Anti-Argonaute RIP-Chip shows that miRNA transfections alter global patterns of mRNA recruitment to microribonucleoprotein complexes

RNA

Volumn 16, Issue 2, 2010, Pages 394-404

  Wang, Wang Xia ^a,b   Wilfred, Bernard R ^a,b   Hu, Yanling ^a,b   Stromberg, Arnold J ^a,b   Nelson, Peter T ^a,b  

^a UNIVERSITY OF KENTUCKY MEDICAL CENTER   (United States)

^b UNIVERSITY OF KENTUCKY   (United States)

Author keywords

Astrocytes; Brain; DBI; Neurons; TXNIP

Indexed keywords

ARGONAUTE ANTIBODY; ARGONAUTE PROTEIN; MESSENGER RNA; MICRORIBONUCLEOPROTEIN; MICRORNA; MIR 107; MIR 124; MIR 128; MIR 320; MONOCLONAL ANTIBODY; PROTEIN ANTIBODY; RIBONUCLEOPROTEIN; UNCLASSIFIED DRUG;

ARTICLE; CANCER CELL CULTURE; COIMMUNOPRECIPITATION; CONTROLLED STUDY; HELA CELL; HUMAN; HUMAN CELL; IMMUNOPRECIPITATION; MICROARRAY ANALYSIS; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; PROTEIN RNA BINDING; VALIDATION PROCESS;

ANIMALS; ANTIBODIES, MONOCLONAL; CELL LINE, TUMOR; EUKARYOTIC INITIATION FACTOR-2; HUMANS; IMMUNOPRECIPITATION; MACROMOLECULAR SUBSTANCES; MICE; MICRORNAS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RIBONUCLEOPROTEINS; RNA, MESSENGER; TRANSFECTION;

EID: 75149163985     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.1905910     Document Type: Article

References (53)

1. Adams BD, Claffey KP, White BA. 2009. Argonaute-2 expression is regulated by epidermal growth factor receptor and mitogen-activated protein kinase signaling and correlates with a transformed phenotype in breast cancer cells. Endocrinology 150: 14-23.
2. Ambros V. 2004. The functions of animal microRNAs. Nature 431: 350-355.
3. Andachi Y. 2008. A novel biochemical method to identify target genes of individual microRNAs: Identification of a new Caenorhabditis elegans let-7 target. RNA 14: 2440-2451.
4. Arnstein P, Taylor DO, Nelson-Rees WA, Huebner RJ, Lennette EH. 1974. Propagation of human tumors in antithymocyte serum-treated mice. J Natl Cancer Inst 52: 71-84.
5. Baek D, Villen J, Shin C, Camargo FD, Gygi SP, Bartel DP. 2008. The impact of microRNAs on protein output. Nature 455: 64-71.
6. Baskerville S, Bartel DP. 2005. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 11: 241-247.
7. Beitzinger M, Peters L, Zhu JY, Kremmer E, Meister G. 2007. Identification of human microRNA targets from isolated argonaute protein complexes. RNA Biol 4: 76-84.
8. 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.
9. Chi SW, Zang JB, Mele A, Darnell RB. 2009. Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 460: 479-486.
10. Chiosea S, Jelezcova E, Chandran U, Acquafondata M, McHale T, Sobol RW, Dhir R. 2006. Up-regulation of dicer, a component of the microRNA machinery, in prostate adenocarcinoma. Am J Pathol 169: 1812-1820.
11. 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.
12. Easow G, Teleman AA, Cohen SM. 2007. Isolation of microRNA targets by miRNP immunopurification. RNA 13: 1198-1204.
13. Eletto D, Russo G, Passiatore G, Del Valle L, Giordano A, Khalili K, Gualco E, Peruzzi F. 2008. Inhibition of SNAP25 expression by HIV-1 Tat involves the activity of mir-128a. J Cell Physiol 216: 764-770.
14. Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS. 2003. MicroRNA targets in Drosophila. Genome Biol 5: R1. doi: 10.1186/gb-2003-5-1-r1.
15. Farh KK, Grimson A, Jan C, Lewis BP, Johnston WK, Lim LP, Burge CB, Bartel DP. 2005. The widespread impact of mammalian microRNAs on mRNA repression and evolution. Science 310: 1817-1821.
16. Godlewski J, Nowicki MO, Bronisz A, Williams S, Otsuki A, Nuovo G, Raychaudhury A, Newton HB, Chiocca EA, Lawler S. 2008. Targeting of the Bmi-1 oncogene/stem cell renewal factor by microRNA-128 inhibits glioma proliferation and self-renewal. Cancer Res 68: 9125-9130.
17. Gopalraj RK, Zhu H, Kelly JF, Mendiondo M, Pulliam JF, Bennett DA, Estus S. 2005. Genetic association of low density lipoprotein receptor and Alzheimer's disease. Neurobiol Aging 26: 1-7.
18. Hammond SM. 2005. Dicing and slicing: The core machinery of the RNA interference pathway. FEBS Lett 579: 5822-5829.
19. Hendrickson DG, Hogan DJ, Herschlag D, Ferrell JE, Brown PO. 2008. Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance. PLoS One 3: e2126. doi: 10.1371/journal.pone. 0002126.
20. Hutvagner G, Simard MJ. 2008. Argonaute proteins: Key players in RNA silencing. Nat Rev Mol Cell Biol 9: 22-32.
21. Karginov FV, Conaco C, Xuan Z, Schmidt BH, Parker JS, Mandel G, Hannon GJ. 2007. A biochemical approach to identifying microRNA targets. Proc Natl Acad Sci 104: 19291-19296.
22. Keene JD, Komisarow JM, Friedersdorf MB. 2006. RIP-Chip: The isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts. Nat Protoc 1: 302-307.
23. Khan AA, Betel D, Miller ML, Sander C, Leslie CS, Marks DS. 2009. Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nat Biotechnol 27: 549-555.
24. Kiriakidou M, Nelson PT, Kouranov A, Fitziev P, Bouyioukos C, Mourelatos Z, Hatzigeorgiou A. 2004. A combined computational-experimental approach predicts human microRNA targets. Genes & Dev 18: 1165-1178.
25. Kirino Y, Mourelatos Z. 2008. Site-specific crosslinking of human microRNPs to RNA targets. RNA 14: 2254-2259.
26. Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M, et al. 2005. Combinatorial microRNA target predictions. Nat Genet 37: 495-500.
27. Krex D, Mohr B, Hauses M, Ehninger G, Schackert HK, Schackert G. 2001. Identification of uncommon chromosomal aberrations in the neuroglioma cell line H4 by spectral karyotyping. J Neurooncol 52: 119-128.
28. Kumar MS, Lu J, Mercer KL, Golub TR, Jacks T. 2007. Impaired microRNA processing enhances cellular transformation and tumorigenesis. Nat Genet 39: 673-677.
29. Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T. 2002. Identification of tissue-specific microRNAs from mouse. Curr Biol 12: 735-739.
30. Landthaler M, Gaidatzis D, Rothballer A, Chen PY, Soll SJ, Dinic L, Ojo T, Hafner M, Zavolan M, Tuschl T. 2008. Molecular characterization of human Argonaute-containing ribonucleoprotein complexes and their bound target mRNAs. RNA 14: 2580-2596.
31. 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.
32. Li KK, Pang JC, Ching AK, Wong CK, Kong X, Wang Y, Zhou L, Chen Z, Ng HK. 2009. miR-124 is frequently down-regulated in medulloblastoma and is a negative regulator of SLC16A1. Hum Pathol 40: 1234-1243.
33. Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS, Johnson JM. 2005. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433: 769-773.
34. Liu J, Carmell MA, Rivas FV, Marsden CG, Thomson JM, Song JJ, Hammond SM, Joshua-Tor L, Hannon GJ. 2004. Argonaute2 is the catalytic engine of mammalian RNAi. Science 305: 1437-1441.
35. Liu X, Fortin K, Mourelatos Z. 2008. MicroRNAs: Biogenesis and molecular functions. Brain Pathol 18: 113-121.
36. Lugli G, Larson J, Martone ME, Jones Y, Smalheiser NR. 2005. Dicer and eIF2c are enriched at postsynaptic densities in adult mouse brain and are modified by neuronal activity in a calpain-dependent manner. J Neurochem 94: 896-905.
37. Lukiw WJ. 2007. Micro-RNA speciation in fetal, adult and Alzheimer's disease hippocampus. Neuroreport 18: 297-300.
38. Makeyev EV, Zhang J, Carrasco MA, Maniatis T. 2007. The microRNA miR-124 promotes neuronal differentiation by triggering brain-specific alternative pre-mRNA splicing. Mol Cell 27: 435-448.
39. Miranda KC, Huynh T, Tay Y, Ang YS, Tam WL, Thomson AM, Lim B, Rigoutsos I. 2006. A pattern-based method for the identification of microRNA binding sites and their corresponding heteroduplexes. Cell 126: 1203-1217.
40. Mourelatos Z, Dostie J, Paushkin S, Sharma A, Charroux B, Abel L, Rappsilber J, Mann M, Dreyfuss G. 2002. miRNPs: A novel class of ribonucleoproteins containing numerous microRNAs. Genes & Dev 16: 720-728.
41. Muinos-Gimeno M, Guidi M, Kagerbauer B, Martin-Santos R, Navines R, Alonso P, Menchon JM, Gratacos M, Estivill X, Espinosa-Parrilla Y. 2009. Allele variants in functional microRNA target sites of the neurotrophin-3 receptor gene (NTRK3) as susceptibility factors for anxiety disorders. Hum Mutat 30: 1062-1071.
42. Nelson PT, Hatzigeorgiou AG, Mourelatos Z. 2004. miRNP:mRNA association in polyribosomes in a human neuronal cell line. RNA 10: 387-394.
43. Nelson PT, De Planell-Saguer M, Lamprinaki S, Kiriakidou M, Zhang P, O'Doherty U, Mourelatos Z. 2007. A novel monoclonal antibody against human Argonaute proteins reveals unexpected characteristics of miRNAs in human blood cells. RNA 13: 1787-1792.
44. Ohkuma S, Katsura M, Tsujimura A. 2001. Alterations in cerebral diazepam binding inhibitor expression in drug dependence: A possible biochemical alteration common to drug dependence. Life Sci 68: 1215-1222.
45. Peterson KJ, Dietrich MR, McPeek MA. 2009. MicroRNAs and metazoan macroevolution: Insights into canalization, complexity, and the Cambrian explosion. Bioessays 31: 736-747.
46. Pierson J, Hostager B, Fan R, Vibhakar R. 2008. Regulation of cyclin dependent kinase 6 by microRNA 124 in medulloblastoma. J Neurooncol 90: 1-7.
47. Rigoutsos I. 2009. New tricks for animal microRNAS: Targeting of amino acid coding regions at conserved and nonconserved sites. Cancer Res 69: 3245-3248.
48. Smirnova L, Grafe A, Seiler A, Schumacher S, Nitsch R, Wulczyn FG. 2005. Regulation of miRNA expression during neural cell specification. Eur J Neurosci 21: 1469-1477.
49. Sun R, Fu X, Li Y, Xie Y, Mao Y. 2009. Global gene expression analysis reveals reduced abundance of putative microRNA targets in human prostate tumours. BMC Genomics 10: 93. doi: 10.1186/1471-2164-10-93.
50. Wang WX, Rajeev BW, Stromberg AJ, Ren N, Tang G, Huang Q, Rigoutsos I, Nelson PT. 2008a. The expression of microRNA miR-107 decreases early in Alzheimer's disease and may accelerate disease progression through regulation of βb-site amyloid precursor protein-cleaving enzyme 1. J Neurosci 28: 1213-1223.
51. Wang WX, Wilfred BR, Baldwin DA, Isett RB, Ren N, Stromberg A, Nelson PT. 2008b. Focus on RNA isolation: Obtaining RNA for microRNA (miRNA) expression profiling analyses of neural tissue. Biochim Biophys Acta 1779: 749-757.
52. Yamawaki H, Haendeler J, Berk BC. 2003. Thioredoxin: A key regulator of cardiovascular homeostasis. Circ Res 93: 1029-1033.
53. Zhang Y, Chao T, Li R, Liu W, Chen Y, Yan X, Gong Y, Yin B, Qiang B, Zhao J, et al. 2009. MicroRNA-128 inhibits glioma cells proliferation by targeting transcription factor E2F3a. J Mol Med 87: 43-51.