Biogenesis of mammalian miRNA

MicroRNAs as Tools in Biopharmaceutical Production

Volumn 9789400751286, Issue , 2012, Pages 15-27

  Clarke, Stephen L ^a   Davis, McKale R ^a   Sunkar, Ramanjulu ^a  

^a OKLAHOMA STATE UNIVERSITY   (United States)

Author keywords

Biogenesis; MicroRNA; Transcription; Translational repression

Indexed keywords

BIOSYNTHESIS; CELL PROLIFERATION; FEEDBACK; MAMMALS; METABOLISM; PHYSIOLOGY; RECOMBINANT PROTEINS; RNA;

BIOGENESIS; CELLULAR DIFFERENTIATION; CELLULAR METABOLISM; CELLULAR PROLIFERATIONS; MESSENGER RNA; MICRORNA; RNA-INDUCED SILENCING COMPLEXES; TARGET MESSENGERS; TRANSLATIONAL REPRESSION; UNTRANSLATED REGIONS;

THERMODYNAMIC STABILITY;

EID: 84935049688     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-94-007-5128-6_2     Document Type: Chapter

References (85)

1. Bartel DP. (2009). MicroRNAs: target recognition and regulatory functions. Cell 136(2): 215-233. doi: 10.1016/j.cell.2009.01.002
2. Baskerville S, Bartel DP. (2005). Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. Rna 11(3): 241-247. doi: 10.1261/rna.7240905
3. Basyuk E, Suavet F, Doglio A, Bordonne R, Bertrand E. (2003). Human let-7 stem-loop precursors harbor features of RNase III cleavage products. Nucleic Acids Res 31(22): 6593-6597
4. Beilharz TH, Humphreys DT, Clancy JL, Thermann R, Martin DI, Hentze MW, Preiss T. (2009). microRNA-mediated messenger RNA deadenylation contributes to translational repression in mammalian cells. PLoS One 4(8): e6783. doi: 10.1371/journal.pone.0006783
5. Berezhna SY, Supekova L, Sever MJ, Schultz PG, Deniz AA. (2011). Dual regulation of hepatitis C viral RNA by cellular RNAi requires partitioning of Ago2 to lipid droplets and P-bodies. Rna. 17(10): 1831-1845. doi: 10.1261/rna.2523911
6. Bernstein E, Caudy AA, Hammond SM, Hannon GJ. (2001). Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409(6818): 363-366. doi: 10.1038/35053110
7. Bohnsack MT, Czaplinski K, Gorlich D. (2004). Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs. Rna 10(2): 185-191
8. Cai X, Hagedorn CH, Cullen BR. (2004). Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. Rna 10(12): 1957-1966. doi: 10.1261/rna.7135204
9. Cannell IG, Kong YW, Bushell M. (2008). How do microRNAs regulate gene expression?. Biochem Soc Trans 36(Pt 6): 1224-1231. doi: 10.1042/BST0361224
10. Carthew RW, Sontheimer EJ. (2009). Origins and Mechanisms of miRNAs and siRNAs. Cell. 136(4): 642-655. doi: 10.1016/j.cell.2009.01.035
11. Chekulaeva M, Filipowicz W. (2009). Mechanisms of miRNA-mediated post-Transcriptional regulation in animal cells. Curr Opin Cell Biol 21(3): 452-460. doi: 10.1016/j.ceb.2009.04.009
12. Chendrimada TP, Gregory RI, Kumaraswamy E, Norman J, Cooch N, Nishikura K, Shiekhattar R. (2005). TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature 436(7051): 740-744. doi: 10.1038/nature03868
13. Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel DP. (2010). Mammalian microRNAs: experimental evaluation of novel and previously annotated genes. Genes Dev 24(10): 992-1009. doi: 10.1101/gad.1884710
14. Czech B, Hannon GJ. (2011). Small RNA sorting: matchmaking for Argonautes. Nat Rev Genet. 12(1): 19-31. doi: 10.1038/nrg2916
15. Denli AM, Tops BB, Plasterk RH, Ketting RF, Hannon GJ. (2004). Processing of primary microRNAs by the Microprocessor complex. Nature 432(7014): 231-235. doi: 10.1038/nature03049
16. Doench JG, Sharp PA. (2004). Specificity of microRNA target selection in translational repression. Genes Dev 18(5): 504-511. doi: 10.1101/gad.1184404
17. Esau C, Davis S, Murray SF, Yu XX, Pandey SK, Pear M, Watts L, Booten SL, Graham M, McKay R, Subramaniam A, Propp S, Lollo BA, Freier S, Bennett CF, Bhanot S, Monia BP. (2006). miR-122 regulation of lipid metabolism revealed by in vivo antisense targeting. Cell Metab 3(2): 87-98. doi: 10.1016/j.cmet.2006.01.005
18. Eulalio A, Huntzinger E, Izaurralde E. (2008). Getting to the root of miRNA-mediated gene silencing. Cell 132(1): 9-14. doi: 10.1016/j.cell.2007.12.024
19. Fabian MR, Mathonnet G, Sundermeier T, Mathys H, Zipprich JT, Svitkin YV, Rivas F, Jinek M, Wohlschlegel J, Doudna JA, Chen CY, Shyu AB, Yates JR, 3rd, Hannon GJ, Filipowicz W, Duchaine TF, Sonenberg N. (2009). Mammalian miRNA RISC recruits CAF1 and PABP to affect PABP-dependent deadenylation. Mol Cell 35(6): 868-880. doi: 10.1016/j.molcel.2009.08.004
20. Fabian MR, Sonenberg N, Filipowicz W. (2010). Regulation of mRNA translation and stability by microRNAs. Annu Rev Biochem 79: 351-379. doi: 10.1146/annurev-biochem-060308-103103
21. Farazi TA, Spitzer JI, Morozov P, Tuschl T. (2011). miRNAs in human cancer. J Pathol 223(2): 102-115. doi: 10.1002/path.2806
22. Forman JJ, Coller HA. (2010). The code within the code: microRNAs target coding regions. Cell Cycle 9(8): 1533-1541
23. Friedman RC, Farh KK, Burge CB, Bartel DP. (2009). Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19(1): 92-105. doi: 10.1101/gr.082701.108
24. Grey F, Tirabassi R, Meyers H, Wu G, McWeeney S, Hook L, Nelson JA. (2010)A viral microRNA down-regulates multiple cell cycle genes through mRNA 5 UTRs. PLoS Pathog 6(6): e1000967. doi: 10.1371/journal.ppat.1000967
25. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. (2008). miRBase: tools for microRNA genomics. Nucleic Acids Res 36(Database issue): D154-158. doi: 10.1093/nar/gkm952
26. Grishok A, Pasquinelli AE, Conte D, Li N, Parrish S, Ha I, Baillie DL, Fire A, Ruvkun G, Mello CC. (2001). Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C elegans developmental timing. Cell 106(1): 23-34
27. Gu S, Jin L, Zhang F, Sarnow P, Kay MA. (2009). Biological basis for restriction of microRNA targets to the 3 untranslated region in mammalian mRNAs. Nat Struct Mol Biol 16(2): 144-150. doi: 10.1038/nsmb.1552
28. Haase AD, Jaskiewicz L, Zhang H, Laine S, Sack R, Gatignol A, Filipowicz W. (2005). TRBP, a regulator of cellular PKR and HIV-1 virus expression, interacts with Dicer and functions in RNA silencing. EMBO Rep 6(10): 961-967. doi: 10.1038/sj.embor.7400509
29. Han J, Lee Y, Yeom KH, Kim YK, Jin H, Kim VN. (2004). The Drosha-DGCR8 complex in primary microRNA processing. Genes Dev 18(24): 3016-3027. doi: 10.1101/gad.1262504
30. Han J, Lee Y, Yeom KH, Nam JW, Heo I, Rhee JK, Sohn SY, Cho Y, Zhang BT, Kim VN. (2006). Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell 125(5): 887-901. doi: 10.1016/j.cell.2006.03.043
31. Hon LS, Zhang Z. (2007). The roles of binding site arrangement and combinatorial targeting in microRNA repression of gene expression. Genome Biol 8(8): R166. doi: 10.1186/gb-2007-8-8-r166
32. Hsu JB, Chiu CM, Hsu SD, Huang WY, Chien CH, Lee TY, Huang HD. (2011). miRTar: an integrated system for identifyingmiRNA-Target interactions in human.BMCBioinformatics 12: 300. doi: 10.1186/1471-2105-12-300
33. Hu R, Liu W, Li H, Yang L, Chen C, Xia ZY, Guo LJ, Xie H, Zhou HD, Wu XP, Luo XH. (2011). A Runx2/miR-3960/miR-2861 regulatory feedback loop during mouse osteoblast differentiation. J Biol Chem 286(14): 12328-12339. doi: 10.1074/jbc.M110.176099
34. Huang J, Townsend C, Dou D, Liu H, Tan M. (2011). OMIT: A Domain-Specific Knowledge Base for MicroRNA Target Prediction. Pharm Res 28(12): 310-314. doi: 10.1007/s11095-011-0573-8
35. Humphreys DT, Westman BJ, Martin DI, Preiss T. (2005). MicroRNAs control translation initiation by inhibiting eukaryotic initiation factor 4E/cap and poly(A). tail function. Proc Natl Acad Sci U S A 102(47): 16961-16966. doi: 10.1073/pnas.0506482102
36. Hutvagner G, McLachlan J, Pasquinelli AE, Balint E, Tuschl T, Zamore PD. (2001). A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293(5531): 834-838. doi: 10.1126/science.1062961
37. John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS. (2004). Human MicroRNA targets. PLoS Biol 2(11): e363. doi: 10.1371/journal.pbio.0020363
38. Kawamata T, Seitz H, Tomari Y. (2009). Structural determinants of miRNAs for RISC loading and slicer-independent unwinding. Nat Struct Mol Biol 16(9): 953-960. doi: 10.1038/nsmb.1630
39. Kawamata T, Tomari Y. (2010). Making RISC. Trends Biochem Sci 35(7): 368-376. doi: 10.1016/j.tibs.2010.03.009
40. Khvorova A, Reynolds A, Jayasena SD. (2003). Functional siRNAs and miRNAs exhibit strand bias. Cell 115(2): 209-216
41. Kim J, Krichevsky A, Grad Y, Hayes GD, Kosik KS, Church GM, Ruvkun G. (2004). Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. Proc Natl Acad Sci U S A 101(1): 360-365. doi: 10.1073/pnas.2333854100
42. Kim VN, Nam JW. (2006). Genomics of microRNA. Trends Genet 22(3): 165-173. doi: 10.1016/j.tig.2006.01.003
43. Kong YW, Cannell IG, de Moor CH, Hill K, Garside PG, Hamilton TL, Meijer HA, Dobbyn HC, Stoneley M, Spriggs KA, Willis AE, Bushell M. (2008). The mechanism of micro-RNA-mediated translation repression is determined by the promoter of the target gene. Proc Natl Acad Sci U S A 105(26): 8866-8871. doi: 10.1073/pnas.0800650105
44. Krol J, Loedige I, Filipowicz W. (2010). The widespread regulation of microRNA biogenesis, function and decay. Nat Rev Genet 11(9): 597-610. doi: 10.1038/nrg2843
45. Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, Lee J, Provost P, Radmark O, Kim S, Kim VN. (2003). The nuclear RNase III Drosha initiates microRNA processing. Nature 425(6956): 415-419. doi: 10.1038/nature01957
46. Lee Y, Hur I, Park SY, Kim YK, Suh MR, Kim VN. (2006). The role of PACT in the RNA silencing pathway. Embo J 25(3): 522-532. doi: 10.1038/sj.emboj.7600942
47. Lee Y, Kim M, Han J, Yeom KH, Lee S, Baek SH, Kim VN. (2004). MicroRNA genes are transcribed by RNA polymerase II. Embo J 23(20): 4051-4060. doi: 10.1038/sj.emboj.7600385
48. Lhakhang TW, Chaudhry MA. (2011). Current approaches to micro-RNA analysis and target gene prediction. J Appl Genet 53(2): 149-158. doi: 10.1007/s13353-011-0060-2
49. Li H, Xie H, Liu W, Hu R, Huang B, Tan YF, Xu K, Sheng ZF, Zhou HD, Wu XP, Luo XH. (2009)A novel microRNA targeting HDAC5 regulates osteoblast differentiation in mice and contributes to primary osteoporosis in humans. J Clin Invest 119(12): 3666-3677. doi: 10.1172/JCI39832
50. Lindenblatt C, Schulze-Osthoff K, Totzke G. (2009). IkappaBzeta expression is regulated by miR-124a. Cell Cycle 8(13): 2019-2023
51. Liu H, Yue D, Chen Y, Gao SJ, Huang Y. (2010). Improving performance of mammalian microRNA target prediction. BMC Bioinformatics 11: 476. doi: 10.1186/1471-2105-11-476
52. Liu X, Fortin K, Mourelatos Z. (2008). MicroRNAs: biogenesis and molecular functions. Brain Pathol 18(1): 113-121. doi: 10.1111/j.1750-3639.2007.00121.x
53. Lund E, Guttinger S, Calado A, Dahlberg JE, Kutay U. (2004). Nuclear export of microRNA precursors. Science 303. (5654): 95-98. doi: 10.1126/science.1090599
54. Macrae IJ, Zhou K, Li F, Repic A, Brooks AN, Cande WZ, Adams PD, Doudna JA. (2006). Structural basis for double-stranded RNA processing by Dicer. Science 311(5758): 195-198. doi: 10.1126/science.1121638
55. Maroney PA, Yu Y, Fisher J, Nilsen TW. (2006). Evidence that microRNAs are associated with translating messenger RNAs in human cells. Nat Struct Mol Biol 13(12): 1102-1107. doi: 10.1038/nsmb1174
56. 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 eIF4 F. Science. 317(5845): 1764-1767. doi: 10.1126/science.1146067
57. Meister G, Landthaler M, Patkaniowska A, Dorsett Y, Teng G, Tuschl T. (2004). Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol Cell 15(2): 185-197. doi: 10.1016/j.molcel.2004.07.007
58. Melo SA, Ropero S, Moutinho C, Aaltonen LA, Yamamoto H, Calin GA, Rossi S, Fernandez AF, Carneiro F, Oliveira C, Ferreira B, Liu CG, Villanueva A, Capella G, Schwartz S, Jr., Shiekhattar R, Esteller M. (2009). A TARBP2 mutation in human cancer impairs microRNA processing and DICER1 function. Nat Genet 41(3): 365-370. doi: 10.1038/ng.317
59. Moretti F, Thermann R, Hentze MW. (2010). Mechanism of translational regulation by miR-2 from sites in the 5 untranslated region or the open reading frame. Rna 16(12): 2493-2502. doi: 10.1261/rna.2384610
60. Nelson PT, Hatzigeorgiou AG, Mourelatos Z. (2004). miRNP: mRNA association in polyribosomes in a human neuronal cell line. Rna 10(3): 387-394
61. Niepmann M. (2009). Activation of hepatitis C virus translation by a liver-specific microRNA. Cell Cycle 8(10): 1473-1477
62. Nottrott S, Simard MJ, Richter JD. (2006). Human let-7a miRNA blocks protein production on actively translating polyribosomes. Nat Struct Mol Biol 13(12): 1108-1114. doi: 10.1038/nsmb1173
63. Okamura K, Phillips MD, Tyler DM, Duan H, Chou YT, Lai EC. (2008). The regulatory activity of micro RNA species has substantial influence on microRNA and 3 UTR evolution. Nat Struct Mol Biol 15(4): 354-363. doi: 10.1038/nsmb.1409
64. Olena AF, Patton JG. (2010). Genomic organization of microRNAs. J Cell Physiol 222(3): 540-545. doi: 10.1002/jcp.21993
65. Ou Z, Wada T, Gramignoli R, Li S, Strom SC, Huang M, Xie W. (2011). MicroRNA hsa-miR-613 targets the human LXRalpha gene and mediates a feedback loop of LXRalpha autoregulation. Mol Endocrinol 25(4): 584-596. doi: 10.1210/me.2010-0360
66. Parker R, Sheth U. (2007). P bodies and the control of mRNA translation and degradation. Mol Cell. 25(5): 635-646. doi: 10.1016/j.molcel.2007.02.011
67. Paroo Z, Ye X, Chen S, Liu Q. (2009). Phosphorylation of the human microRNA-generating complex mediates MAPK/Erk signaling. Cell 139(1): 112-122. doi: 10.1016/j.cell.2009.06.044
68. Petersen CP, Bordeleau ME, Pelletier J, Sharp PA. (2006). Short RNAs repress translation after initiation in mammalian cells. Mol Cell 21(4): 533-542. doi: 10.1016/j.molcel.2006.01.031
69. Pillai RS, Bhattacharyya SN, Artus CG, Zoller T, Cougot N, Basyuk E, Bertrand E, Filipowicz W. (2005). Inhibition of translational initiation by Let-7 MicroRNA in human cells. Science. 309(5740): 1573-1576. doi: 10.1126/science.1115079
70. Pothof J, van Gent DC. (2011). Spatiotemporal Aspects of MicroRNA-Mediated Gene Regulation. Adv Exp Med Biol 722: 75-85. doi: 10.1007/978-1-4614-0332-6-5
71. Ricci EP, Limousin T, Soto-Rifo R, Allison R, Poyry T, Decimo D, Jackson RJ, Ohlmann T. (2011). Activation of a microRNA response in trans reveals a new role for poly(A). in translational repression. Nucleic Acids Res 39(12): 5215-5231. doi: 10.1093/nar/gkr086
72. Roberts AP, Lewis AP, Jopling CL. (2011). miR-122 activates hepatitis C virus translation by a specialized mechanism requiring particular RNA components. Nucleic Acids Res 39(17): 7716-7729. doi: 10.1093/nar/gkr426
73. Rodriguez A, Griffiths-Jones S, Ashurst JL, Bradley A. (2004). Identification of mammalian microRNA host genes and transcription units. Genome Res 14(10A): 1902-1910. doi: 10.1101/gr.2722704
74. Schwarz DS, Hutvagner G, Du T, Xu Z, Aronin N, Zamore PD. (2003). Asymmetry in the assembly of the RNAi enzyme complex. Cell 115(2): 199-208
75. Vasudevan S, Tong Y, Steitz JA. (2007). Switching from repression to activation: microRNAs can up-regulate translation. Science 318(5858): 1931-1934. doi: 10.1126/science.1149460
76. Vella MC, Choi EY, Lin SY, Reinert K, Slack FJ. (2004). The C elegans microRNA let-7 binds to imperfect let-7 complementary sites from the lin-41 3 UTR. Genes Dev 18(2): 132-137. doi: 10.1101/gad.1165404
77. Wakiyama M, Takimoto K, Ohara O, Yokoyama S. (2007). Let-7 microRNA-mediated mRNA deadenylation and translational repression in a mammalian cell-free system. Genes Dev. 21(15): 1857-1862. doi: 10.1101/gad.1566707
78. Wang B, Yanez A, Novina CD. (2008). MicroRNA-repressed mRNAs contain 40 S but not 60 S components. Proc Natl Acad Sci U S A 105(14): 5343-5348. doi: 10.1073/pnas.0801102105
79. Westholm JO, Lai EC. (2011). Mirtrons: microRNAbiogenesis via splicing. Biochimie 93(11): 1897-1904. doi: 10.1016/j.biochi.2011.06.017
80. Williams AE. (2008). Functional aspects of animal microRNAs. Cell Mol Life Sci 65(4): 545-562. doi: 10.1007/s00018-007-7355-9
81. Yang JS, Phillips MD, Betel D, Mu P, Ventura A, Siepel AC, Chen KC, Lai EC. (2011). Widespread regulatory activity of vertebrate microRNA species. Rna 17(2): 312-326. doi: 10.1261/rna.2537911
82. Yi R, Qin Y, Macara IG, Cullen BR. (2003). Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev 17(24): 3011-3016. doi: 10.1101/gad.1158803
83. Yoda M, Kawamata T, Paroo Z, Ye X, Iwasaki S, Liu Q, Tomari Y. (2010). ATP-dependent human RISC assembly pathways. Nat Struct Mol Biol 17(1): 17-23. doi: 10.1038/nsmb.1733
84. Yuan X, Liu C, Yang P, He S, Liao Q, Kang S, Zhao Y. (2009). Clustered microRNAs coordination in regulating protein-protein interaction network. BMC Syst Biol 3: 65. doi: 10.1186/1752-0509-3-65
85. Zeng Y, Cullen BR. (2005). Efficient processing of primary microRNA hairpins by Drosha requires flanking nonstructured RNA sequences. J Biol Chem 280(30): 27595-27603. doi: 10.1074/jbc.M504714200