Mature miRNAs form secondary structure, which suggests their function beyond RISC

PLoS ONE

Volumn 9, Issue 11, 2014, Pages

  Belter, Agnieszka ^a   Gudanis, Dorota ^a   Rolle, Katarzyna ^a   Piwecka, Monika ^a   Gdaniec, Zofia ^a   Naskre¸t Barciszewska, Mirosława Z ^a   Barciszewski, Jan ^a  

^a INSTITUTE OF BIOORGANIC CHEMISTRY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

APTAMER; MICRORNA; MICRORNA 21; MICRORNA 93; OLIGONUCLEOTIDE; PROTEIN ANTIBODY; TENASCIN; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; CANCER INHIBITION; CELLULAR PARAMETERS; CONTROLLED STUDY; GENE CONTROL; GENE OVEREXPRESSION; GLIOBLASTOMA; HUMAN; HUMAN CELL; MIRNA INDUCED SILENCING COMPLEX; PROTEIN FUNCTION; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY; RNA BINDING; STRUCTURAL HOMOLOGY; STRUCTURE ANALYSIS; WORLD HEALTH ORGANIZATION; CHEMISTRY; CONFORMATION; GENETICS; NUCLEOTIDE SEQUENCE; SEQUENCE HOMOLOGY;

BASE SEQUENCE; HUMANS; MICRORNAS; NUCLEIC ACID CONFORMATION; SEQUENCE HOMOLOGY, NUCLEIC ACID;

EID: 84913569025     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0113848     Document Type: Article

References (64)

1. Griffths-Jones S, Grocock RJ, Van Dongen S, Bateman A, Enright AJ (2006) miRBase: microRNA sequences, targets and gene nomenclature. Nucl Acids Res 34: D140-D144.
2. Liu J, Carmell MA, Rivas FV, Marsden CG, Thomson JM, et al. (2004) Argonaute2 is the catalytic engine of mammalian RNAi. Science 305: 1437-1441.
3. Hutvagner G, Zamore PD (2002) A microRNA in multiple-turnover RNAi enzyme complex. Science 297: 2056-2060.
4. Gaur A, Jewell DA, Liang Y, Ridzon D, Moore JH, et al. (2007) Characterization of microRNA expression levels and their biological correlates in human cancer cell lines. Cancer Res 67: 2456-2468.
5. Godlewski J, Nowicki MO, Bronisz A, Williams S, Stsuki A, et al. (2012) Targeting of the Bmi-1 oncogene/stem cell renewal factor by microRNA-128 inhibits glioma proliferation and self-renewal. Cancer Res 68: 9125-9130.
6. Kim H, Huang W, Jiang X, Pennicooke B, Park PJ, et al. (2010) Integrative genome analysis reveals an oncomir/oncogene cluster regulating glioblastoma survivorship. Proc Natl Acad Sci USA 107: 2183-2188.
7. Cui Q, Yu Z, Purisima EO, Wang E (2006) Principles of microRNA regulation of a human cellular signaling network. Mol Syst Biol 2: 46.
8. Mercer TR, Dinger ME, Sunkin SM, Mehler MF, Mattick JS (2008) Specific expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci USA 105: 716-721.
9. Farazi TA, Spitzer JI, Morozov P, Tuschl T (2011) miRNAs in human cancer. J Pathol 223: 102-115.
10. Ming L, Qipeng Z, Deng M, Miao J, Guo Y, et al. (2008) An analysis of human microRNA and disease associations. PLOS One 3: e3420-e3425.
11. Volinia S, Calin GA, Liu CG, Ambs S, Cimmino A, et al. (2006) A microRNA expression signature of human solid tumors defines cancer gene targets. PNAS 103: 2257-2261.
12. Calin GA, Ferracino A, Di Leva G, Shimizu M, Wojcik SE, et al. (2005) A microRNA signature associated with prognosis and progression in chronic lymphocytic leukemia. N Engl J Med 353: 1793-1801.
13. Lee Y, Kim M, Han J, Yeom KH, Lee S, et al. (2004) MicroRNA genes are transcribed by RNA polymerase II. EMBO J 23: 4051-4060.
14. Denli AM, Tops BB, Plasterek RH, Ketting GJ (2004) Processing the primary microRNAs by the microprocessor complex. Nature 432: 231-235.
15. Krol J, Loedige I, Filipowicz W (2010) The widespread regulation of microRNA biogenesis, function and decay. Nat Rev Genet 11: 597-610.
16. Winter J, Jung S, Keller S, Gregory RI, Diederichs S (2009) Many roads to maturity: microRNA biogenesis pathways and their regulation. Nat Cell Biol 11: 228-234.
17. Lund E, Guttinger S, Calado A, Dahlberg JE, Kutay U (2004) Nuclear export of microRNA precursors. Science 303: 95-98.
18. Zeng Y, Cullen BR (2004) Structural requirements for pre-microRNA binding and nuclear export by exportin 5. Nucl Acids Res 32: 4776-4785.
19. Khvorova A, Reynolds A, Jayasena SD (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell 115: 209-216.
20. Schwarz DS, Zamore PD (2002) Why do miRNAs live in the miRNP? Genes Dev 16: 1025-1031.
21. Lambert NJ, Gu SG, Zahler AM (2011) The conformation of microRNA seed region in tetivemicroRPNs is prearanged for presentation to miRNA target. Nucleic Acid Res 39: 4827-4835.
22. Cevec M, Thibaudeau C, Plavec J (2008) Solution structure of a let-7 miRNA:lin-41 mRNA complex from C. elegans. Nucl Acids Res 36: 2330-2337.
23. Lewis BP, Shih IH, Jones-RHoades MW, Bartel DP, Burge CB (2003) Prediction of mammalian microRNA targets. Cell 115: 787-798.
24. Shomron N, Golan D, Hornstein E (2009) An evolutionry perspective of animal microRNAs and their targets. J Biomed Biotechnol 2009: 594738.
25. Baek D, Villen J, Shin C, Camargo FD, Gygi SP, et al. (2008) The impact of microRNAs on protein output. Nature 455: 64-71.
26. Selbach M, Schwanhausser B, Thierfelder N, Fang Z, Khanin R, et al. (2008) Widespread changes in protein synthesis induced by microRNAs. Nature 455: 58-63.
27. Gan HH, Gunsalus KC (2013) Tertiary structure-based analysis of microRNA-target interactions. RNA 19: 539-551.
28. Robins H, Li Y, Radgett RW (2005) Incorporating structure to predict microRNA targets. Proc Natl Acad Sci USA 102: 4006-4009.
29. Harharan M, Scaria V, Brahmachari SK (2009) dbSMR: a novel resource of genome-wide SNPs affecting microRNA mediated regulation. BMC Bioinformatics 10: 108.
30. Brennecke J, Stark A, Russell RB, Cohen SM (2005) Principles of microRNA-target recognition. PLOS Biol 3: e85.
31. Parker JS, Parizotto EA, Wang M, Roe SM, Barford D (2009) Enhancement of the seed-target recognition step in RNA silencing by a PIWI/MID domain protein. Mol Cell 33: 204-214.
32. Bartel DP (2009) MicroRNAs: target recognition and regulatory function. Cell 136: 215-233.
33. Barciszewska M, Mashkova TD, Kisselev LL, Barciszewski J (1985) The primary structure of maize and tabacco 5 S rRNA. FEBS Letter 192: 289-293.
34. Ragan Ch, Zuker M, Ragan MA (2011) Quantitative prediction of miRNA-mRNA interaction based on equilibrium concentrations. PLOS Computional Biology 7: e1001090.
35. Available: www.bioNumbers.org. Accessed 2013 Nov 4.
36. Gruber AR, Lorenz R, Bernhart SH, Neubock R, Hofacker IL (2008) The Vienna RNA Websuite. Nucl Acids Res 36: W70-W74.
37. Bernhart SH, Tafer H, Muckstein U, Flamm C, Stadler PF, et al. (2006) Partition function and base pairing probabilities of RNA heterdimers. Algorithms Mol Biol 16: 3.
38. Hochsmann M, Bjorn-Voss, Giegerich R (2004) Pure multiple RNA secondary structure aligments: a progressive profile approach in IEEE/ACM transactions on computational biology and bioinformatics 1: 53-62.
39. Piwecka M, Rolle K, Wyszko E, Zukiel R, Nowak S, et al. (2011) Nucleic acid-based technologies in therapy of malignant gliomas. Curr Pharm Biotechnol 12: 1805-1822.
40. Cheong C, Varani G, Tinoco IJr (1990) Solution structure of an unusually stable RNA hairpin, 5'GGAC(UUCG)GUCC. Nature 346: 680-682.
41. Maiti M, Nauwelaerts K, Lescrinier E, Schuit FC, Herdewijn P (2010) Self-complementary sequence context in mature miRNAs. Biochem Biophys Res Commun 392: 572-576.
42. Adhikary M, Ganguli S, Das SG, Datta A (2011) Secondary structural analyses of microRNAs and precursors in Pan troglodytes. Int J Comp Biol 2: 35-37.
43. Das AK, Ganguli S, Gupta S, Datta A (2011) Secondary structural analysis of microRNA and their precursors in plants. IJAS 3: 62-64.
44. Guo L, Sun B, Wu Q, Yang S, Chen F (2012) miRNA-miRNA interaction implicates for potential mutual regulatory pattern. Gene 511: 187-194.
45. Janas MM, Wang B, Harris AS, Aquiar M, Shaffer JM, et al. (2012) Alternative RISC assembly: binding and repression of microRNA-mRNA duplexes by human Ago proteins. RNA 18: 2041-2055.
46. Stalder L, Heusermann W, Sokol L, Trojer D, Wirz J, et al. (2013) The rough endoplastic reticulum is a nucleation site of siRNA-mediated RNA silencing. EMBP J 32: 1115-1127.
47. Flores O, Nakayama S, Whisnant AW, Javanbakht H, Cullen BR, et al. (2013) Mutational inactivation of herpex virus 1 microRNAs identifies viral mRNA targets and reveals phenotypic effects in culture. J Virol 87: 6589-6603.
48. Gantier MP, McCoy CE, Rusinova I, Saulep D, Wang D, et al. (2011) Analysis of microRNA turnover in mammalian cells following Dicer1 ablation. Nucleic Acids Res 39: 5692-5703.
49. Tavazoie SF, Alarcon C, Oskarsson T, Padua D, Wang Q, et al. (2008) Endogenous human microRNAs that suppress breast cancer metastasis. Nature 451: 147-154.
50. Nowakowski J, Tinoco IJr (1997) RNA structure and stability. Seminars of Virology 8: 153-165.
51. Li L, Zhu D, Huang L, Bian Z, Chen X, et al. (2012) Argonaute2 complexes selectivity protect the circulating miRNAs in cell secreted microvasicles. PLOS One 7: e46957.
52. Aqil M, Naqvi AR, Bano AS, Jameel S (2013) The HIV-1 Nef protein binds Argonaute-2 and functions as a viral suppressor of RNA interference. PLOS One 8: e74472.
53. Liu J, Rivas FV, Wohlschlegel J, Yates JR 3rd, Parker R, et al. (2005) A role for the P-body component GW182 in microRNA function. Nat Cell Biol 7: 1261-1266.
54. Zamudio JR, Kelly TJ, Sharp PA (2014) Argonaute bound small RNAs from promoter-proximal RNA polymerase II. Cell 156: 920-934.
55. Hicke BJ, Marion Ch, Chang YF, Gould T, Lynott CK, et al. (2001) Tenascin-C aptamers are generated using tumor cells and purified protein. J Biol Chem 276: 48644-48654.
56. Chen AK, Sengupta P, Waki K, van Engelenbureg SB, Ochiya T, et al. (2014) MicroRNA binding to the HIV-1 Gag protein inhibits Gag assembly and virus production. PNAS 111:E2676-E2683.
57. Held DM, Kissel JD, Patterson IT, Nickens DG, Burke DH (2006) HIV-1 interaction by nucleic acid aptamers. Frontiers in Bioscience 11: 89-112.
58. Ramalingam D, Duclair S, Datta SAK, Ellington A, Rein A, et al. (2011) RNA aptamers directed to human immunodeficiency virus type 1 Gag polyprotein bind to the matrix and nucleocapsid domain and inhibit virus production. J Virol 85: 305-314.
59. King IN, Yartseva V, Salas D, Kumar A, Heidersbach A, et al. (2014) The RNA-binding protein TDP-43 selectively disrupts microRNA-1/206 incorporation into the RNA silenting complex. J Biol Chem 289: 14271.
60. Tang R, Li L, Zhu D, Hou D, Cao T, et al. (2012) Mouse miRNA-709 directly regulated miRNA-15a/16-1 biogenesis at the posttranscriptional level in the nucleus: evidence for a microRNA hierarchy system. Cell Res 22: 504-515.
61. Liu J, Hu J, Corey DR (2012) Expanding the action of duplex RNAs into the nucleus: redirecting alternative splicing. Nucl Acids Res 40: 1240-1250.
62. KIm DH, Satrom P, Snove O, Rossi JJ (2008) MicroRNA-directed transcriptional gene silencing in mammalian cells. Proc Natl Acad Sci USA 105: 16230-16235.
63. Zardo G, Ciolfi A, Vian L, Starnes LM, Billi M, et al. (2012) Colycombs and microRNA-223 regulate human granulopoiesis by transcriptional control of target gene expression. Blood 119: 4034-4046.
64. Adilakshmi T, Sudol I, Tapinos N (2012) Combinatorial action of miRNAs regulates transcriptional and post-transcriptional gene silencing following in vivo PNS jury. PLOS One 7: e39674.