoloni P, Tocchini-Valentini GP. Coevolution of tRNA intron motifs and tRNA endonuclease architecture in Archaea. Proc Natl Acad Sci USA 2005; 102:15418-22; PMID:16221764; https://doi.org/10.1073/pnas.0506750102
   PubMed Web of Science ®Google Scholar
• Salgia SR, Singh SK, Gurha P, Gupta R. Two reactions of Haloferax volcanii RNA splicing enzymes: joining of exons and circularization of introns. RNA 2003; 9:319-30; PMID:12592006; https://doi.org/10.1261/rna.2118203
   PubMed Web of Science ®Google Scholar
• Xue S, Calvin K, Li H. RNA recognition and cleavage by a splicing endonuclease. Science 2006; 312:906-10; PMID:16690865; https://doi.org/10.1126/science.1126629
   PubMed Web of Science ®Google Scholar
• Yoshihisa T. Handling tRNA introns, archaeal way and eukaryotic way. Front Genet 2014; 5:1-16; PMID:24567736; https://doi.org/10.3389/fgene.2014.00213
   PubMed Web of Science ®Google Scholar
• Chan PP, Lowe TM. GtRNAdb: A database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res 2009; 37:93-7; PMID:18984615; https://doi.org/10.1093/nar/gkn787
   PubMed Web of Science ®Google Scholar
• Danan M, Schwartz S, Edelheit S, Sorek R. Transcriptome-wide discovery of circular RNAs in Archaea. Nucleic Acids Res 2012; 40:3131-42; PMID:22140119; https://doi.org/10.1093/nar/gkr1009
   PubMed Web of Science ®Google Scholar
• Burggraf S, Larsen N, Woese CR, Stetter KO. An intron within the 16S ribosomal RNA gene of the archaeon Pyrobaculum aerophilum. Proc Natl Acad Sci U S A 1993; 90:2547-50; PMID:8460170; https://doi.org/10.1073/pnas.90.6.2547
   PubMed Web of Science ®Google Scholar
• Singh SK, Gurha P, Tran EJ, Maxwell ES, Gupta R. Sequential 2′-O-methylation of archaeal pre-tRNA Trp nucleotides is guided by the intron-encoded but trans-acting box C/D ribonucleoprotein of pre-tRNA. J Biol Chem 2004; 279:47661-71; PMID:15347671; https://doi.org/10.1074/jbc.M408868200
   PubMed Web of Science ®Google Scholar
• Trotta CR, Miao F, Arn EA, Stevens SW, Ho CK, Rauhut R, Abelson JN. The yeast tRNA splicing endonuclease: a tetrameric enzyme with two active site subunits homologous to the archaeal tRNA endonucleases. Cell 1997; 89:849-58; PMID:9200603; https://doi.org/10.1016/S0092-8674(00)80270-6
   PubMed Web of Science ®Google Scholar
• Di Segni G, Borghese L, Sebastiani S, Tocchini-Valentini GP. A pre-tRNA carrying intron features typical of Archaea is spliced in yeast. RNA 2005; 11:70-6; PMID:15574514; https://doi.org/10.1261/rna.7138805
   PubMed Web of Science ®Google Scholar
• Reyes VM, Abelson J. Substrate recognition and splice site determination in yeast tRNA splicing. Cell 1988; 55:719-30; PMID:3141064; https://doi.org/10.1016/0092-8674(88)90230-9
   PubMed Web of Science ®Google Scholar
• Greer CL, Soll D, Willis I. Substrate recognition and identification of splice sites by the tRNA-splicing endonuclease and ligase from Saccharomyces cerevisiae. Mol Cell Biol 1987; 7:76-84; PMID:3550427; https://doi.org/10.1128/MCB.7.1.76
   PubMed Web of Science ®Google Scholar
• Phizicky EM, Schwartz RC, Abelson J. Saccharomyces cerevisiae tRNA ligase. Purification of the protein and isolation of the structural gene. J Biol Chem 1986; 261:2978-86; PMID:3512545
   PubMed Web of Science ®Google Scholar
• Englert M, Beier H. Plant tRNA ligases are multifunctional enzymes that have diverged in sequence and substrate specificity from RNA ligases of other phylogenetic origins. Nucleic Acids Res 2005; 33:388-99; PMID:15653639; https://doi.org/10.1093/nar/gki174
   PubMed Web of Science ®Google Scholar
• Wang LK, Schwer B, Englert M, Beier H, Shuman S. Structure-function analysis of the kinase-CPD domain of yeast tRNA ligase (Trl1) and requirements for complementation of tRNA splicing by a plant Trl1 homolog. Nucleic Acids Res 2006; 34:517-27; PMID:16428247; https://doi.org/10.1093/nar/gkj441
   PubMed Web of Science ®Google Scholar
• Popow J, Englert M, Weitzer S, Schleiffer A, Mierzwa B, Mechtler K, Trowitzsch S, Will CL, Lührmann R, Söll D, et al. HSPC117 is the essential subunit of a human tRNA splicing ligase complex. Science 2011; 331:760-4; PMID:21311021; https://doi.org/10.1126/science.1197847
   PubMed Web of Science ®Google Scholar
• Englert M, Sheppard K, Aslanian A, Yates JR, Söll D. Archaeal 3′-phosphate RNA splicing ligase characterization identifies the missing component in tRNA maturation. Proc Natl Acad Sci USA 2011; 108:1290-5; PMID:21209330; https://doi.org/10.1073/pnas.1018307108
   PubMed Web of Science ®Google Scholar
• Peschek J, Acosta-Alvear D, Mendez AS, Walter P. A conformational RNA zipper promotes intron ejection during non-conventional XBP1 mRNA splicing. EMBO Rep 2015; 16:1688-98; PMID:26483401; https://doi.org/10.15252/embr.201540955
   PubMed Web of Science ®Google Scholar
• Jurkin J, Henkel T, Nielsen AF, Minnich M, Popow J, Kaufmann T, Heindl K, Hoffmann T, Busslinger M, Martinez J. The mammalian tRNA ligase complex mediates splicing of XBP1 mRNA and controls antibody secretion in plasma cells. EMBO J 2014; 33:2922-36; PMID:25378478; https://doi.org/10.15252/embj.201490332
   PubMed Web of Science ®Google Scholar
• Kosmaczewski SG, Edwards TJ, Han SM, Eckwahl MJ, Meyer BI, Peach S, Hesselberth JR, Wolin SL, Hammarlund M. The RtcB RNA ligase is an essential component of the metazoan unfolded protein response. EMBO Rep 2014; 15:1278-85; PMID:25366321; https://doi.org/10.15252/embr.201439531
   PubMed Web of Science ®Google Scholar
• Lu Y, Liang FX, Wang X. A synthetic biology approach identifies the mammalian UPR RNA ligase RtcB. Mol Cell 2014; 55:758-70; PMID:25087875; https://doi.org/10.1016/j.molcel.2014.06.032
   PubMed Web of Science ®Google Scholar
• Sidrauski C, Cox JS, Walter P. tRNA ligase is required for regulated mRNA splicing in the unfolded protein response. Cell 1996; 87:405-13; PMID:8898194; https://doi.org/10.1016/S0092-8674(00)81361-6
   PubMed Web of Science ®Google Scholar
• Wang Y, Wang Z. Efficient backsplicing produces translatable circular mRNAs. RNA 2015; 21:172-9; PMID:25449546; https://doi.org/10.1261/rna.048272.114
   PubMed Web of Science ®Google Scholar
• Schmidt CA, Noto JJ, Filonov GS, Matera AG. A method for expressing and imaging abundant, stable, circular RNAs in vivo using tRNA splicing. Methods Enzymol 2016; 572:215-36. PMID:27241756; https://doi.org/10.1016/bs.mie.2016.02.018
   PubMed Web of Science ®Google Scholar
• Lebbink RJ, Lowe M, Chan T, Khine H, Wang X, McManus MT. Polymerase II promoter strength determines efficacy of microRNA adapted shRNAs. PLoS One 2011; 6:e26213; PMID:22031824; https://doi.org/10.1371/journal.pone.0026213
   PubMed Web of Science ®Google Scholar
• Qin JY, Zhang L, Clift KL, Hulur I, Xiang AP, Ren BZ, Lahn BT. Systematic comparison of constitutive promoters and the doxycycline-inducible promoter. PLoS One 2010; 5:e10611; PMID:20485554; https://doi.org/10.1371/journal.pone.0010611
   PubMed Web of Science ®Google Scholar
• Filonov GS, Moon JD, Svensen N, Jaffrey SR. Broccoli: Rapid selection of an RNA mimic of green fluorescent protein by fluorescence-based selection and directed evolution. J Am Chem Soc 2014; 136:16299-308; PMID:25337688; https://doi.org/10.1021/ja508478x
   PubMed Web of Science ®Google Scholar
• Filonov GS, Kam CW, Song W, Jaffrey SR. In-gel imaging of RNA processing using broccoli reveals optimal aptamer expression strategies. Chem Biol 2015; 22:649-60; PMID:26000751; https://doi.org/10.1016/j.chembiol.2015.04.018
   PubMedGoogle Scholar
• Sakharkar MK, Chow VTK, Kangueane P. Distributions of exons and introns in the human genome. In Silico Biol 2004; 4:387-93; PMID:15217358
   PubMedGoogle Scholar
• Good P, Krikos A, Li S, Bertrand E, Lee N, Giver L, Ellington A, Zaia J, Rossi J, Engelke D. Expression of small, therapeutic RNAs in human cell nuclei. Gene Ther 1997; 4:45-54; PMID:9068795; https://doi.org/10.1038/sj.gt.3300354
   PubMed Web of Science ®Google Scholar