Microarray analysis shows that some microRNAs downregulate large numbers of-target mRNAs

Nature

Volumn 433, Issue 7027, 2005, Pages 769-773

  Lim, Lee P ^a   Lau, Nelson C ^b   Garrett Engele, Philip ^a   Grimson, Andrew ^b   Schelter, Janell M ^a   Castle, John ^a   Bartel, David P ^b   Linsley, Peter S ^a   Johnson, Jason M ^a  

^a ROSETTA INPHARMATICS   (United States)

^b WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARRAYS; CELLS; GENES; GENETIC ENGINEERING; MUSCLE; PROTEINS;

GENE EXPRESSION; MICROARRAYS; MICRORNAS;

RNA;

MESSENGER RNA; MICRORNA;

GENE EXPRESSION; RNA;

3' UNTRANSLATED REGION; ARTICLE; CONTROLLED STUDY; DNA MICROARRAY; DOWN REGULATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE SEQUENCE; GENETIC TRANSCRIPTION; HELA CELL; HUMAN; HUMAN CELL; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; REGULATORY MECHANISM; SEQUENCE ANALYSIS; TRANSCRIPTION REGULATION; ANTIBODY SPECIFICITY; BRAIN; ENZYME SPECIFICITY; GENETICS; METABOLISM; MOLECULAR GENETICS; MUSCLE; MUTATION; NUCLEOTIDE SEQUENCE; REPORTER GENE;

ANIMALIA; METAZOA;

3' UNTRANSLATED REGIONS; BASE SEQUENCE; BRAIN; DOWN-REGULATION; GENES, REPORTER; HUMANS; MICRORNAS; MOLECULAR SEQUENCE DATA; MUSCLES; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ORGAN SPECIFICITY; RNA, MESSENGER; SUBSTRATE SPECIFICITY;

EID: 13944282215     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/nature03315     Document Type: Article

References (30)

1. Bartel, D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281-297 (2004).
2. Carrington, J. C. & Ambros, V. Role of microRNAs in plant and animal development. Science 301, 336-338 (2003).
3. Lewis, B. P., Shih, I. H., Jones-Rhoades, M. W., Bartel, D. P. & Burge, C. B. Prediction of mammalian microRNA targets. Cell 115, 787-798 (2003).
4. Palatnik,J. F. et al. Control of leaf morphogenesis by microRNAs. Nature 425, 257-263 (2003).
5. Jackson, A. L. et al. Expression profiling reveals off-target gene regulation by RNAi. Nature Biotechnol. 21, 635-637 (2003).
6. Hutvagner, G. & Zamore, P. D. A microRNA in a multiple-turnover RNAi enzyme complex Science 297, 2056-2060 (2002).
7. Zeng, Y., Yi, R. & Cullen, B. R. MicroRNAs and small interfering RNAs can inhibit mRNA expression by similar mechanisms. Proc. Natl Acad. Sci. USA 100, 9779-9784 (2003).
8. Doench, J. G., Petersen, C. P. & Sharp, P. A. siRNAs can function as miRNAs. Genes Dev. 17, 438-442 (2003).
9. Yekta, S., Shih, I. H. & Bartel, D. P. MicroRNA-directed cleavage of HOXB8 mRNA. Science 304, 594-596 (2004).
10. Lagos-Quintana, M. et al. Identification of tissue-specific microRNAs from mouse. Curr. Biol. 12, 735-739 (2002).
11. Sempere, L. F. et al. Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation. Genome Biol. 5, R13 (2004).
12. Pruitt, K. D. & Maglott, D. R. RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Res. 29, 137-140 (2001).
13. Johnson, J. M. et al. Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science 302, 2141-2144 (2003).
14. Bailey, T. L. & Elkan, C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 2, 28-36 (1994).
15. Lim, L. P. et al. The microRNAs of Caenorhabditis elegans. Genes Dev. 17, 991-1008 (2003).
16. Wightman, B., Ha, I. & Ruvkun, G. Posttranscriptional regulation of the heterochronic gene lin-14by lin-4 mediates temporal pattern formation in C. elegans. Cell 75, 855-862 (1993).
17. Lai, E. C. Micro RNAs are complementary to 3′ UTR sequence motifs that mediate negative posttranscriptional regulation. Nature Genet. 30, 363-364 (2002).
18. Doench, J. G. & Sharp, P. A. Specificity of microRNA target selection in translational repression. Genes Dev. 18, 504-511 (2004).
19. John, B. et al. Human MicroRNA targets. PLoS Biol. 2, e363 (2004).
20. Rhoades, M. W. et al. Prediction of plant microRNA targets. Cell 110, 513-520 (2002).
21. Haley, B. & Zamore, P. D. Kinetic analysis of the RNAi enzyme complex. Nature Struct. Mol. Biol. 11, 599-606 (2004).
22. Martinez, J. & Tuschl, T. RISC is a 5′ phosphomonoester- producing RNA endonuclease. Genes Dev. 18, 975-980 (2004).
23. Janz, R. & Sudhof, T. C. Cellugyrin, a novel ubiquitous form of synaptogyrin that is phosphorylatedby pp60c-src. J. Biol. Chem. 273, 2851-2857 (1998).
24. Vartiainen, M. K., Sarkkinen, E. M., Matilainen, T., Salminen, M. & Lappalainen, P. Mammals have two twinfilin isoforms whose subcellular localizations and tissue distributions are differentially regulated. J. Biol. Chem. 278, 34347-34355 (2003).
25. Bartel, D. P. & Chen, C. Z. Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nature Rev. Genet. 5, 396-400 (2004).
26. Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genet. 25, 25-29 (2000).
27. Schwarz, D. S. et al. Asymmetry in the assembly of the RNAi enzyme complex. Cell 115, 199-208 (2003).
28. Khvorova, A., Reynolds, A. & Jayasena, S. D. Functional siRNAs and miRNAs exhibit strand bias. Cell 115, 209-216 (2003).
29. Hughes, T. R. et al. Functional discovery via a compendium of expression profiles. Cell 102, 109-126 (2000).
30. Thompson, J. D., Higgins, D. G. & Gibson, T. J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680 (1994).