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Pursuing gene regulation 'logic' via RNA interference and chromatin immunoprecipitation

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RNA interference and chromatin immunoprecipitation are now firmly established as useful methods for studying mechanisms of gene regulation in vivo. Their combined use can help elucidate gene regulation 'logic' by aiding in target gene identification for transcription factors and chromatin-modifying complexes.

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Figure 1: Use of RNAi and ChIP to categorize LPS-induced genes in mouse macrophages on the basis of their requirement for ATP-dependent nucleosome-remodeling complexes, their kinetics of activation and their protein synthesis requirements.

Katie Ris

References

  1. Carey, M. & Smale, S.T. in Transcriptional Regulation in Eukaryotes: Concepts, Strategies, and Techniques, 137–191 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 2000).

    Google Scholar 

  2. Taniuchi, I., Sunshine, M.J., Festenstein, R. & Littman, D.R. Mol. Cell 10, 1083–1096 (2002).

    Article  CAS  Google Scholar 

  3. Yannoutsos, N. et al. Nat. Immunol. 5, 443–450 (2004).

    Article  CAS  Google Scholar 

  4. Hsu, L.Y. et al. Immunity 19, 105–117 (2003).

    Article  CAS  Google Scholar 

  5. McManus, M.T. & Sharp, P.A. Nat. Rev. Genet. 3, 737–747 (2002).

    Article  CAS  Google Scholar 

  6. Huppi, K., Martin, S.E. & Caplen, N.J. Mol. Cell 17, 1–10 (2005).

    Article  CAS  Google Scholar 

  7. Engelke, D.R. & Rossi, J.J. Methods in Enzymology 1–454 Vol. 392 (Elsevier, San Diego, 2005).

    Google Scholar 

  8. Kuo, M.H. & Allis, C.D. Methods 19, 425–433 (1999).

    Article  CAS  Google Scholar 

  9. Hanlon, S.E. & Lieb, J.D. Curr. Opin. Genet. Dev. 14, 697–705 (2004).

    Article  CAS  Google Scholar 

  10. Sikder, D. & Kodadek, T. Curr. Opin. Chem. Biol. 9, 38–45 (2005).

    Article  CAS  Google Scholar 

  11. Rocheleau, C.E. et al. Cell 90, 707–716 (1997).

    Article  CAS  Google Scholar 

  12. Fire, A. et al. Nature 391, 806–811 (1998).

    Article  CAS  Google Scholar 

  13. Hannon, G.J. Nature 418, 244–251 (2002).

    Article  CAS  Google Scholar 

  14. Mello, C.C. & Conte, D., Jr. Nature 431, 338–342 (2004).

    Article  CAS  Google Scholar 

  15. Bartel, D.P. Cell 116, 281–297 (2004).

    Article  CAS  Google Scholar 

  16. Valencia-Sanchez, M.A., Liu, J., Hannon, G.J. & Parker, R. Genes Dev. 20, 515–524 (2006).

    Article  CAS  Google Scholar 

  17. Elbashir, S.M. et al. Nature 411, 494–498 (2001).

    Article  CAS  Google Scholar 

  18. Brummelkamp, T.R., Bernards, R. & Agami, R. Science 296, 550–553 (2002).

    Article  CAS  Google Scholar 

  19. Cullen, B.R. Nat. Genet. 37, 1163–1165 (2005).

    Article  CAS  Google Scholar 

  20. Mak, T.W., Penninger, J.M. & Ohashi, P.S. Nat. Rev. Immunol. 1, 11–19 (2001).

    Article  CAS  Google Scholar 

  21. Ramirez-Carrozzi, V.R. et al. Genes Dev. 20, 282–296 (2006).

    Article  CAS  Google Scholar 

  22. Moffat, J. & Sabatini, D.M. Nat. Rev. Mol. Cell Biol. 7, 177–187 (2006).

    Article  CAS  Google Scholar 

  23. Ui-Tei, K. et al. Nucleic Acids Res. 32, 936–948 (2004).

    Article  CAS  Google Scholar 

  24. Jackson, A.L. et al. Nat. Biotechnol. 21, 635–637 (2003).

    Article  CAS  Google Scholar 

  25. Birmingham, A. et al. Nat. Methods 3, 199–204 (2006).

    Article  CAS  Google Scholar 

  26. Dequiedt, F. et al. Immunity 18, 687–698 (2003).

    Article  CAS  Google Scholar 

  27. Scheeren, F.A. et al. Nat. Immunol. 6, 303–313 (2005).

    Article  CAS  Google Scholar 

  28. Dedon, P.C., Soults, J.A., Allis, C.D. & Gorovsky, M.A. Anal. Biochem. 197, 83–90 (1991).

    Article  CAS  Google Scholar 

  29. Orlando, V. & Paro, R. Cell 75, 1187–1198 (1993).

    Article  CAS  Google Scholar 

  30. Hecht, A., Strahl-Bolsinger, S. & Grunstein, M. Nature 383, 92–96 (1996).

    Article  CAS  Google Scholar 

  31. Lieb, J.D., Liu, X., Botstein, D. & Brown, P.O. Nat. Genet. 28, 327–334 (2001).

    Article  CAS  Google Scholar 

  32. Weinmann, A.S. Nat. Rev. Immunol. 4, 381–386 (2004).

    Article  CAS  Google Scholar 

  33. Kim, J., Bhinge, A.A., Morgan, X.C. & Iyer, V.R. Nat. Methods 2, 47–53 (2005).

    Article  CAS  Google Scholar 

  34. Walter, J., Dever, C.A. & Biggin, M.D. Genes Dev. 8, 1678–1692 (1994).

    Article  CAS  Google Scholar 

  35. Li, Q. & Johnston, S.A. Mol. Cell. Biol. 21, 2467–2474 (2001).

    Article  CAS  Google Scholar 

  36. Weinmann, A.S., Yan, P.S., Oberley, M.J., Huang, T.H. & Farnham, P.J. Genes Dev. 16, 235–244 (2002).

    Article  CAS  Google Scholar 

  37. Spilianakis, C.G., Lalioti, M.D., Town, T., Lee, G.R. & Flavell, R.A. Nature 435, 637–645 (2005).

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Howard Hughes Medical Institute and Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, 90095-1662, California, USA

    Caiyi C Li, Vladimir R Ramirez-Carrozzi & Stephen T Smale

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  1. Caiyi C Li
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  2. Vladimir R Ramirez-Carrozzi
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  3. Stephen T Smale
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Li, C., Ramirez-Carrozzi, V. & Smale, S. Pursuing gene regulation 'logic' via RNA interference and chromatin immunoprecipitation. Nat Immunol 7, 692–697 (2006). https://doi.org/10.1038/ni0706-692

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