Widespread changes in protein synthesis induced by microRNAs (original) (raw)

• Ambros, V. The functions of animal microRNAs. Nature 431, 350–355 (2004)
  Article ADS CAS Google Scholar
• Bartel, D. P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281–297 (2004)
  Article CAS Google Scholar
• Bushati, N. & Cohen, S. M. microRNA functions. Annu. Rev. Cell Dev. Biol. 23, 175–205 (2007)
  Article CAS Google Scholar
• He, L. & Hannon, G. J. MicroRNAs: small RNAs with a big role in gene regulation. Nature Rev. Genet. 5, 522–531 (2004)
  Article CAS Google Scholar
• Lai, E. C. miRNAs: whys and wherefores of miRNA-mediated regulation. Curr. Biol. 15, R458–R460 (2005)
  Article CAS Google Scholar
• Filipowicz, W., Bhattacharyya, S. N. & Sonenberg, N. Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nature Rev. Genet. 9, 102–114 (2008)
  Article CAS Google Scholar
• Shyu, A. B., Wilkinson, M. F. & van Hoof, A. Messenger RNA regulation: to translate or to degrade. EMBO J. 27, 471–481 (2008)
  Article CAS Google Scholar
• Mathonnet, G. et al. MicroRNA inhibition of translation initiation in vitro by targeting the cap-binding complex eIF4F. Science 317, 1764–1767 (2007)
  Article ADS CAS Google Scholar
• Thermann, R. & Hentze, M. W. Drosophila miR2 induces pseudo-polysomes and inhibits translation initiation. Nature 447, 875–878 (2007)
  Article ADS CAS Google Scholar
• Wakiyama, M., Takimoto, K., Ohara, O. & Yokoyama, S. Let-7 microRNA-mediated mRNA deadenylation and translational repression in a mammalian cell-free system. Genes Dev. 21, 1857–1862 (2007)
  Article CAS Google Scholar
• Liu, J. Control of protein synthesis and mRNA degradation by microRNAs. Curr. Opin. Cell. Biol. 20, 214–221 (2008)
  Article CAS Google Scholar
• Lim, L. P. et al. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433, 769–773 (2005)
  Article ADS CAS Google Scholar
• Bentwich, I. Prediction and validation of microRNAs and their targets. FEBS Lett. 579, 5904–5910 (2005)
  Article CAS Google Scholar
• Hofacker, I. L. How microRNAs choose their targets. Nature Genet. 39, 1191–1192 (2007)
  Article CAS Google Scholar
• Rajewsky, N. microRNA target predictions in animals. Nature Genet. 38 (Suppl). S8–S13 (2006)
  Article CAS Google Scholar
• Sethupathy, P., Megraw, M. & Hatzigeorgiou, A. G. A guide through present computational approaches for the identification of mammalian microRNA targets. Nature Methods 3, 881–886 (2006)
  Article CAS Google Scholar
• Beitzinger, M. et al. Identification of human microRNA targets from isolated argonaute protein complexes. RNA Biol. 4, 76–84 (2007)
  Article CAS Google Scholar
• Easow, G., Teleman, A. A. & Cohen, S. M. Isolation of microRNA targets by miRNP immunopurification. RNA 13, 1198–1204 (2007)
  Article CAS Google Scholar
• Karginov, F. V. et al. A biochemical approach to identifying microRNA targets. Proc. Natl Acad. Sci. USA 104, 19291–19296 (2007)
  Article ADS CAS Google Scholar
• Hendrickson, D. G. et al. Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance. PLoS ONE 3, e2126 (2008)
  Article ADS Google Scholar
• Aleman, L. M., Doench, J. & Sharp, P. A. Comparison of siRNA-induced off-target RNA and protein effects. RNA 13, 385–395 (2007)
  Article CAS Google Scholar
• Vinther, J. et al. Identification of miRNA targets with stable isotope labeling by amino acids in cell culture. Nucleic Acids Res. 34, e107 (2006)
  Article Google Scholar
• Stefani, G. & Slack, F. J. Small non-coding RNAs in animal development. Nature Rev. Mol. Cell Biol. 9, 219–230 (2008)
  Article CAS Google Scholar
• Mann, M. Functional and quantitative proteomics using SILAC. Nature Rev. Mol. Cell Biol. 7, 952–958 (2006)
  Article CAS Google Scholar
• Ong, S. E. et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 1, 376–386 (2002)
  Article CAS Google Scholar
• Schwanhaeusser, B., Gossen, M., Dittmar, G. & Selbach, M. Global analysis of cellular protein translation by pulsed SILAC. Proteomics (in the press)
• Milner, E., Barnea, E., Beer, I. & Admon, A. The turnover kinetics of major histocompatibility complex peptides of human cancer cells. Mol. Cell. Proteomics 5, 357–365 (2006)
  Article CAS Google Scholar
• Pratt, J. M. et al. Dynamics of protein turnover, a missing dimension in proteomics. Mol. Cell. Proteomics 1, 579–591 (2002)
  Article CAS Google Scholar
• Lam, Y. W., Lamond, A. I., Mann, M. & Andersen, J. S. Analysis of nucleolar protein dynamics reveals the nuclear degradation of ribosomal proteins. Curr. Biol. 17, 749–760 (2007)
  Article CAS Google Scholar
• Cox, J. & Mann, M. Is proteomics the new genomics? Cell 130, 395–398 (2007)
  Article CAS Google Scholar
• Cravatt, B. F., Simon, G. M. & Yates, J. R. The biological impact of mass-spectrometry-based proteomics. Nature 450, 991–1000 (2007)
  Article ADS CAS Google Scholar
• Domon, B. & Aebersold, R. Mass spectrometry and protein analysis. Science 312, 212–217 (2006)
  Article ADS CAS Google Scholar
• Landgraf, P. et al. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129, 1401–1414 (2007)
  Article CAS Google Scholar
• Sood, P. et al. Cell-type-specific signatures of microRNAs on target mRNA expression. Proc. Natl Acad. Sci. USA 103, 2746–2751 (2006)
  Article ADS CAS Google Scholar
• Nielsen, C. B. et al. Determinants of targeting by endogenous and exogenous microRNAs and siRNAs. RNA 13, 1894–1910 (2007)
  Article CAS Google Scholar
• Grimson, A. et al. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol. Cell 27, 91–105 (2007)
  Article CAS Google Scholar
• Haley, B. & Zamore, P. D. Kinetic analysis of the RNAi enzyme complex. Nature Struct. Mol. Biol. 11, 599–606 (2004)
  Article CAS Google Scholar
• Martinez, J. & Tuschl, T. RISC is a 5′ phosphomonoester-producing RNA endonuclease. Genes Dev. 18, 975–980 (2004)
  Article CAS Google Scholar
• Schwarz, D. S. et al. Designing siRNA that distinguish between genes that differ by a single nucleotide. PLoS Genet. 2, e140 (2006)
  Article Google Scholar
• Vasudevan, S., Tong, Y. & Steitz, J. A. Switching from repression to activation: microRNAs can up-regulate translation. Science 318, 1931–1934 (2007)
  Article ADS CAS Google Scholar
• Doench, J. G., Petersen, C. P. & Sharp, P. A. siRNAs can function as miRNAs. Genes Dev. 17, 438–442 (2003)
  Article CAS Google Scholar
• Stenvang, J. et al. The utility of LNA in microRNA-based cancer diagnostics and therapeutics. Semin. Cancer Biol. 18, 89–102 (2008)
  Article CAS Google Scholar
• Wahlestedt, C. et al. Potent and nontoxic antisense oligonucleotides containing locked nucleic acids. Proc. Natl Acad. Sci. USA 97, 5633–5638 (2000)
  Article ADS CAS Google Scholar
• Boyerinas, B. et al. Identification of let-7-regulated oncofetal genes. Cancer Res. 68, 2587–2591 (2008)
  Article CAS Google Scholar
• Kuster, B., Schirle, M., Mallick, P. & Aebersold, R. Scoring proteomes with proteotypic peptide probes. Nature Rev. Mol. Cell Biol. 6, 577–583 (2005)
  Article CAS Google Scholar
• Eulalio, A., Behm-Ansmant, I. & Izaurralde, E. P bodies: at the crossroads of post-transcriptional pathways. Nature Rev. Mol. Cell Biol. 8, 9–22 (2007)
  Article CAS Google Scholar
• Nottrott, S., Simard, M. J. & Richter, J. D. Human let-7a miRNA blocks protein production on actively translating polyribosomes. Nature Struct. Mol. Biol. 13, 1108–1114 (2006)
  Article CAS Google Scholar
• Ong, S. E. & Mann, M. A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC). Nature Protocols 1, 2650–2660 (2007)
  Article Google Scholar
• Elias, J. E. & Gygi, S. P. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nature Methods 4, 207–214 (2007)
  Article CAS Google Scholar