Labeled microRNA pull-down assay system: An experimental approach for high-throughput identification of microRNA-target mRNAs

Nucleic Acids Research

Volumn 37, Issue 10, 2009, Pages

  Hsu, Ren Jun ^a   Yang, Hsin Jung ^a   Tsai, Huai Jen ^a  

^a NATIONAL TAIWAN UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

CELL EXTRACT; COMPLEMENTARY DNA; DIGOXIGENIN; GENE PRODUCT; LUCIFERASE; MESSENGER RNA; MICRORNA; PROTEIN HAND2; UNCLASSIFIED DRUG; BASIC HELIX LOOP HELIX TRANSCRIPTION FACTOR; HAND2 PROTEIN, ZEBRAFISH; RNA PRECURSOR; ZEBRAFISH PROTEIN;

ARTICLE; CAENORHABDITIS ELEGANS; CHEMICAL LABELING; CONTROLLED STUDY; DNA SEQUENCE; FALSE POSITIVE RESULT; GENE IDENTIFICATION; GENE TARGETING; IMMUNOPRECIPITATION; IN SITU HYBRIDIZATION; LABELED MIRNA PULL DOWN ASSAY SYSTEM; MICROARRAY ANALYSIS; MOLECULAR CLONING; NONHUMAN; PRIORITY JOURNAL; REPORTER GENE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; ZEBRA FISH; 3' UNTRANSLATED REGION; ANIMAL; CELL STRAIN COS1; CERCOPITHECUS; CHEMISTRY; DNA MICROARRAY; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; METHODOLOGY; RNA INTERFERENCE; VALIDATION STUDY;

CAENORHABDITIS ELEGANS; DANIO RERIO;

3' UNTRANSLATED REGIONS; ANIMALS; BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTORS; CAENORHABDITIS ELEGANS; CERCOPITHECUS AETHIOPS; COS CELLS; IMMUNOPRECIPITATION; MICRORNAS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA INTERFERENCE; RNA PRECURSORS; RNA, MESSENGER; ZEBRAFISH; ZEBRAFISH PROTEINS;

EID: 67249160019     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp274     Document Type: Article

References (35)

1. Grishok,A., Pasquinelli,A.E., Conte,D., Li,N., Parrish,S., Ha,I., Baillie,DL., Fire,A., Ruvkun,G. and Mello,C.C. (2001) Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell, 106, 23-24.
2. Hutvágner,G., McLachlan,J., Pasquinelli,A.E., Bálint,E., Tuschl,T. and Zamore,P.D. (2001) A cellular function for the RNAinterference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science, 293, 834-838.
3. Lee,Y., Ahn,C., Han,J., Choi,H., Kim,J., Yim,J., Lee,J., Provost,P., Rådmark,O., Kim,S. et al. (2003) The nuclear RNase III Drosha initiates microRNA processing. Nature, 425, 415-419.
4. Bernstein,E., Caudy,A.A., Hammond,S.M. and Hannon,G.J. (2001) Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature, 409, 363-366.
5. Chen,C.Z., Li,L., Lodish,H.F. and Bartel,D.P. (2004) MicroRNAs modulate hematopoietic lineage differentiation. Science, 303, 83-86.
6. Yekta,S., Shih,I.H. and Bartel,D.P. (2004) MicroRNA-directed cleavage of HOXB8 mRNA. Science, 304, 594-596.
7. Wienholds,E., Koudijs,M.J., Eeden,F.J., Cuppen,E. and Plasterk,R.H. (2003) The microRNA-producing enzyme Dicer1 is essential for zebrafish development. Nat. Genet., 35, 217-218.
8. Giraldez,A.J., Cinalli,R.M., Glasner,M.E., Enright,A.J., Thomson,J.M., Baskerville,S., Hammond,S.M., Bartel,D.P. and Schier,A.F. (2005) MicroRNAs regulate brain morphogenesis in zebrafish. Science, 308, 833-838.
9. Lee,R.C., Feinbaum,R.L. and Ambros,V. (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 75, 843-854.
10. Moss,E.G., Lee,R.C. and Ambros,V. (1997) The cold shock domain protein LIN-28 controls developmental timing in C. elegans and is regulated by the lin-4 RNA. Cell, 88, 637-641.
11. Rooij,Van.E., Sutherland,L.B., Qi,X., Richardson,J.A., Hill,J. and Olson,E.N. (2007) Control of stress-dependent cardiac growth and gene expression by a microRNA. Science, 316, 575-579.
12. Berezikov,E., Guryev,V., Belt,J., Wienholds,E., Plasterk,R.H. and Cuppen,E. (2005) Phylogenetic shadowing and computational identification of human microRNA genes. Cell, 120, 21-24.
13. Lewis,B.P., Shih,I.H., Jones-Rhoades,M.W., Bartel,D.P. and Burge,C.B. (2003) Prediction of mammalian microRNA targets. Cell, 115, 787-798.
14. Wienholds,E., Kloosterman,W.P., Miska,E., Alvarez-Saavedra,E., Berezikov,E., Bruijn,E., Horvitz,H.R., Kauppinen,S. and Plasterk,R.H. (2005) MicroRNA expression in zebrafish embryonic development. Science, 309, 310-311.
15. Enright,A.J., John,B., Gaul,U., Tuschl,T., Sander,C. and Marks,D.S. (2003) MicroRNA targets in Drosophila. Genome Biol., 5, R1.
16. Doench,J.G. and Sharp,P.A. (2004) Specificity of microRNA target selection in translational repression. Genes Dev., 18, 504-511.
17. Li,N., Flynt,A.S., Kim,H.R., Solnica-Krezel,L. and Patton,J.G. (2008) Dispatched Homolog 2 is targeted by miR-214 through a combination of three weak microRNA recognition sites. Nucleic Acids Res., 13 4277-4285.
18. Esquela-Kerscher,A., Johnson,S.M., Bai,L., Saito,K., Partridge,J., Reinert,K.L. and Slack,F.J. (2005) Post-embryonic expression of C. elegans microRNAs belonging to the lin-4 and let-7 families in the hypodermis and the reproductive system. Dev. Dyn., 234, 868-877.
19. Easow,G., Teleman,A.A. and Cohen,S.M. (2007) Isolation of microRNA targets by miRNP immunopurification. RNA, 13, 1198-1204.
20. Beitzinger,M., Peters,L., Zhu,J.Y., Kremmer,E. and Meister,G. (2007) Identification of human microRNA targets from isolated argonaute protein complexes. RNA Biol., 2, 76-84.
21. Mili,S. and Steitz,J.A. (2004) Evidence for reassociation of RNA-binding proteins after cell lysis: Implications for the interpretation of immunoprecipitation analyses. RNA, 10, 1692-1694.
22. Brenner,S. (1974) The genetics of Caenorhabditis elegans. Genetics 77, 71-94.
23. Chen,Y.H., Lee,W.C., Liu,C.F. and Tsai,H.J. (2001) Molecular structure, dynamic expression, and promoter analysis of zebrafish (Danio rerio) myf-5 gene. Genesis, 29, 22-35.
24. Huang,C.J., Tu,C.T., Hsiao,C.D., Hsieh,F.J. and Tsai,H.J. (2003) Germ-line transmission of a myocardium-specific GFP transgene reveals critical regulatory elements in the cardiac myosin light chain 2 promoter of zebrafish. Dev. Dyn., 228, 30-40.
25. Wang,T.M., Chen,Y.H., Liu,C.F. and Tsai,H.J. (2002) Functional analysis of the proximal promoter regions of fish rhodopsin and myf-5 genes using transgenesis. Mar. Biotechnol., 4, 247-255.
26. Ørom,U.A., Nielsen,F.C. and Lund,A.H. (2008) MicroRNA-10a binds the 5′UTR of ribosomal protein mRNAs and enhances their translation. Mol. Cell, 30, 460-47.
27. Zhao,Y., Samal,E. and Srivastava,D. (2005) Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature, 436, 214-220.
28. Kloosterman,W.P., Wienholds,E., Ketting,R.F. and Plasterk,R.H. (2004) Substrate requirements for let-7 function in the developing zebrafish embryo. Nucleic Acids Res., 32, 6284-6291.
29. Lin,S.Y., Johnson,S.M., Abraham,M., Vella,M.C., Pasquinelli,A., Gamberi,C., Gottlieb,E. and Slack,F.J. (2003) The C. elegans hunchback homolog, hbl-1, controls temporal patterning and is a probable microRNA target. Dev. Cell, 4, 639-650.
30. Vella,M.C., Choi,E.Y., Lin,S.Y., Reinert,K. and Slack,F.J. (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.
31. Griffiths-Jones,S. (2004) The microRNA Registry. Nucleic Acids Res. 32, D109-D111.
32. Kim,H.K., Lee,Y.S., Sivaprasad,U., Malhotra,A. and Dutta,A. (2006) Muscle-specific microRNA miR-206 promotes muscle differentiation. J. Cell Biol., 174, 677-687.
33. Rosenberg,M.I., Georges,S.A., Asawachaicharn,A., Analau,E. and Tapscott,S.J. (2006) MyoD inhibits Fstl1 and Utrn expression by inducing transcription of miR-206. J. Cell Biol., 175, 77-85.
34. Thisse,B., Heyer,V., Lux,A., Alunni,V., Degrave,A., Seiliez,I., Kirchner,J., Parkhill,J.P. and Thisse,C. (2004) Spatial and temporal expression of the zebrafish genome by large-scale in situ hybridization screening. Methods Cell Biol., 77, 505-519.
35. Varambally,S., Cao,Q., Mani,R.S., Shankar,S., Wang,X., Ateeq,B., Laxman,B., Cao,X., Jing,X. and Ramnarayanan,K. (2008) Genomic loss of microRNA-101 leads to overexpression of histone methyltransferase EZH2 in cancer. Science, 322, 1695-1699.