MicroRNAs: Biogenesis and molecular functions

Brain Pathology

Volumn 18, Issue 1, 2008, Pages 113-121

  Liu, Xuhang ^a   Fortin, Kristine ^a   Mourelatos, Zissimos ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

Ago; Argonaute; Dicer; microRNA; miRNA; miRNP; mRNA transcription; RISC; RNA intereference; RNAi; siRNA

Indexed keywords

AMINO ACID TRANSPORTER; ARGONAUTE 2 PROTEIN; ARGONAUTE PROTEIN; DNA DIRECTED RNA POLYMERASE III; DOUBLE STRANDED RNA; MESSENGER RNA; MICRORNA; PLANT RNA; RIBONUCLEASE III; RNA BINDING PROTEIN; RNA POLYMERASE II; RNA PRECURSOR; SMALL INTERFERING RNA;

AMINO TERMINAL SEQUENCE; BIOGENESIS; CARBOXY TERMINAL SEQUENCE; CONFERENCE PAPER; CYTOPLASM; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE SILENCING; HUMAN; MAMMAL; MOLECULAR BIOLOGY; NEMATODE; NEUROPATHOLOGY; NONHUMAN; PROTEIN ASSEMBLY; PROTEIN DOMAIN; PROTEIN FUNCTION; RNA ANALYSIS; RNA BINDING; RNA CLEAVAGE; RNA INTERFERENCE; RNA TRANSLATION; TRANSCRIPTION REGULATION;

ANIMALS; DROSOPHILA PROTEINS; GENE EXPRESSION REGULATION; HUMANS; MACROMOLECULAR SUBSTANCES; MICRORNAS; MODELS, ANIMAL; PROTEIN BIOSYNTHESIS; RNA INTERFERENCE; RNA, MESSENGER; RNA, SMALL INTERFERING;

EID: 38349131954     PISSN: 10156305     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1750-3639.2007.00121.x     Document Type: Conference Paper

References (103)

1. Ambros V (2004) The functions of animal microRNAs. Nature 431 : 350 355.
2. Ameres SL, Martinez J, Schroeder R (2007) Molecular basis for target RNA recognition and cleavage by human RISC. Cell 130 : 101 112.
3. Aravin AA, Hannon GJ, Brennecke J (2007) The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science 318 : 761 764.
4. Bagga S, Bracht J, Hunter S, Massirer K, Holtz J, Eachus R et al (2005) Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell 122 : 553 563.
5. Bartel DP, Chen CZ (2004) Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nat Rev Genet 5 : 396 400.
6. Berezikov E, Chung WJ, Willis J, Cuppen E, Lai EC (2007) Mammalian mirtron genes. Mol Cell 28 : 328 336.
7. Bernstein E, Caudy AA, Hammond SM, Hannon GJ (2001) Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409 : 363 366.
8. Bhattacharyya SN, Habermacher R, Martine U, Closs EI, Filipowicz W (2006) Relief of microRNA-mediated translational repression in human cells subjected to stress. Cell 125 : 1111 1124.
9. 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 : 185 191.
10. Brennecke J, Hipfner DR, Stark A, Russell RB, Cohen SM (2003) Bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell 113 : 25 36.
11. Brennecke J, Stark A, Russell RB, Cohen SM (2005) Principles of microRNA-target recognition. PLoS Biol 3 : e85.
12. Cai X, Cullen BR (2007) The imprinted H19 noncoding RNA is a primary microRNA precursor. RNA 13 : 313 316.
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. Carmell MA, Xuan Z, Zhang MQ, Hannon GJ (2002) The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes Dev 16 : 2733 2742.
15. Chendrimada TP, Finn KJ, Ji X, Baillat D, Gregory RI, Liebhaber SA et al (2007) MicroRNA silencing through RISC recruitment of eIF6. Nature 447 : 823 828.
16. Denli AM, Tops BB, Plasterk RH, Ketting RF, Hannon GJ (2004) Processing of primary microRNAs by the Microprocessor complex. Nature 432 : 231 235.
17. Doench JG, Sharp PA (2004) Specificity of microRNA target selection in translational repression. Genes Dev 18 : 504 511.
18. Dugas DV, Bartel B (2004) MicroRNA regulation of gene expression in plants. Curr Opin Plant Biol 7 : 512 520.
19. Elbashir SM, Lendeckel W, Tuschl T (2001) RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev 15 : 188 200.
20. Eulalio A, Behm-Ansmant I, Schweizer D, Izaurralde E (2007) P-body formation is a consequence, not the cause, of RNA-mediated gene silencing. Mol Cell Biol 27 : 3970 3981.
21. Eulalio A, Behm-Ansmant I, Izaurralde E (2007) P bodies: at the crossroads of post-transcriptional pathways. Nat Rev Mol Cell Biol 8 : 9 22.
22. Faller M, Matsunaga M, Yin S, Loo JA, Guo F (2007) Heme is involved in microRNA processing. Nat Struct Mol Biol 14 : 23 29.
23. Filipowicz W, Jaskiewicz L, Kolb FA, Pillai RS (2005) Post-transcriptional gene silencing by siRNAs and miRNAs. Curr Opin Struct Biol 15 : 331 341.
24. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391 : 806 811.
25. Forstemann K, Horwich MD, Wee L, Tomari Y, Zamore PD (2007) Drosophila microRNAs are sorted into functionally distinct argonaute complexes after production by dicer-1. Cell 130 : 287 297.
26. Fukuda T, Yamagata K, Fujiyama S, Matsumoto T, Koshida I, Yoshimura K et al (2007) DEAD-box RNA helicase subunits of the Drosha complex are required for processing of rRNA and a subset of microRNAs. Nat Cell Biol 9 : 604 611.
27. Gebauer F, Hentze MW (2004) Molecular mechanisms of translational control. Nat Rev Mol Cell Biol 5 : 827 835.
28. Giraldez AJ, Mishima Y, Rihel J, Grocock RJ, Van Dongen S, Inoue K et al (2006) Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science 312 : 75 79.
29. Gregory RI, Yan KP, Amuthan G, Chendrimada T, Doratotaj B, Cooch N et al (2004) The Microprocessor complex mediates the genesis of microRNAs. Nature 432 : 235 240.
30. Gregory RI, Chendrimada TP, Cooch N, Shiekhattar R (2005) Human RISC couples microRNA biogenesis and posttranscriptional gene silencing. Cell 123 : 631 640.
31. Griffiths-Jones S, Saini HK, Dongen SV, Enright AJ (2007) miRBase: tools for microRNA genomics. Nucleic Acids Res, in press.
32. Guil S, Caceres JF (2007) The multifunctional RNA-binding protein hnRNP A1 is required for processing of miR-18a. Nat Struct Mol Biol 14 : 591 596.
33. Hamilton AJ, Baulcombe DC (1999) A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 286 : 950 952.
34. Hammond SM, Boettcher S, Caudy AA, Kobayashi R, Hannon GJ (2001) Argonaute2, a link between genetic and biochemical analyses of RNAi. Science 293 : 1146 1150.
35. Han J, Lee Y, Yeom KH, Kim YK, Jin H, Kim VN (2004) The Drosha-DGCR8 complex in primary microRNA processing. Genes Dev 18 : 3016 3027.
36. Han J, Lee Y, Yeom KH, Nam JW, Heo I, Rhee JK et al (2006) Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell 125 : 887 901.
37. 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 USA 102 : 16961 16966.
38. Hutvagner G, Zamore PD (2002) A microRNA in a multiple-turnover RNAi enzyme complex. Science 297 : 2056 2060.
39. Kim J, Krichevsky A, Grad Y, Hayes GD, Kosik KS, Church GM et al (2004) Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. Proc Natl Acad Sci USA 101 : 360 365.
40. Kim VN (2006) Small RNAs just got bigger: Piwi-interacting RNAs (piRNAs) in mammalian testes. Genes Dev 20 : 1993 1997.
41. Kiriakidou M, Nelson PT, Kouranov A, Fitziev P, Bouyioukos C, Mourelatos Z et al (2004) A combined computational-experimental approach predicts human microRNA targets. Genes Dev 18 : 1165 1178.
42. Kiriakidou M, Tan GS, Lamprinaki S, De Planell-Saguer M, Nelson PT, Mourelatos Z (2007) An mRNA m7G cap binding-like motif within human Ago2 represses translation. Cell 129 : 1141 1151.
43. Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, Epstein EJ et al (2005) Combinatorial microRNA target predictions. Nat Genet 37 : 495 500.
44. Lai EC (2002) Micro RNAs are complementary to 3′ UTR sequence motifs that mediate negative post-transcriptional regulation. Nat Genet 30 : 363 364.
45. Landthaler M, Yalcin A, Tuschl T (2004) The human DiGeorge syndrome critical region gene 8 and its D. melanogaster homolog are required for miRNA biogenesis. Curr Biol 14 : 2162 2167.
46. Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75 : 843 854.
47. Lee Y, Jeon K, Lee JT, Kim S, Kim VN (2002) MicroRNA maturation: stepwise processing and subcellular localization. EMBO J 21 : 4663 4670.
48. Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J et al (2003) The nuclear RNase III Drosha initiates microRNA processing. Nature 425 : 415 419.
49. Lee Y, Kim M, Han J, Yeom KH, Lee S, Baek SH et al (2004) MicroRNA genes are transcribed by RNA polymerase II. EMBO J 23 : 4051 4060.
50. Lee YS, Nakahara K, Pham JW, Kim K, He Z, Sontheimer EJ et al (2004) Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell 117 : 69 81.
51. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB (2003) Prediction of mammalian microRNA targets. Cell 115 : 787 798.
52. Lingel A, Simon B, Izaurralde E, Sattler M (2004) Nucleic acid 3′-end recognition by the Argonaute2 PAZ domain. Nat Struct Mol Biol 11 : 576 577.
53. Liu J, Carmell MA, Rivas FV, Marsden CG, Thomson JM, Song JJ et al (2004) Argonaute2 is the catalytic engine of mammalian RNAi. Science 305 : 1437 1441.
54. Liu Q, Rand TA, Kalidas S, Du F, Kim HE, Smith DP et al (2003) R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway. Science 301 : 1921 1925.
55. Llave C, Xie Z, Kasschau KD, Carrington JC (2002) Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297 : 2053 2056.
56. Long D, Lee R, Williams P, Chan CY, Ambros V, Ding Y (2007) Potent effect of target structure on microRNA function. Nat Struct Mol Biol 14 : 287 294.
57. Lund E, Guttinger S, Calado A, Dahlberg JE, Kutay U (2004) Nuclear export of microRNA precursors. Science 303 : 95 98.
58. Ma JB, Yuan YR, Meister G, Pei Y, Tuschl T, Patel DJ (2005) Structural basis for 5′-end-specific recognition of guide RNA by the A. fulgidus Piwi protein. Nature 434 : 666 670.
59. Maniataki E, Mourelatos Z (2005) A human, ATP-independent, RISC assembly machine fueled by pre-miRNA. Genes Dev 19 : 2979 2990.
60. 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 : 1102 1107.
61. Martinez J, Tuschl T (2004) RISC is a 5′ phosphomonoester-producing RNA endonuclease. Genes Dev 18 : 975 980.
62. Mathonnet G, Fabian MR, Svitkin YV, Parsyan A, Huck L, Murata T et al (2007) MicroRNA inhibition of translation initiation in vitro by targeting the cap-binding complex eIF4F. Science 317 : 1764 1767.
63. Matranga C, Tomari Y, Shin C, Bartel DP, Zamore PD (2005) Passenger-strand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes. Cell 123 : 607 620.
64. Miranda KC, Huynh T, Tay Y, Ang YS, Tam WL, Thomson AM et al (2006) A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell 126 : 1203 1217.
65. Mourelatos Z, Dostie J, Paushkin S, Sharma A, Charroux B, Abel L et al (2002) miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev 16 : 720 728.
66. Nelson PT, Hatzigeorgiou AG, Mourelatos Z (2004) miRNP:mRNA association in polyribosomes in a human neuronal cell line. RNA 10 : 387 394.
67. Nottrott S, Simard MJ, Richter JD (2006) Human let-7a miRNA blocks protein production on actively translating polyribosomes. Nat Struct Mol Biol 13 : 1108 1114.
68. Okamura K, Hagen JW, Duan H, Tyler DM, Lai EC (2007) The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila. Cell 130 : 89 100.
69. Olsen PH, Ambros V (1999) The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiation of translation. Dev Biol 216 : 671 680.
70. Parker JS, Roe SM, Barford D (2004) Crystal structure of a PIWI protein suggests mechanisms for siRNA recognition and slicer activity. EMBO J 23 : 4727 4737.
71. Parker JS, Roe SM, Barford D (2005) Structural insights into mRNA recognition from a PIWI domain-siRNA guide complex. Nature 434 : 663 666.
72. Parker R, Sheth U (2007) P bodies and the control of mRNA translation and degradation. Mol Cell 25 : 635 646.
73. Petersen CP, Bordeleau ME, Pelletier J, Sharp PA (2006) Short RNAs repress translation after initiation in mammalian cells. Mol Cell 21 : 533 542.
74. 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.
75. Pillai RS, Bhattacharyya SN, Artus CG, Zoller T, Cougot N, Basyuk E et al (2005) Inhibition of translational initiation by Let-7 MicroRNA in human cells. Science 309 : 1573 1576.
76. Provost P, Dishart D, Doucet J, Frendewey D, Samuelsson B, Radmark O (2002) Ribonuclease activity and RNA binding of recombinant human Dicer. EMBO J 21 : 5864 5874.
77. Rajewsky N, Socci ND (2004) Computational identification of microRNA targets. Dev Biol 267 : 529 535.
78. Rand TA, Petersen S, Du F, Wang X (2005) Argonaute2 cleaves the anti-guide strand of siRNA during RISC activation. Cell 123 : 621 629.
79. Rehwinkel J, Behm-Ansmant I, Gatfield D, Izaurralde E (2005) A crucial role for GW182 and the DCP1:DCP2 decapping complex in miRNA-mediated gene silencing. RNA 11 : 1640 1647.
80. Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE et al (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403 : 901 906.
81. Richter JD, Sonenberg N (2005) Regulation of cap-dependent translation by eIF4E inhibitory proteins. Nature 433 : 477 480.
82. Rigoutsos I, Huynh T, Miranda K, Tsirigos A, McHardy A, Platt D (2006) Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes. Proc Natl Acad Sci USA 103 : 6605 6610.
83. Rivas FV, Tolia NH, Song JJ, Aragon JP, Liu J, Hannon GJ et al (2005) Purified Argonaute2 and an siRNA form recombinant human RISC. Nat Struct Mol Biol 12 : 340 349.
84. Rodriguez A, Griffiths-Jones S, Ashurst JL, Bradley A (2004) Identification of mammalian microRNA host genes and transcription units. Genome Res 14 : 1902 1910.
85. Ruby JG, Jan CH, Bartel DP (2007) Intronic microRNA precursors that bypass Drosha processing. Nature 448 : 83 86.
86. Saetrom P, Heale BS, Snove O, Jr., Aagaard, L, Alluin J, Rossi JJ (2007) Distance constraints between microRNA target sites dictate efficacy and cooperativity. Nucleic Acids Res 35 : 2333 2342.
87. Schwarz DS, Tomari Y, Zamore PD (2004) The RNA-induced silencing complex is a Mg2+-dependent endonuclease. Curr Biol 14 : 787 791.
88. Seggerson K, Tang L, Moss EG (2002) Two genetic circuits repress the Caenorhabditis elegans heterochronic gene lin-28 after translation initiation. Dev Biol 243 : 215 225.
89. Song JJ, Smith SK, Hannon GJ, Joshua-Tor L (2004) Crystal structure of Argonaute and its implications for RISC slicer activity. Science 305 : 1434 1437.
90. Thermann R, Hentze MW (2007) Drosophila miR2 induces pseudo-polysomes and inhibits translation initiation. Nature 447 : 875 878.
91. Tomari Y, Zamore PD (2005) Perspective: machines for RNAi. Genes Dev 19 : 517 529.
92. Tomari Y, Matranga C, Haley B, Martinez N, Zamore PD (2004) A protein sensor for siRNA asymmetry. Science 306 : 1377 1380.
93. Tomari Y, Du T, Zamore PD (2007) Sorting of Drosophila small silencing RNAs. Cell 130 : 299 308.
94. 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 : 132 137.
95. 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 : 1857 1862.
96. Wightman B, Ha I, Ruvkun G (1993) Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75 : 855 862.
97. Wu L, Fan J, Belasco JG (2006) MicroRNAs direct rapid deadenylation of mRNA. Proc Natl Acad Sci USA 103 : 4034 4039.
98. Yang W, Steitz TA (1995) Recombining the structures of HIV integrase, RuvC and RNase H. Structure 3 : 131 134.
99. Yekta S, Shih IH, Bartel DP (2004) MicroRNA-directed cleavage of HOXB8 mRNA. Science 304 : 594 596.
100. 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 : 3011 3016.
101. Yuan YR, Pei Y, Ma JB, Kuryavyi V, Zhadina M, Meister G et al (2005) Crystal structure of A. aeolicus argonaute, a site-specific DNA-guided endoribonuclease, provides insights into RISC-mediated mRNA cleavage. Mol Cell 19 : 405 419.
102. Zhang H, Kolb FA, Brondani V, Billy E, Filipowicz W (2002) Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP. EMBO J 21 : 5875 5885.
103. Zhang H, Kolb FA, Jaskiewicz L, Westhof E, Filipowicz W (2004) Single processing center models for human Dicer and bacterial RNase III. Cell 118 : 57 68.