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Research Paper

Circular versus linear RNA topology: different modes of RNA–RNA interactions in vitro and in human cells

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Pages 674-683 | Received 03 May 2021, Accepted 06 Sep 2021, Published online: 28 Nov 2021

References

  • Rong D, Sun H, Li Z, et al. An emerging function of circRNA-miRNAs-mRNA axis in human diseases. Oncotarget. 2017;8(42):73271–73281.
  • Ebbesen KK, Kjems J, Hansen TB. Circular RNAs: identification, biogenesis and function. Biochim Biophys Acta. 2016;1859(1):163–168.
  • Petkovic S, Muller S. RNA circularization strategies in vivo and in vitro. Nucleic Acids Res. 2015;43(4):2454–2465.
  • Jeck WR, Sorrentino JA, Wang K, et al. Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA. 2013;19(2):141–157.
  • Welden JR, Pawluchin A, Van Doorn J, et al. 2020. Use of alu element containing minigenes to analyze circular RNAs. J Vis Exp. 157. 10.3791/59760.
  • Metge F, Czaja-Hasse LF, Reinhardt R, et al. FUCHS-towards full circular RNA characterization using RNAseq. PeerJ. 2017;5:e2934.
  • Ivanov A, Memczak S, Wyler E, et al. Analysis of intron sequences reveals hallmarks of circular RNA biogenesis in animals. Cell Rep. 2015;10(2):170–177.
  • Chuang TJ, Wu CS, Chen CY, et al. 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.
  • Luo Y, Liu S, Yao K. Transcriptome-wide Investigation of mRNA/circRNA in miR-184 and Its r.57c > u mutant type treatment of human lens epithelial cells. Mol Ther Nucleic Acids. 2017;7:71–80.
  • Raz O, Granot G, Pasmanik-Chor M, et al. Profiling and bioinformatics analyses reveal chronic lymphocytic leukemia cells share a unique circular RNA expression pattern. Exp Hematol. 2020;85:8–12.
  • Haque S, Ames RM, Moore K, et al. Islet-expressed circular RNAs are associated with type 2 diabetes status in human primary islets and in peripheral blood. BMC Med Genomics. 2020;13(1):64.
  • Barrett SP, Salzman J. Circular RNAs: analysis, expression and potential functions. Development. 2016;143(11):1838–1847.
  • Kristensen LS, Andersen MS, Stagsted LVW, et al. The biogenesis, biology and characterization of circular RNAs, Nature reviews. Genetics. 2019;20:675–691.
  • Kleaveland B, Shi CY, Stefano J, et al. A network of noncoding regulatory rnas acts in the mammalian brain. Cell. 2018;174(2):350–362.e317.
  • Memczak S, Jens M, Elefsinioti A, et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 2013;495(7441):333–338.
  • Salzman J, Chen RE, Olsen MN, et al. Cell-type specific features of circular RNA expression. PLoS Genet. 2013;9(9):e1003777.
  • Rybak-Wolf A, Stottmeister C, Glažar P, et al. Circular RNAs in the mammalian brain are highly abundant, conserved, and dynamically expressed. Mol Cell. 2015;58(5):870–885.
  • Maass PG, Glažar P, Memczak S, et al. A map of human circular RNAs in clinically relevant tissues. J Mol Med (Berl). 2017;95(11):1179–1189.
  • Rittner K, Burmester C, Sczakiel G. In vitro selection of fast-hybridizing and effective antisense RNAs directed against the human immunodeficiency virus type 1. Nucleic Acids Res. 1993;21(6):1381–1387.
  • Persson C, Wagner EG, Nordstrom K. Control of replication of plasmid R1: formation of an initial transient complex is rate-limiting for antisense RNA–target RNA pairing. EMBO J. 1990;9(11):3777–3785.
  • Rehmsmeier M, Steffen P, Hochsmann M, et al. Fast and effective prediction of microRNA/target duplexes. RNA. 2004;10(10):1507–1517.
  • Ghosal S, Das S, Sen R, et al. Circ2Traits: a comprehensive database for circular RNA potentially associated with disease and traits. Front Genet. 2013;4:283.
  • Petkovic S, Badelt S, Block S, et al. Sequence-controlled RNA self-processing: computational design, biochemical analysis, and visualization by AFM. RNA. 2015;21(7):1249–1260.
  • Patzel V, Sczakiel G. Theoretical design of antisense RNA structures substantially improves annealing kinetics and efficacy in human cells. Nat Biotechnol. 1998;16(1):64–68.
  • Lorenz R, Bernhart SH, Siederdissen HZ, et al. ViennaRNA Package 2.0. Algorithms for molecular biology: AMB. 2011;6(1):26
  • Kerpedjiev P, Hammer S, Hofacker IL. Forna (force-directed RNA): simple and effective online RNA secondary structure diagrams. Bioinformatics. 2015;31(20):3377–3379.
  • Wunsche W, Sczakiel G. The activity of siRNA in mammalian cells is related to the kinetics of siRNA-target recognition in vitro: mechanistic implications. J Mol Biol. 2005;345(2):203–209.
  • Patzel V, Sczakiel G. Length dependence of RNA-RNA annealing. J Mol Biol. 1999;294(5):1127–1134.
  • Homann M, Nedbal W, Sczakiel G. Dissociation of long-chain duplex RNA can occur via strand displacement in vitro: biological implications. Nucleic Acids Res. 1996;24(22):4395–4400.
  • Mayr C, Hemann MT, Bartel DP. Disrupting the pairing between let-7 and Hmga2 enhances oncogenic transformation. Science. 2007;315(5818):1576–1579.
  • Hansen TB, Jensen TI, Clausen BH, et al. Natural RNA circles function as efficient microRNA sponges. Nature. 2013;495(7441):384–388.
  • Fang X, Bai Y, Zhang L, et al. Silencing circSLAMF6 represses cell glycolysis, migration, and invasion by regulating the miR-204-5p/MYH9 axis in gastric cancer under hypoxia. Biosci Rep. 2020;40(6). 10.1042/BSR20201275
  • Ye M, Hou H, Shen M, et al., Circular RNA circFOXM1 Plays a Role in Papillary Thyroid Carcinoma by Sponging miR-1179 and Regulating HMGB1 Expression, Molecular therapy. Nucleic acids. 2020; 19:741–750.
  • Ebert MS, Neilson JR, Sharp PA. MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells. Nat Methods. 2007;4(9):721–726.
  • Franco-Zorrilla JM, Valli A, Todesco M, et al. Target mimicry provides a new mechanism for regulation of microRNA activity. Nat Genet. 2007;39(8):1033–1037.
  • Hansen TB, Kjems J, Damgaard CK. Circular RNA and miR-7 in cancer. Cancer Res. 2013;73(18):5609–5612.
  • Chen S, Li T, Zhao Q, et al. Using circular RNA hsa_circ_0000190 as a new biomarker in the diagnosis of gastric cancer. Clin Chim Acta. 2017;466:167–171.
  • Nair AA, Niu N, Tang X, et al. Circular RNAs and their associations with breast cancer subtypes. Oncotarget. 2016;7:80967–80979.
  • Lavenniah A, Luu TDA, Li YP, et al. Engineered circular RNA sponges act as mirna inhibitors to attenuate pressure overload-induced cardiac hypertrophy. Mol Ther. 2020;28(6):1506–1517.
  • Pasman Z, Been MD, Garcia-Blanco MA. Exon circularization in mammalian nuclear extracts. RNA. 1996;2:603–610.
  • Petkovic S, Muller S. RNA self-processing: formation of cyclic species and concatemers from a small engineered RNA. FEBS Lett. 2013;587(15):2435–2440.
  • Dyer BW, Ferrer FA, Klinedinst DK, et al. A noncommercial dual luciferase enzyme assay system for reporter gene analysis. Anal Biochem. 2000;282(1):158–161.