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Senescence is an endogenous trigger for microRNA-directed transcriptional gene silencing in human cells

Abstract

Cellular senescence is a tumour-suppressor mechanism that is triggered by cancer-initiating or promoting events in mammalian cells. The molecular underpinnings for this stable arrest involve transcriptional repression of proliferation-promoting genes regulated by the retinoblastoma (RB1)/E2F repressor complex. Here, we demonstrate that AGO2, RB1 and microRNAs (miRNAs), as exemplified here by let-7, physically and functionally interact to repress RB1/E2F-target genes in senescence, a process that we call senescence-associated transcriptional gene silencing (SA-TGS). Herein, AGO2 acts as the effector protein for let-7-directed implementation of silent-state chromatin modifications at target promoters, and inhibition of the let-7/AGO2 effector complex perturbs the timely execution of senescence. Thus, we identify cellular senescence as the an endogenous signal of miRNA/AGO2-mediated TGS in human cells. Our results suggest that miRNA/AGO2-mediated SA-TGS may contribute to tumour suppression by stably repressing proliferation-promoting genes in premalignant cancer cells.

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Figure 1: Identification of AGO-bound E2F-target genes and heterochromatin-bound miRNAs.
Figure 2: AGO2 accumulates in the nucleus of senescent cells and is recruited to promoters of repressed E2F-target genes.
Figure 3: AGO2 cooperates with RB1 to regulate E2F-target gene expression.
Figure 4: Depletion of AGO2 delays senescence arrest in W38 fibroblasts.
Figure 5: Overexpression of AGO2 induces proliferative arrest with features of premature senescence.
Figure 6: AGO2 and let-7f cooperate to induce TGS of E2F-target promoters.
Figure 7: Inhibition of let-7f perturbs timely execution of senescence and SA-TGS.
Figure 8: Model for AGO2 and miRNA function in SA-TGS of E2F-target genes.

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References

  1. Collado, M. & Serrano, M. Senescence in tumours: evidence from mice and humans. Nat. Rev. Cancer 10, 51–57 (2010).

    Article  CAS  Google Scholar 

  2. Narita, M. et al. Rb-mediated heterochromatin formation and silencing of E2F target genes during cellular senescence. Cell 113, 703–716 (2003).

    Article  CAS  Google Scholar 

  3. Adams, P. D. Remodeling chromatin for senescence. Aging Cell 6, 425–427 (2007).

    Article  CAS  Google Scholar 

  4. Moazed, D. Small RNAs in transcriptional gene silencing and genome defence. Nature 457, 413–420 (2009).

    Article  CAS  Google Scholar 

  5. Morris, K. V. RNA-mediated transcriptional gene silencing in human cells. Curr. Top. Microbiol. Immunol. 320, 211–224 (2008).

    CAS  PubMed  Google Scholar 

  6. Janowski, B. A. et al. Involvement of AGO1 and AGO2 in mammalian transcriptional silencing. Nat. Struct. Mol. Biol. 13, 787–792 (2006).

    Article  CAS  Google Scholar 

  7. Kim, D. H., Saetrom, P., Snove, O. Jr. & Rossi, J. J. MicroRNA-directed transcriptional gene silencing in mammalian cells. Proc. Natl Acad. Sci. USA 105, 16230–16235 (2008).

    Article  CAS  Google Scholar 

  8. Rabinovich, A., Jin, V. X., Rabinovich, R., Xu, X. & Farnham, P. J. E2F in vivo binding specificity: comparison of consensus versus nonconsensus binding sites. Genome Res. 18, 1763–1777 (2008).

    Article  CAS  Google Scholar 

  9. Xu, X. et al. A comprehensive ChIP–chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members. Genome Res. 17, 1550–1561 (2007).

    Article  CAS  Google Scholar 

  10. Ross, J. F., Naar, A., Cam, H., Gregory, R. & Dynlacht, B. D. Active repression and E2F inhibition by pRB are biochemically distinguishable. Genes Dev. 15, 392–397 (2001).

    Article  CAS  Google Scholar 

  11. Bieda, M., Xu, X., Singer, M. A., Green, R. & Farnham, P. J. Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome. Genome Res. 16, 595–605 (2006).

    Article  CAS  Google Scholar 

  12. Rudel, S., Flatley, A., Weinmann, L., Kremmer, E. & Meister, G. A multifunctional human Argonaute2-specific monoclonal antibody. RNA 14, 1244–1253 (2008).

    Article  Google Scholar 

  13. Zhou, Y. et al. High-risk myeloma is associated with global elevation of miRNAs and overexpression of EIF2C2/AGO2. Proc. Natl Acad. Sci. USA 107, 7904–7909 (2010).

    Article  CAS  Google Scholar 

  14. Kim, M. S. et al. Somatic mutations and losses of expression of microRNA regulation-related genes AGO2 and TNRC6A in gastric and colorectal cancers. J. Pathol. 221, 139–146 (2010).

    Article  CAS  Google Scholar 

  15. Li, L., Yu, C., Gao, H. & Li, Y. Argonaute proteins: potential biomarkers for human colon cancer. BMC Cancer 10, 38 (2010).

    Article  Google Scholar 

  16. Michaloglou, C. et al. BRAFE600-associated senescence-like cell cycle arrest of human naevi. Nature 436, 720–724 (2005).

    Article  CAS  Google Scholar 

  17. Dhomen, N. et al. Oncogenic Braf induces melanocyte senescence and melanoma in mice. Cancer Cell 15, 294–303 (2009).

    Article  CAS  Google Scholar 

  18. Gray-Schopfer, V. C. et al. Cellular senescence in naevi and immortalisation in melanoma: a role for p16? Br. J. Cancer 95, 496–505 (2006).

    Article  CAS  Google Scholar 

  19. Sporn, J. C. et al. Histone macroH2A isoforms predict the risk of lung cancer recurrence. Oncogene 28, 3423–3428 (2009).

    Article  CAS  Google Scholar 

  20. Zhang, R. et al. Formation of MacroH2A-containing senescence-associated heterochromatin foci and senescence driven by ASF1a and HIRA. Dev. Cell 8, 19–30 (2005).

    Article  CAS  Google Scholar 

  21. Ricke, R. M. & Bielinsky, A. K. Easy detection of chromatin binding proteins by the Histone Association Assay. Biol. Proced Online 7, 60–69 (2005).

    Article  CAS  Google Scholar 

  22. Nielsen, S. J. et al. Rb targets histone H3 methylation and HP1 to promoters. Nature 412, 561–565 (2001).

    Article  CAS  Google Scholar 

  23. Luo, R. X., Postigo, A. A. & Dean, D. C. Rb interacts with histone deacetylase to repress transcription. Cell 92, 463–473 (1998).

    Article  CAS  Google Scholar 

  24. Brehm, A. et al. Retinoblastoma protein recruits histone deacetylase to repress transcription. Nature 391, 597–601 (1998).

    Article  CAS  Google Scholar 

  25. Magnaghi-Jaulin, L. et al. Retinoblastoma protein represses transcription by recruiting a histone deacetylase. Nature 391, 601–605 (1998).

    Article  CAS  Google Scholar 

  26. Ohtani, K., DeGregori, J. & Nevins, J. R. Regulation of the cyclin E gene by transcription factor E2F1. Proc. Natl Acad. Sci. USA 92, 12146–12150 (1995).

    Article  CAS  Google Scholar 

  27. Ro, S. et al. Cloning and expression profiling of testis-expressed piRNA-like RNAs. RNA 13, 1693–1702 (2007).

    Article  CAS  Google Scholar 

  28. Krueger, J. & Rehmsmeier, M. RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acid Res. 34, W451–W454 (2006).

    Article  CAS  Google Scholar 

  29. Dalton, S. Cell cycle regulation of the human cdc2 gene. EMBO J. 11, 1797–1804 (1992).

    Article  CAS  Google Scholar 

  30. Han, J., Kim, D. & Morris, K. V. Promoter-associated RNA is required for RNA-directed transcriptional gene silencing in human cells. Proc. Natl Acad. Sci. USA 104, 12422–12427 (2007).

    Article  CAS  Google Scholar 

  31. Bischof, O. et al. The E3 SUMO ligase PIASy is a regulator of cellular senescence and apoptosis. Mol. Cell 22, 783–794 (2006).

    Article  CAS  Google Scholar 

  32. Ji, P. et al. An Rb-Skp2-p27 pathway mediates acute cell cycle inhibition by Rb and is retained in a partial-penetrance Rb mutant. Mol. Cell 16, 47–58 (2004).

    Article  CAS  Google Scholar 

  33. Chang, B. D. et al. A senescence-like phenotype distinguishes tumor cells that undergo terminal proliferation arrest after exposure to anticancer agents. Cancer Res. 59, 3761–3767 (1999).

    CAS  PubMed  Google Scholar 

  34. Bischof, O, Nacerddine, K. & Dejean, A. Human papillomavirus oncoprotein E7 targets the promyelocytic leukemia protein and circumvents cellular senescence via the Rb and p53 tumor suppressor pathways. Mol. Cell Biol. 25, 1013–1024 (2005).

    Article  CAS  Google Scholar 

  35. Kumar, P. P. et al. Functional interaction between PML and SATB1 regulates chromatin-loop architecture and transcription of the MHC class I locus. Nat. Cell Biol. 9, 45–56 (2007).

    Article  Google Scholar 

  36. Frank, S. R., Schroeder, M., Fernandez, P., Taubert, S. & Amati, B. Binding of c-Myc to chromatin mediates mitogen-induced acetylation of histone H4 and gene activation. Genes Dev. 15, 2069–2082 (2001).

    Article  CAS  Google Scholar 

  37. Meng, L., Bregitzer, P., Zhang, S. & Lemaux, P. G. Methylation of the exon/intron region in the Ubi1 promoter complex correlates with transgene silencing in barley. Plant Mol. Biol. 53, 327–340 (2003).

    Article  CAS  Google Scholar 

  38. Huang, D. W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protocols 4, 44–57 (2008).

    Article  Google Scholar 

  39. Liu, C. G., Spizzo, R., Calin, G. A. & Croce, C. M. Expression profiling of microRNA using oligo DNA arrays. Methods 44, 22–30 (2008).

    Article  Google Scholar 

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Acknowledgements

We would like to thank A. Verdel and M. Yaniv for discussions and critical reading of the manuscript. We are grateful to P. Adams for providing the anti-macroH2A antibody to U.H. and N. Mirani for technical help with histopathology as well as S. Volinia and C. Croce for miRNA profiling and J. Doudement (GenomeQuest, France) for bioinformatics analysis. This work was supported by grants from Ligue Nationale Contre le Cancer (Equipe labellisée), Association for International Cancer Research, Agence Nationale de la Recherche, Association pour la Recherche sur le Cancer (ARC), OdysseyRe and the New Jersey Commission on Cancer Research 09-1124-CCR-EO to U.H. O.B. is a CNRS (Centre National de la Recherche Scientifique) fellow, A.D. Institut National de la Santé et de la Recherche Médicale (INSERM)/Institut Pasteur and M.B. was supported by ARC.

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Contributions

O.B. and M.B. conceived the project. M.B. carried out experiments. O.B., M.B. and A.D. analysed the data. U.H. carried out immunohistochemical staining on nevi and melanomas. T.Y. carried out bioinformatic analysis. O.B. and A.D. wrote the manuscript.

Corresponding authors

Correspondence to Anne Dejean or Oliver Bischof.

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The authors declare no competing financial interests.

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Benhamed, M., Herbig, U., Ye, T. et al. Senescence is an endogenous trigger for microRNA-directed transcriptional gene silencing in human cells. Nat Cell Biol 14, 266–275 (2012). https://doi.org/10.1038/ncb2443

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