Systematic identification of mrNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance

PLoS ONE

Volumn 3, Issue 5, 2008, Pages

  Hendrickson, David G ^a   Hogan, Daniel J ^a   Herschlag, Daniel ^a   Ferrell, James E ^a   Brown, Patrick O ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARGONAUTE 2 PROTEIN; EPITOPE; MESSENGER RNA; MICRORNA; MIR 1 PROTEIN; MIR 124 PROTEIN; RIBONUCLEOPROTEIN; RNA INDUCED SILENCING COMPLEX; ARGONAUTE 2 PROTEIN, DROSOPHILA; DROSOPHILA PROTEIN;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; CELL STRAIN HEK293; CONTROLLED STUDY; DNA MICROARRAY; GENE EXPRESSION; GENETIC TRANSFECTION; HUMAN; HUMAN CELL; IMMUNOPRECIPITATION; MICROARRAY ANALYSIS; QUANTITATIVE ANALYSIS; ANIMAL; CELL LINE; GENE EXPRESSION REGULATION; GENE SILENCING; GENETIC TRANSCRIPTION; GENETICS; KIDNEY; KINETICS;

3' UNTRANSLATED REGIONS; 5' UNTRANSLATED REGIONS; ANIMALS; CELL LINE; DROSOPHILA PROTEINS; GENE EXPRESSION REGULATION; GENE SILENCING; HUMANS; KIDNEY; KINETICS; MICRORNAS; RNA, MESSENGER; RNA-INDUCED SILENCING COMPLEX; TRANSCRIPTION, GENETIC; TRANSFECTION;

EID: 47749154078     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0002126     Document Type: Article

References (76)

1. Ambros V (2004) The functions of animal microRNAs. Nature 431: 350-355.
2. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
3. Carthew RW (2006) Gene regulation by microRNAs. Curr Opin Genet Dev 16: 203-208.
4. Chen PY, Meister G (2005) microRNA-guided posttranscriptional gene regulation. Biol Chem 386: 1205-1218.
5. Farh KK, Grimson A, Jan C, Lewis BP, Johnston WK, et al. (2005) The widespread impact of mammalian MicroRNAs on mRNA repression and evolution. Science 310: 1817-1821.
6. 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.
7. Abbott AL, Alvarez-Saavedra E, Miska EA, Lau NC, Bartel DP, et al. (2005) The let-7 MicroRNA family members mir-48, mir-84, and mir-241 function together to regulate developmental timing in Caenorhabditis elegans. Dev Cell 9: 403-414.
8. Alvarez-Garcia I, Miska EA (2005) MicroRNA functions in animal development and human disease. Development 132: 4653-4662.
9. Hatfield SD, Shcherbata HR, Fischer KA, Nakahara K, Carthew RW, et al. (2005) Stem cell division is regulated by the microRNA pathway. Nature 435: 974-978.
10. Kloosterman WP, Plasterk RH (2006) The diverse functions of microRNAs in animal development and disease. Dev Cell 11: 441-450.
11. Linsley PS, Schelter J, Burchard J, Kibukawa M, Martin MM, et al. (2007) Transcripts targeted by the microRNA-16 family cooperatively regulate cell cycle progression. Mol Cell Biol 27: 2240-2252.
12. Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, et al. (2005) MicroRNA expression profiles classify human cancers. Nature 435: 834-838.
13. 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.
14. Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, et al. (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403: 901-906.
15. Gregory RI, Chendrimada TP, Cooch N, Shiekhattar R (2005) Human RISC couples microRNA biogenesis and posttranscriptional gene silencing. Cell 123: 631-640.
16. Hammond SM, Bernstein E, Beach D, Hannon GJ (2000) An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 404: 293-296.
17. 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.
18. Chendrimada TP, Gregory RI, Kumaraswamy E, Norman J, Cooch N, et al. (2005) TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature 436: 740-744.
19. Okamura K, Ishizuka A, Siomi H, Siomi MC (2004) Distinct roles for Argonaute proteins in small RNA-directed RNA cleavage pathways. Genes Dev 18: 1655-1666.
20. Rand TA, Petersen S, Du F, Wang X (2005) Argonaute2 cleaves the anti-guide strand of siRNA during RISC activation. Cell 123: 621-629.
21. Meister G, Landthaler M, Patkaniowska A, Dorsett Y, Teng G, et al. (2004) Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol Cell 15: 185-197.
22. Pham JW, Pellino JL, Lee YS, Carthew RW, Sontheimer EJ (2004) A Dicer-2-dependent 80s complex cleaves targeted mRNAs during RNAi in Drosophila. Cell 117: 83-94.
23. Peters L, Meister G (2007) Argonaute proteins: mediators of RNA silencing. Mol Cell 26: 611-623.
24. 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.
25. Hall TM (2005) Structure and function of argonaute proteins. Structure 13: 1403-1408.
26. 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.
27. Meister G, Tuschl T (2004) Mechanisms of gene silencing by double-stranded RNA. Nature 431: 343-349.
28. Hutvagner G, Zamore PD (2002) A microRNA in a multiple-turnaver RNAi enzyme complex. Science 297: 2056-2060.
29. Yekta S, Shih IH, Bartel DP (2004) MicroRNA-directed cleavage of HOXB8 mRNA. Science 304: 594-596.
30. Doench JG, Sharp PA (2004) Specificity of microRNA target selection in translational repression. Genes Dev 18: 504-511.
31. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB (2003) Prediction of mammalian microRNA targets. Cell 115: 787-798.
32. Jackson RJ, Standart N (2007) How do microRNAs regulate gene expression? Sci STYE 2007: re1.
33. Bagga S, Bracht J, Hunter S, Massirer K, Holtz J, et al. (2005) Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell 122: 553-563.
34. Behm-Ansmant I, Rehwinkel J, Doerks T, Stark A, Bork P, et al. (2006) mRNA degradation by miPNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes. Genes Dev 20: 1885-1898.
35. Esau C, Davis S, Murray SF, Yu XX, Pandey SK, et al. (2006) miR-122 regulation of lipid metabolism revealed by in vivo antisense targeting. Cell Metab 3: 87-98.
36. Eulalio A, Rehwinkel J, Stricker M, Huntzinger E, Yang SF, et al. (2007) Target-specific requirements for enhancers of decapping in miRNA-mediated gene silencing. Genes Dev 21: 2558-2570.
37. Giraldez AJ, Mishima Y, Rihel J, Grocock RJ, Van Dongen S, et al. (2006) Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science 312: 75-79.
38. Krutzfeldt J, Rajewsky N, Braich R, Rajeev KG, Tuschl T, et al. (2005) Silencing of microRNAs in vivo with 'antagomirs'. Nature 438: 685-689.
39. Rehwinkel J, Natalin P, Stark A, Brennecke J, Cohen SM, et al. (2006) Genome-wide analysis of mRNAs regulated by Drosha and Argonaute proteins in Drosophila melanogaster. Mol Cell Biol 26: 2965-2975.
40. Schmitter D, Filkowski J, Sewer A, Pillai RS, Oakeley EJ, et al. (2006) Effects of Dicer and Argonaute down-regulation on mRNA levels in human HEK293 cells. Nucleic Acids Res 34: 4801-4815.
41. Wu L, Belasco JG (2005) Micro-RNA regulation of the mammalian lin-28 gene during neuronal differentiation of embryonal carcinoma cells. Mol Cell Biol 25: 9198-9208.
42. Wu I, Fan J, Belasco JG (2006) MicroRNAs direct rapid deadenylation of mRNA. Proc Natl Acad Sci U S A 103: 4034-4039.
43. Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, et al. (2005) Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433: 769-773.
44. Nilsen TW (2007) Mechanisms of microRNA-mediated gene regulation in animal cells. Trends Genet 23: 243-249.
45. Valencia-Sanchez MiA, Liu J, Hannon GJ, Parker R (2006) Control of translation and mRNA degradation by miRNAs and siRNAs. Genes Dev 20: 515-524.
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. Piilai RS, Bhattacharyya SN, Artus CG, Zoller T, Cougot N, et al. (2005) Inhibition of translational initiation by Let-7 MicroRNA in human cells. Science 309: 1573-1576.
48. Brennecke J, Stark A, Russell RB, Cohen SM (2005) Principles of microRNA-target recognition. PLoS Biol 3: c85.
49. Enright AJ, John B, Gaul U, Tuschl T, Sander C, et al. (2003) MicroRNA targets in Drosophila. Genome Biol 5: R1.
50. Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, et al. (2007) MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 27: 91-105.
51. John B, Enright AJ, Aravin A, Tuschl T, Sander C, et al. (2004) Human MicroRNA targets. PLoS Biol 2: e363.
52. Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, et al. (2005) Combinatorial microRNA target predictions. Nat Genet 37: 495-500.
53. Easow G, Teleman AA, Cohen SM (2007) Isolation of microRNA targets by miRNP immunopurification. Rna 13: 1198-1204.
54. Lytle JR, Yario TA, Steitz 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 U S A 104: 9667-9672.
55. Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, et al. (2007) Discovery of functional elements in 12 Droscphila genornes using evolutionary signatures. Nature 450: 219-232.
56. Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, et al. (2005) Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature 434: 338-345.
57. Sethupathy P, Megraw M, Hatzigeorgiou AG (2006) A guide through present computational approaches for the identification of mammalian microRNA targets. Nat Methods 3: 881-886.
58. Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E (2007) The role of site accessibility in microRNA target recognition. Nat Genet 39: 1278-1284.
59. Miranda KC, Huynh T, Tay Y, Ang YS, Tam WL, et al. (2006) A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell 126: 1203-1217.
60. Didiano D, Hobert O (2006) Perfect seed pairing is not a generally reliable predictor for miRNA-target interactions. Nat Struct Mol Biol 13: 849-851.
61. SFGF (2008) Human Exonic Evidence Based Oligonucleotide (HEEBO) Arrays.
62. Ambion (2008) mirVana™ miRNA Probe Set.
63. Ferea TL, Brown PO (1999) Observing the living genome. Curr Opin Genet Dev 9: 715-722.
64. Tusher VG, Tibshirani R, Chu G (200 1) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 98: 5116-5121.
65. Efron B, Tibshirani R (2002) Empirical bayes methods and false discovery rates for microarrays. Genet Epidemiol 23: 70-86.
66. Bailey TL, Elkan C (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2: 28-36.
67. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 102: 15545-15550.
68. Beitzinger M, Peters L, Zhu JY, Kremmer E, Meister G (2007) Identification of Human microRNA Targets From Isolated Argonaute Protein Complexes. RNA Biol 4.
69. Karginov FV, Conaco C, Xuan Z, Schmidt BH, Parker JS, et al. (2007) A biochemical approach to identifying microRNA targets. Proc Natl Acad Sci U S A 104: 19291-19296.
70. Zhang L, Ding L, Cheung TH, Dong MQ Chen J, et al. (2007) Systematic identification of C. elegans miRISC proteins, miRNAs, and mRNA targets by their interactions with GW182 proteins AIN-1 and AIN-2. Mol Cell 28: 598-613.
71. Myers JW, Ferrell JE (2005) Silencing gene expression with Dicer-generated siRNA pools. Methods Mol Biol 309: 93-196.
72. Fare TL, Coffey EM, Dai H, He YD, Kessler DA, et al. (2003) Effects of atmospheric ozone on microarray data quality. Anal Chem 75: 4672-4675.
73. Demeter J, Beauheim C, Gollub J, Hernandez-Boussard T, Jin H, et al. (2007) The Stanford Microarray Database: implementation of new analysis tools and open source release of software. Nucleic Acids Res 35: D766-770.
74. Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 95: 14863-14868.
75. Saldanha AJ (2004) Java Treeview-extensible visualization of microarray data. Bioinformatics 20: 3246-3248.
76. Hosack DA, Dennis G Jr, Sherman BT, Lane HC, Lempicki RA (2003) Identifying biological themes within lists of genes with EASE. Genome Biol 4: R70.