Ruiz EGR, Velázquez-Flores MÁ

Language: Spanish
References: 74
Page: 55-70
PDF size: 787.90 Kb.

ABSTRACT

MicroRNAs (miRNAs) are small non coding RNAs (~22 nt), whose transcription is regulated by different molecular mechanisms. To date, four pathways of biogenesis are known and originate conventional miRNAs, mirtrons, simtrons, and miRNAs flanked by Alu elements. Remarkably, all these miRNAs act in conjunction with the RNA-induced silencing complex (RISC); however, other mechanisms cannot be ruled out. While attenuation of gene expression is the best characterized effect, currently there is evidence indicating the induction of gene expression by miRNAs. The mechanisms of action used by miRNAs –to regulate gene expression- include the translation inhibition and/or the mRNA target destabilization; however, miRNA action at the transcriptional level and as ligands of the Toll-like receptors 7 and 8 has also been observed. Thus, the divergence of the mechanisms of biogenesis and action of miRNAs seem to ensure the regulation of gene expression in specific cell moments.

REFERENCES

1. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu- Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu S, Zhao S, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF, Guigó R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glades A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X (2001) The sequence of the human genome. Science 291: 1304–1351.

2. International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409: 860–921.

3. Hall LL, Lawrence JB (2016) RNA as a fundamental component of interphase chromosomes: could repeats prove key? Curr Opin Genet Dev 37: 137-147.

4. de Andres-Pablo A, Morillon A, Wery M (2016) LncRNAs, lost in translation or licence to regulate? Curr Genet [Epub ahead of print]

5. Zou Y, Liu W, Zhang J, Xiang D (2016) miR- 153 regulates apoptosis and autophagy of cardiomyocytes by targeting Mcl-1. Mol Med Rep doi: 10.3892/mmr.2016.5309. [Epub ahead of print]

6. Zaho L, Kunst L (2016) SUPERKILLER complex components are required for the RNA exosome-mediated control of cuticular wax biosynthesis in Arabidopsis inflorescence stems. Plant Physiol pii: pp.00450.2016. [Epub ahead of print]

7. Wen J, Ladewig E, Shenker S, Mohammed J, Lai EC (2015) Analysis of Nearly One Thousand Mammalian Mirtrons Reveals Novel Features of Dicer Substrates. PLoS Comput Biol 11: e1004441.

8. Havens MA, Reich AA, Duelli DM, Hastings ML (2012) Biogenesis of mammalian microRNAs by a non-canonical processing pathway. Nucleic Acids Res 40: 4626-4640.

9. Fabbri M, Paone A, Calore F, Galli R, Gaudio E, Santhanam R, Lovat F, Fadda P, Mao C, Nuovo GJ, Zanesi N, Crawford M, Ozer GH, Wernicke D, Alder H, Caligiuri MA, Nana-Sinkam P, Perrotti D, Croce CM (2012) MicroRNAs bind to Toll-like receptors to induce prometastatic inflammatory response. Proc Natl Acad Sci U S A 109: E2110-6.

10. Mah SM, Buske C, Humphries RK, Kuchenbauer F (2010) miRNA*: a passenger stranded in RNA-induced silencing complex? Crit Rev Eukaryot Gene Expr 20: 141-8.

11. Jazdzewski K, Liyanarachchi S, Swierniak M, Pachucki J, Ringel MD, Jarzab B, de la Chapelle A (2009) Polymorphic mature microRNAs from passenger strand of pre-miR-146a contribute to thyroid cancer. Proc Natl Acad Sci U S A 106: 1502-1505.

12. Lewis BP, Burge BC, Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120: 15-20.

13. Cai X, Hagedorn CH, Cullen BR (2004) Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA 10: 1957–1966.

14. Smalheiser NR, Torvik VI (2005) Mammalian microRNAs derived from genomic repeats. Tremés Genet 21: 322–326.

15. Borchert GM, Lanier W, Davidson BL. RNA polymerase III transcribes human microRNAs. Nat Struct Mol Biol. 2006 13: 1097-1101.

16. Chung Wj, Agius P, Westholm JO, Chen M, Okamura K, Robine N, Leslie CS, LAi EC (2011) Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans. Genome Res 21: 286- 300.

17. Cai Y, Yu X, Hu S, Yu J (2009) A brief review on the mechanisms of miRNA regulation. Genomics, proteomics & Bioinformatics 7: 147-154.

18. Steitz A, Vasudevan S (2009) miRNPs: versatile regulators of gene expression in vertebrate cells. Biochem Society Transactions 37: 931-935.

19. Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120: 15–20.

20. Lee I, Ajay SS, Book KL, Kim HS, Hong SH, Kim NH, Dhanasekaran SM, Chinnaiyan AM, Athey BD (2009) New class of microRNA targets containing simultaneous 5´-UTR and 3´-UTR interaction sites. Genome Res 19: 1175-1183.

21. Brummer A, Hausser J (2014) MicroRNA binding sites in the coding region of mRNA: extending the repertoire of post-transcripcional gene regulation. BioEssays 36: 617-626.

22. Brodersen P, Voinnet O (2009) Revisiting the principles of microRNA target recognition and mode of action. Nature Reviews Molecular Cell Biology 10: 141-148.

23. Majoros WH, Ohler U (2007) Spatial preferences of microRNA targets in 3´untranslated regions. BMC Genomics 8: article 152.

24. Ohler U, Yekta S, Lim LP, Bartel DP, Burge CB (2004) Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification. RNA 10: 1309-1322.

25. Grewal SIS, Elgin SCR (2007) Transcription and RNA interference in the formation of heterochromatin. Nature 447: 399-406.

26. Finnegan EJ, Matzke MA (2003) The small world. Journal of Cell Science 116: 4689-4693.

27. Fabian ME, Sonenberg N, Filipowicz (2010) Regulation of mRNA translation an stability by microRNAs. Annual Review of Biochemistry 79: 351-379.

28. Garneau NL, Wilus CJ (2007) The highways and byways of mRNA decay. Nat Rev Mol Cell Biol 8: 113-126.

29. Valencia-Sánchez MA, Liu J, Hannon GJ, Parker R (2006) Control of translation and mRNA degradation by miRNAs and siRNAs. Genes and Development 20: 515-524.

30. Bagga S, Bracht J, Hunter J, Massirer K, Holtz J, Eachus R, Pasquinelli AE (2005) Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell 122: 553-563.

31. Mathonnet G, Fabian MR, Svitkin YV, Parsyan A, Huck L, Murata T, Biffo S, Merrick WC, Darzynkiewicz E, Pillai et al. RS, Fillipowicz W, Duchaine TF, Sonenberg N (2007) MicroRNA inhibition of translation initiation in vitro by targeting the cap-binding complex eIF4F. Science 317: 1764-1767.

32. Iwasaki S, Tomari Y (2009) Argonautemediated translational repression (and activation). Fly 3: 204-206.

33. Wang B, Yane, A Novina CD (2008) MicroRNArepressed mRNAs contain 40S but not 60S components. Proc Natl Acad Sci USA 105: 5343-5348.

34. Lytle JR, Yario TA, Steits JA (2007) Target mRNAs are repressed as efficiently by microRNA-binding sites in the 5´ UTR as in the 3’ UTR. Proc Natl Acad Sci USA 104: 9667- 9672.

35. Eulalio A, Huntinger E, Izaurralde E (2008) Getting to the root of miRNA-mediated gene silencing. Cell 132: 9-14.

36. Ding XC, Grosshans H (2009) Repression of C. elegans microRNA targets at the initiation level of translation requires GW182 proteins. EMBO J 28: 213-222.

37. Chendrimada TP, Finn KJ, Ji X, Baillat D, Gregory RI, Liebhaber SA, Pasquinelli AE, Shiekhattar R (2007) MicroRNA silencing through RISC recruitment of eIF6. Nature 447: 823-828.

38. Mathonnet G, Fabian MR, Svitkin YV, Parsyan A, Huck L, Murata T, Biffo S, Merrick WC, Darzynkiewicz E, Pillai RS, Filipowicz W, Duchaine TF, Sonenberg N (2007) MicroRNA inhibition of translation initiation in vitro by targeting the cap-binding complex eIF4F. Science 317: 1764-1767.

39. Pillai RS, Bhattacharyya SN, Filipowicz W (2007) Repression of protein synthesis by miRNAs: how many mechanisms? Trends Cell Biol 17: 118-126.

40. Andrei MA, Ingelfinger D, Heintzmann R, Achsel T, Rivera-Pomar R, Luhrmann R (2005) A role for eIF4E and eIF4E-transporter in targeting mRNPs to mammalian processing bodies. RNA 11: 717-727.

41. Sen GL, Blau HM (2005) Argonaute 2/RISC resides in sites of mammalian mRNA decay known as cytoplasmic bodies. Nat Cell Biol 7: 633-636.

42. Eystathioy T, Jakymiw A, Chan EK, Séraphin B, Cougot N, Fritzler MJ (2003) The GW182 protein colocalizes with mRNA degradation associated proteins hDcp1 and hLSm4 in cytoplasmic GW bodies. RNA 9: 1171-1173.

43. Vasudevan S and Steitz JA (2007) “AU-richelement- mediated upregulation of translation by FXR1 and Argonaute 2”. Cell 128: 1105- 1118.

44. Place RF, Li LC, Pookot D, Noonan EJ, Dahiya R (2008) MicroRNA-373 induces expression of genes with complementary promoter sequences. Proc Natl Acad Sci USA 105: 1608- 1613.

45. Li E, Zahng J, Yuan T, Ma B (2014) miR-145 inhibits osteosarcoma cell proliferation and invasion by targeting ROCK1. Tumour Biol 35: 7645-7650.

46. Cordes KR, Sheehy NT, White MP, Berry EC, Morton SU, Muth AN, Lee TH, Miano JM, Ivey KN, Srivastava D (2009) miR-145 and miR-143 regulate smooth muscle cell fate and plasticity. Nature 460: 705-710.

47. Lin CC, Liu LZ, Addison JB, Wonderlin WF, Ivanov AV, Ruppert JM (2011) A KLF4- miRNA-206 autoregulatory feedback loop can promote or inhibit protein translation depending upon cell context. Mol Cell Biol 31: 2513-2527.

48. Turchinovich A, Burwinkel B (2012) Distinct AGO1 and AGO2 associated miRNA profiles in human cells and blood plasma. RNA Biol 9: 1066-1075.

49. Pillai RS, Artus CG, Filipowicz W (2004) Tethering of human Ago proteins to mRNA mimics the miRNA-mediated repression of protein synthesis. RNA 10: 1518-1525.

50. Li LC, Okino ST, Zhao H, Pookot D, Place RF, Urakami S, Enokida H, Dahiya R. (2006) Small dsRNAs induce transcriptional activation in human cells. Proc Natl Acad Sci U S A 103: 17337-173342.

51. Yang Z, Jakymiw A, Wood MR, Eystathioy T, Rubin RL, Fritzler MJ, Chan EK (2004) GW182 is critical for the stability of GW bodies expressed during the cell cycle and cell proliferation. J Cell Sci 117: 5567-5578.

52. Bhattacharyya SN, Filipowicz W (2007) Argonautes and company: sailing against the wind. Cell 128: 1027-1028.

53. Vasudevan S, Tong Y, Steitz JA (2007) Switching from repression to activation: microRNAs can up-regulate translation. Science 318: 1931- 1934.

54. Truesdell SS, Mortensen RD, Seo M, Schroeder JC, Lee JH, LeTonqueze O, Vasudevan S (2012) MicroRNA-mediated mRNA translation activation in quiescent cells and oocytes involves recruitment of a nuclear microRNP. Sci Rep 2: 842.

55. Lund E, Sheets MD, Imboeden SB, Dahlberg Je (2011) Limiting Ago protein restricts RNAi and microRNA biogenesis during early development in Xenopus laevis. Genes Dev 25: 1121-1131.

56. Mortensen RD, Serra M, Steitz JA, Vasudevan S (2011) Posttranscriptional activation of gene expression in Xenopus laevis oocytes by microRNA-protein complexes (microRNPs). Proc Natl Acad Sci USA 108: 8281-8286.

57. Kim HH, Kuwano Y, Srikantan S, Lee EK, Martindale JL, Gorospe M. (2009) HuR recruits let-7/RISC to repress c-Myc expression. Genes Dev 23: 1743-1748.

58. Mertens-Talcott SU, Chintharlapalli S, Li X, Safe S (2007) The oncogenic microRNA-27a targets genes that regulate specificity protein transcription factors and the G2-M checkpoint in MDA-MB-231 breast cancer cells. Cancer Res 67: 11001-11011.

59. Jopling CL, Schütz S, Sarnow (2008) Positiondependent function of a tandem microRNA miR-122-binding site located in the hepatitis C virus RNA genome. Cell Host and Microbe 4: 77-85.

60. Niepmann M (2009) Activation of hepatitis C virus translation by a liver-specific microRNA. Cell Cycle 8: 1473-1477.

61. Henke JI, Goergen D, Zheng J, Song Y, Schüttler CG, Fehr C, Jünemann C, Niepmann M (2008) microRNA-122 stimulates translation of hepatitis C virus RNA. The EMBO Journal 27: 3300-3310.

62. Machlin ES, Sarnow P, Sagan SM (2011) Masking the 5´terminal nucleotides of the hepatitis C virus genome by an unconventional microRNA-target RNA complex. PNAS 108: 3193-3198.

63. Li Y, Masaki T, Yamane D, McGivern DR, Lemon M (2013) Competing and non-competing activities of miR-122 and the 5´exonuclease Xrn1 in regulation of hepatitis C virus replication. PNAS 110: 1881-1886.

64. Shimakami T, Yamane D, Jangra RK, Kempf BJ, Spaniel C, Barton DJ, Lemon SM (2012) Stabilization of hepatitis C virus RNA by an Ago2-miR-122 complex. Proc Natl Acad Sci U S A 109: 941-946.

65. Tsai NP, Lin YL, Wei LN (2009) MicroRNA mir-346 targets the 5’ untranslated region of receptor-interacting protein 140 (RIP140) mRNA and up-regulates its protein expression. Biochem J 424: 411-418.

66. Chan SW, Henderson IR, Jacobsen SE (2005) Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat Rev Genet 6: 351–360.

67. Matzke M, Kanno T, Salinger L, Huettel B, Matzke AJ (2009). RNA- mediated chromatinbased silencing in plants. Curr Opin Cell Biol 21: 367–376.

68. Wassenegger M, Heimes S, Riedel L, Sanger HL (1994) RNA-directed de novo methylation of genomic sequences in plants. Cell 76: 567–576.

69. Wu L, Zhou H, Zhang Q, Zhang J, Ni F, Liu C, Qi Y (2010) DNA methylation mediated by a microRNA pathway. Mol Cell 38: 465-475.

70. Balaj L, Lessard R, Dai L, Cho YJ, Pomeroy SL, Breakefield XO, Skog J (2011) Tumour microvesicles contain retrotransposon elements and amplified oncogene sequences. Nat Commun 2: 180.

71. Al-Nedawi Km Meehan B, Micallef J, Lhotak V, May L, Guha A, Rak J (2008) Intercellular transfer of the oncogenic receptor EGFRvIII by microvesicles derived from tumour cells. Nat Cell Biol 10: 619–624.

72. Valadi H, Ekstrom K, Bossios A, Sjostrand M, Lee JJ, Lotvall JO (2007) Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells. Nat. Cell Biol 9: 654–659.

73. Yamaguchi T, Izumi Y, Nakamura Y, Yamazaki T, Shiota M, Sano S, Tanaka M, Osada- Oka M, Shimada K, Miura K, Yoshiyama M, Iwao H (2015) Repeated remote ischemic conditioning attenuates left ventricular remodeling via exosome-mediated intercellular communication on chronic heart failure after myocardial infarction. Int J Cardiol 178: 239– 246.

74. Valinezhad Orang A, Safaralizadeh R, Kazemzadeh-Bavili M (2014) Mechanisms of miRNA Mediated Gene Regulation from Common Downregulation to mRNA-Specific Upregulation. Int J Genomics 2014: 970607.