The impact of microRNAs on protein output (original) (raw)

References

1. 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)
   Article CAS PubMed Google Scholar
2. Lewis, B. P., Burge, C. B. & Bartel, D. P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15–20 (2005)
   Article CAS PubMed Google Scholar
3. Brennecke, J., Stark, A., Russell, R. B. & Cohen, S. M. Principles of microRNA-target recognition. PLoS Biol. 3, e85 (2005)
   Article PubMed PubMed Central Google Scholar
4. Krek, A. et al. Combinatorial microRNA target predictions. Nature Genet. 37, 495–500 (2005)
   Article CAS PubMed Google Scholar
5. Farh, K. K. et al. The widespread impact of mammalian microRNAs on mRNA repression and evolution. Science 310, 1817–1821 (2005)
   Article ADS CAS PubMed Google Scholar
6. Stark, A., Brennecke, J., Bushati, N., Russell, R. B. & Cohen, S. M. Animal microRNAs confer robustness to gene expression and have a significant impact on 3′UTR evolution. Cell 123, 1133–1146 (2005)
   Article CAS PubMed Google Scholar
7. Grimson, A. et al. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol. Cell 27, 91–105 (2007)
   Article CAS PubMed PubMed Central Google Scholar
8. Nielsen, C. B. et al. Determinants of targeting by endogenous and exogenous microRNAs and siRNAs. RNA 13, 1894–1910 (2007)
   Article CAS PubMed PubMed Central Google Scholar
9. Lim, L. P. et al. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433, 769–773 (2005)
   ADS CAS PubMed Google Scholar
10. Krutzfeldt, J. et al. Silencing of microRNAs in vivo with ‘antagomirs’. Nature 438, 685–689 (2005)
    Article ADS PubMed Google Scholar
11. Giraldez, A. J. et al. Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science 312, 75–79 (2006)
    Article ADS CAS PubMed Google Scholar
12. Beitzinger, M., Peters, L., Zhu, J. Y., Kremmer, E. & Meister, G. Identification of human microRNA targets from isolated argonaute protein complexes. RNA Biol. 4, 76–84 (2007)
    Article CAS PubMed Google Scholar
13. Easow, G., Teleman, A. A. & Cohen, S. M. Isolation of microRNA targets by miRNP immunopurification. RNA 13, 1198–1204 (2007)
    Article CAS PubMed PubMed Central Google Scholar
14. Karginov, F. V. et al. A biochemical approach to identifying microRNA targets. Proc. Natl Acad. Sci. USA 104, 19291–19296 (2007)
    Article ADS CAS PubMed PubMed Central Google Scholar
15. Zhang, L. et al. 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 (2007)
    Article CAS PubMed PubMed Central Google Scholar
16. Vinther, J., Hedegaard, M. M., Gardner, P. P., Andersen, J. S. & Arctander, P. Identification of miRNA targets with stable isotope labeling by amino acids in cell culture. Nucleic Acids Res. 34, e107 (2006)
    Article PubMed PubMed Central Google Scholar
17. 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 PubMed Google Scholar
18. Kloosterman, W. P., Wienholds, E., Ketting, R. F. & Plasterk, R. H. Substrate requirements for let-7 function in the developing zebrafish embryo. Nucleic Acids Res. 32, 6284–6291 (2004)
    Article CAS PubMed PubMed Central Google Scholar
19. Chen, C. Z., Li, L., Lodish, H. F. & Bartel, D. P. MicroRNAs modulate hematopoietic lineage differentiation. Science 303, 83–86 (2004)
    Article ADS CAS PubMed Google Scholar
20. Fazi, F. et al. A minicircuitry comprised of microRNA-223 and transcription factors NFI-A and C/EBPα regulates human granulopoiesis. Cell 123, 819–831 (2005)
    Article CAS PubMed Google Scholar
21. Johnnidis, J. B. et al. Regulation of progenitor cell proliferation and granulocyte function by microRNA-223. Nature 451, 1125–1129 (2008)
    Article ADS CAS PubMed Google Scholar
22. Griffiths-Jones, S., Saini, H. K., van Dongen, S. & Enright, A. J. miRBase: tools for microRNA genomics. Nucleic Acids Res. 36, D154–D158 (2008)
    Article CAS PubMed Google Scholar
23. John, B. et al. Human microRNA targets. PLoS Biol. 2, e363 (2004)
    Article PubMed PubMed Central Google Scholar
24. Betel, D., Wilson, M., Gabow, A., Marks, D. S. & Sander, C. The microRNA.org resource: targets and expression. Nucleic Acids Res. 36, D149–D153 (2008)
    Article CAS PubMed Google Scholar
25. Lall, S. et al. A genome-wide map of conserved microRNA targets in C. elegans . Curr. Biol. 16, 460–471 (2006)
    Article CAS PubMed Google Scholar
26. Kertesz, M., Iovino, N., Unnerstall, U., Gaul, U. & Segal, E. The role of site accessibility in microRNA target recognition. Nature Genet. 39, 1278–1284 (2007)
    Article CAS PubMed Google Scholar
27. Gaidatzis, D., van Nimwegen, E., Hausser, J. & Zavolan, M. Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC Bioinformatics 8, 69 (2007)
    Article PubMed PubMed Central Google Scholar
28. Miranda, K. C. et al. A pattern-based method for the identification of microRNA binding sites and their corresponding heteroduplexes. Cell 126, 1203–1217 (2006)
    Article CAS PubMed Google Scholar
29. Robins, H., Li, Y. & Padgett, R. W. Incorporating structure to predict microRNA targets. Proc. Natl Acad. Sci. USA 102, 4006–4009 (2005)
    Article ADS CAS PubMed PubMed Central Google Scholar
30. Zhao, Y., Samal, E. & Srivastava, D. Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature 436, 214–220 (2005)
    Article ADS CAS PubMed Google Scholar
31. Long, D. et al. Potent effect of target structure on microRNA function. Nature Struct. Mol. Biol. 14, 287–294 (2007)
    Article CAS Google Scholar
32. Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genet. 25, 25–29 (2000)
    Article CAS PubMed Google Scholar
33. Reddy, V. Y., Zhang, Q. Y. & Weiss, S. J. Pericellular mobilization of the tissue-destructive cysteine proteinases, cathepsins B, L, and S, by human monocyte-derived macrophages. Proc. Natl Acad. Sci. USA 92, 3849–3853 (1995)
    Article ADS CAS PubMed PubMed Central Google Scholar
34. Menzel, K. et al. Cathepsins B, L and D in inflammatory bowel disease macrophages and potential therapeutic effects of cathepsin inhibition in vivo . Clin. Exp. Immunol. 146, 169–180 (2006)
    Article CAS PubMed PubMed Central Google Scholar
35. Fu, Y. K., Arkins, S., Wang, B. S. & Kelley, K. W. A novel role of growth hormone and insulin-like growth factor-I. Priming neutrophils for superoxide anion secretion. J. Immunol. 146, 1602–1608 (1991)
    CAS PubMed Google Scholar
36. Bjerknes, R. & Aarskog, D. Priming of human polymorphonuclear neutrophilic leukocytes by insulin-like growth factor I: increased phagocytic capacity, complement receptor expression, degranulation, and oxidative burst. J. Clin. Endocrinol. Metab. 80, 1948–1955 (1995)
    CAS PubMed Google Scholar
37. Everley, P. A. et al. Enhanced analysis of metastatic prostate cancer using stable isotopes and high mass accuracy instrumentation. J. Proteome Res. 5, 1224–1231 (2006)
    Article CAS PubMed Google Scholar
38. Guo, A. et al. Signaling networks assembled by oncogenic EGFR and c-Met. Proc. Natl Acad. Sci. USA 105, 692–697 (2008)
    Article ADS CAS PubMed PubMed Central Google Scholar
39. Kersey, P. J. et al. The International Protein Index: an integrated database for proteomics experiments. Proteomics 4, 1985–1988 (2004)
    Article CAS PubMed Google Scholar
40. Pruitt, K. D., Katz, K. S., Sicotte, H. & Maglott, D. R. Introducing RefSeq and LocusLink: curated human genome resources at the NCBI. Trends Genet. 16, 44–47 (2000)
    Article CAS PubMed Google Scholar
41. Imanishi, T. et al. Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol. 2, e162 (2004)
    Article PubMed PubMed Central Google Scholar
42. Kent, W. J. BLAT–the BLAST-like alignment tool. Genome Res. 12, 656–664 (2002)
    Article CAS PubMed PubMed Central Google Scholar
43. Baek, D., Davis, C., Ewing, B., Gordon, D. & Green, P. Characterization and predictive discovery of evolutionarily conserved mammalian alternative promoters. Genome Res. 17, 145–155 (2007)
    Article CAS PubMed PubMed Central Google Scholar
44. Okazaki, Y. et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420, 563–573 (2002)
    Article ADS PubMed Google Scholar
45. Bolstad, B. M., Irizarry, R. A., Astrand, M. & Speed, T. P. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19, 185–193 (2003)
    Article CAS PubMed Google Scholar
46. Karolchik, D. et al. The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res. 36, D773–D779 (2008)
    Article CAS PubMed Google Scholar
47. Ruby, J. G. et al. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans . Cell 127, 1193–1207 (2006)
    Article CAS PubMed Google Scholar
48. Pall, G. S., Codony-Servat, C., Byrne, J., Ritchie, L. & Hamilton, A. Carbodiimide-mediated cross-linking of RNA to nylon membranes improves the detection of siRNA, miRNA and piRNA by northern blot. Nucleic Acids Res. 35, e60 (2007)
    Article PubMed PubMed Central Google Scholar

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