Dicer-independent, Ago2-mediated microRNA biogenesis in vertebrates

Cell Cycle

Volumn 9, Issue 22, 2010, Pages 4455-4460

  Yang, Jr Shiuan ^a,b   Lai, Eric C ^a  

^a Department of Obstetrics Gynecology   (United States)

^b Weill Cornell Graduate School of Biomedical Sciences   (United States)

Author keywords

Ago2; Dicer independent; Erythropoiesis; mir 451; Slicer

Indexed keywords

ARGONAUTE 2 PROTEIN; DICER; MICRORNA; MICRORNA 451; PROTEIN DROSHA; RIBONUCLEASE; SHORT HAIRPIN RNA; SMALL INTERFERING RNA; UNCLASSIFIED DRUG;

BIOGENESIS; DNA HAIRPIN; GENE EXPRESSION; GENE LOCUS; GENE SILENCING; GENE STRUCTURE; HUMAN; MOLECULAR CLONING; NONHUMAN; REVIEW; VERTEBRATE;

ANIMALIA; VERTEBRATA;

EID: 78649894176     PISSN: 15384101     EISSN: 15514005     Source Type: Journal    
DOI: 10.4161/cc.9.22.13958     Document Type: Review

References (72)

1. Flynt AS, Lai EC. Biological principles of microRNA- mediated regulation: shared themes amid diversity. Nat Rev Genet 2008; 9:831-42.
2. Herranz H, Cohen SM. MicroRNAs and gene regulatory networks: Managing the impact of noise in biological systems. Genes Dev 2010; 24:1339-44.
3. Filipowicz W, Bhattacharyya SN, Sonenberg N. Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat Rev Genet 2008; 9:102-14.
4. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB. Prediction of mammalian microRNA targets. Cell 2003; 115:787-98.
5. Lai EC. microRNAs are complementary to 3′ UTR sequence motifs that mediate negative post-transcriptional regulation. Nat Genet 2002; 30:363-4.
6. Friedman RC, Farh KK, Burge CB, Bartel DP. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 2009; 19:92-105.
7. Bartel DP. MicroRNAs: Target recognition and regulatory functions. Cell 2009; 136:215-33.
8. Kim VN, Han J, Siomi MC. Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol 2009; 10:126-39.
9. Winter J, Jung S, Keller S, Gregory RI, Diederichs S. Many roads to maturity: microRNA biogenesis pathways and their regulation. Nat Cell Biol 2009; 11:228-34.
10. Miyoshi K, Miyoshi T, Siomi H. Many ways to generate microRNA-like small RNAs: Non-canonical pathways for microRNA production. Mol Genet Genomics 2010; 284:95-103.
11. Okamura K, Lai EC. Diversity and complexity of dicer dependent small RNA networks in animals. Seikagaku 2009; 81:904-9.
12. Okamura K, Hagen JW, Duan H, Tyler DM, Lai EC. The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila. Cell 2007; 130:89-100.
13. Ruby JG, Jan CH, Bartel DP. Intronic microRNA precursors that bypass Drosha processing. Nature 2007; 448:83-6.
14. Berezikov E, Chung WJ, Willis J, Cuppen E, Lai EC. Mammalian mirtron genes. Mol Cell 2007; 28:328-36.
15. Babiarz JE, Ruby JG, Wang Y, Bartel DP, Blelloch R. Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs. Genes Dev 2008; 22:2773-85.
16. Glazov EA, Cottee PA, Barris WC, Moore RJ, Dalrymple BP, Tizard ML. A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. Genome Res 2008; 18:957-64.
17. Flynt AS, Chung WJ, Greimann JC, Lima CD, Lai EC. microRNA biogenesis via splicing and exosome-mediated trimming in Drosophila. Mol Cell 2010; 38:900-7.
18. Ender C, Krek A, Friedlander MR, Beitzinger M, Weinmann L, Chen W, et al. A human snoRNA with microRNA-like functions. Mol Cell 2008; 32:519-28.
19. Glazov EA, Kongsuwan K, Assavalapsakul W, Horwood PF, Mitter N, Mahony TJ. Repertoire of bovine miRNA and miRNA-like small regulatory RNAs expressed upon viral infection. PLoS ONE 2009; 4:6349.
20. Taft RJ, Glazov EA, Lassmann T, Hayashizaki Y, Carninci P, Mattick JS. Small RNAs derived from snoRNAs. Rna 2009; 15:1233-40.
21. Brameier M, Herwig A, Reinhardt R, Walter L, Gruber J. Human box C/D snoRNAs with miRNA like functions: Expanding the range of regulatory RNAs. Nucleic Acids Res 2010.
22. Cole C, Sobala A, Lu C, Thatcher SR, Bowman A, Brown JW, et al. Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. Rna 2009; 15:2147-60.
23. Haussecker D, Huang Y, Lau A, Parameswaran P, Fire AZ, Kay MA. Human tRNA-derived small RNAs in the global regulation of RNA silencing. Rna 2010; 16:673-95.
24. Bogerd HP, Karnowski HW, Cai X, Shin J, Pohlers M, Cullen BR. A mammalian herpesvirus uses noncanonical expression and processing mechanisms to generate viral MicroRNAs. Mol Cell 2010; 37:135-42.
25. Okamura K, Lai EC. Endogenous small interfering RNAs in animals. Nat Rev Mol Cell Biol 2008; 9:673-8.
26. Altuvia Y, Landgraf P, Lithwick G, Elefant N, Pfeffer S, Aravin A, et al. Clustering and conservation patterns of human microRNAs. Nucleic Acids Res 2005; 33:2697-706.
27. Rathjen T, Nicol C, McConkey G, Dalmay T. Analysis of short RNAs in the malaria parasite and its red blood cell host. FEBS Lett 2006; 580:5185-8.
28. Nelson PT, De Planell-Saguer M, Lamprinaki S, Kiriakidou M, Zhang P, O'Doherty U, et al. A novel monoclonal antibody against human Argonaute proteins reveals unexpected characteristics of miRNAs in human blood cells. RNA 2007; 13:1787-92.
29. Siolas D, Lerner C, Burchard J, Ge W, Linsley PS, Paddison PJ, et al. Synthetic shRNAs as potent RNAi triggers. Nat Biotechnol 2005; 23:227-31.
30. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: Tools for microRNA genomics. Nucleic Acids Res 2008; 36:154-8.
31. Lai EC, Tomancak P, Williams RW, Rubin GM. Computational identification of Drosophila microRNA genes. Genome Biol 2003; 4:1-20.
32. Berezikov E, Guryev V, van de Belt J, Wienholds E, Plasterk RH, Cuppen E. Phylogenetic shadowing and computational identification of human microRNA genes. Cell 2005; 120:21-4.
33. Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, et al. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 2007; 450:219-32.
34. Lai EC. microRNAs: Runts of the genome assert themselves. Curr Biol 2003; 13:925-36.
35. Yang JS, Maurin T, Robine N, Rasmussen KD, Jeffrey KL, Chandwani R, et al. Conserved vertebrate mir-451 provides a platform for dicer-independent, Ago2-mediated microRNA biogenesis. Proc Natl Acad Sci USA 2010; 107:15163-8.
36. Kawamata T, Seitz H, Tomari Y. Structural determinants of miRNAs for RISC loading and slicer-independent unwinding. Nat Struct Mol Biol 2009; 16:953-60.
37. Cheloufi S, Dos Santos CO, Chong MM, Hannon GJ. A dicer-independent miRNA biogenesis pathway that requires Ago catalysis. Nature 2010; 465:584-9.
38. Cifuentes D, Xue H, Taylor DW, Patnode H, Mishima Y, Cheloufi S, et al. A novel miRNA processing pathway independent of dicer requires argonaute2 catalytic activity. Science 2010; 328:1694-8.
39. Han J, Lee Y, Yeom KH, Nam JW, Heo I, Rhee JK, et al. Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell 2006; 125:887-901.
40. Diederichs S, Haber DA. Dual role for argonautes in microRNA processing and posttranscriptional regulation of microRNA expression. Cell 2007; 131:1097-108.
41. Rasmussen KD, Simmini S, Abreu-Goodger C, Bartonicek N, Di Giacomo M, Bilbao-Cortes D, et al. The miR-144/451 locus is required for erythroid homeostasis. J Exp Med 2010; 207:1351-8.
42. O'Carroll D, Mecklenbrauker I, Das PP, Santana A, Koenig U, Enright AJ, et al. A Slicer-independent role for Argonaute 2 in hematopoiesis and the microRNA pathway. Genes Dev 2007; 21:1999-2004.
43. Dore LC, Amigo JD, Dos Santos CO, Zhang Z, Gai X, Tobias JW, et al. A GATA-1-regulated microRNA locus essential for erythropoiesis. Proc Natl Acad Sci USA 2008; 105:3333-8.
44. Pase L, Layton JE, Kloosterman WP, Carradice D, Waterhouse PM, Lieschke GJ. miR-451 regulates zebrafish erythroid maturation in vivo via its target gata2. Blood 2009; 113:1794-804.
45. Papapetrou EP, Korkola JE, Sadelain M. A genetic strategy for single and combinatorial analysis of mirna function in mammalian hematopoietic stem cells. Stem Cells 2010; 28:287-96.
46. Yu D, dos Santos CO, Zhao G, Jiang J, Amigo JD, Khandros E, et al. miR-451 protects against erythroid oxidant stress by repressing 14-3-3zeta. Genes Dev 24:1620-33.
47. Patrick DM, Zhang CC, Tao Y, Yao H, Qi X, Schwartz RJ, et al. Defective erythroid differentiation in miR-451 mutant mice mediated by 14-3-3zeta. Genes Dev 24:1614-9.
48. Chang K, Elledge SJ, Hannon GJ. Lessons from Nature: microRNA-based shRNA libraries. Nat Methods 2006; 3:707-14.
49. Tan GS, Garchow BG, Liu X, Yeung J, Morris JPt, Cuellar TL, et al. Expanded RNA-binding activities of mammalian Argonaute 2. Nucleic Acids Res 2009; 37:7533-45.
50. Giraldez AJ, Mishima Y, Rihel J, Grocock RJ, Van Dongen S, Inoue K, et al. Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science 2006; 312:75-9.
51. Giraldez AJ, Cinalli RM, Glasner ME, Enright AJ, Thomson JM, Baskerville S, et al. MicroRNAs regulate brain morphogenesis in zebrafish. Science 2005; 308:833-8.
52. Koralov SB, Muljo SA, Galler GR, Krek A, Chakraborty T, Kanellopoulou C, et al. Dicer ablation affects antibody diversity and cell survival in the B lymphocyte lineage. Cell 2008; 132:860-74.
53. Ventura A, Young AG, Winslow MM, Lintault L, Meissner A, Erkeland SJ, et al. Targeted deletion reveals essential and overlapping functions of the miR-17 through 92 family of miRNA clusters. Cell 2008; 132:875-86.
54. Silva JM, Li MZ, Chang K, Ge W, Golding MC, Rickles RJ, et al. Second-generation shRNA libraries covering the mouse and human genomes. Nat Genet 2005; 37:1281-8.
55. Jackson AL, Burchard J, Schelter J, Chau BN, Cleary M, Lim L, et al. Widespread siRNA "off-target" transcript silencing mediated by seed region sequence complementarity. Rna 2006; 12:1179-87.
56. Schwarz DS, Hutvagner G, Du T, Xu Z, Aronin N, Zamore PD. Asymmetry in the assembly of the RNAi enzyme complex. Cell 2003; 115:199-208.
57. Khvorova A, Reynolds A, Jayasena SD. Functional siRNAs and miRNAs exhibit strand bias. Cell 2003; 115:209-16.
58. Kumar MS, Lu J, Mercer KL, Golub TR, Jacks T. Impaired microRNA processing enhances cellular transformation and tumorigenesis. Nat Genet 2007; 39:673-7.
59. Kumar MS, Pester RE, Chen CY, Lane K, Chin C, Lu J, et al. Dicer1 functions as a haploinsufficient tumor suppressor. Genes Dev 2009; 23:2700-4.
60. Lin RJ, Lin YC, Chen J, Kuo HH, Chen YY, Diccianni MB, et al. microRNA signature and expression of Dicer and Drosha can predict prognosis and delineate risk groups in neuroblastoma. Cancer Res 2010; 70:7841-50.
61. Pampalakis G, Diamandis EP, Katsaros D, Sotiropoulou G. Downregulation of dicer expression in ovarian cancer tissues. Clin Biochem 43:324-7.
62. Karube Y, Tanaka H, Osada H, Tomida S, Tatematsu Y, Yanagisawa K, et al. Reduced expression of Dicer associated with poor prognosis in lung cancer patients. Cancer Sci 2005; 96:111-5.
63. Merritt WM, Lin YG, Han LY, Kamat AA, Spannuth WA, Schmandt R, et al. Dicer, Drosha and outcomes in patients with ovarian cancer. N Engl J Med 2008; 359:2641-50.
64. Hill DA, Ivanovich J, Priest JR, Gurnett CA, Dehner LP, Desruisseau D, et al. DICER1 mutations in familial pleuropulmonary blastoma. Science 2009; 325:965.
65. Heo I, Joo C, Kim YK, Ha M, Yoon MJ, Cho J, et al. TUT4 in concert with Lin28 suppresses microRNA biogenesis through pre-microRNA uridylation. Cell 2009; 138:696-708.
66. Hagan JP, Piskounova E, Gregory RI. Lin28 recruits the TUTase Zcchc11 to inhibit let-7 maturation in mouse embryonic stem cells. Nat Struct Mol Biol 2009; 16:1021-5.
67. Ameres SL, Horwich MD, Hung JH, Xu J, Ghildiyal M, Weng Z, et al. Target RNA-directed trimming and tailing of small silencing RNAs. Science 2010; 328:1534-9.
68. Song JJ, Smith SK, Hannon GJ, Joshua-Tor L. Crystal structure of Argonaute and its implications for RISC slicer activity. Science 2004; 305:1434-7.
69. Parker JS, Roe SM, Barford D. Crystal structure of a PIWI protein suggests mechanisms for siRNA recognition and slicer activity. EMBO J 2004; 23:4727-37.
70. Yuan YR, Pei Y, Ma JB, Kuryavyi V, Zhadina M, Meister G, et al. Crystal structure of A. aeolicus argonaute, a site-specific DNA-guided endoribonuclease, provides insights into RISC-mediated mRNA cleavage. Mol Cell 2005; 19:405-19.
71. Halic M, Moazed D. Dicer-independent primal RNAs trigger RNAi and heterochromatin formation. Cell 2010; 140:504-16.
72. Lee HC, Li L, Gu W, Xue Z, Crosthwaite SK, Pertsemlidis A, et al. Diverse pathways generate microRNA-like RNAs and Dicer-independent small interfering RNAs in fungi. Mol Cell 38:803-14.