p53-mediated heterochromatin reorganization regulates its cell fate decisions

Journal name:
Nature Structural & Molecular Biology
Volume:
19,
Pages:
478–484
Year published:
DOI:
doi:10.1038/nsmb.2271
Received
Accepted
Published online

Abstract

p53 is a major sensor of cellular stresses, and its activation influences cell fate decisions. We identified SUV39H1, a histone code 'writer' responsible for the histone H3 Lys9 trimethylation (H3K9me3) mark for 'closed' chromatin conformation, as a target of p53 repression. SUV39H1 downregulation was mediated transcriptionally by p21 and post-translationally by MDM2. The H3K9me3 repression mark was found to be associated with promoters of representative p53 target genes and was decreased upon p53 activation. Overexpression of SUV39H1 maintained higher levels of the H3K9me3 mark on these promoters and was associated with decreased p53 promoter occupancy and decreased transcriptional induction in response to p53. Conversely, SUV39H1 pre-silencing decreased H3K9me3 levels on these promoters and enhanced the p53 apoptotic response. These findings uncover a new layer of p53-mediated chromatin regulation through modulation of histone methylation at p53 target promoters.

At a glance

Figures

  1. p53 downregulates SUV39H1 expression.
    Figure 1: p53 downregulates SUV39H1 expression.

    (a) Real-time quantitative PCR (qrtPCR) of EJ-p53 cells induced for p53 for the indicated time points. (b) qrtPCR of B5/589 cells treated with either Nutlin3a or MI-219. (c) qrtPCR of EJ-p53 and EJ-p21 cells induced for p53 or p21, respectively, for the indicated time points. (d) qrtPCR of EJ-p53 cells stably expressing either sh-GFP or sh-p21 and induced for different levels of p53 for 24 h at the indicated tetracycline concentrations. (e) Western blot analysis of indicated proteins in EJ-p53 and EJ-p21 cells induced for either p53 or p21, respectively, for the indicated time points. All error bars represent s.e.m. of representative experiments done in triplicate.

  2. Induction of p53 abrogates the H3K9me3 heterochromatin mark.
    Figure 2: Induction of p53 abrogates the H3K9me3 heterochromatin mark.

    (a) Western blot analysis of EJ-p53 cells induced for p53 for the indicated time points by the complete removal of tetracycline from the medium. (b) Western blot analysis of B5/589 cells expressing either sh-GFP or sh-p53 and treated with MI-219. (c) Western blot analysis of HCT116 p53 WT and HCT116 p53−/− cells treated with 0, 0.05, 0.1 or 0.2 μg ml−1 of doxorubicin for 48 h. (d) ChIP analysis showing H3K9me3 occupancy on p53 target promoters in B5/589 cells treated with MI-219 for 24 h. The target sequences were detected by qrtPCR analysis of eluted DNA. The relative H3K9me3 occupancy over the input percentage is shown as a bar diagram. Acetylcholine receptor (AChR) is used as a negative control. All error bars represent s.e.m. of representative experiments done in triplicate.

  3. Overexpression of SUV39H1 inhibits p53-dependent apoptosis.
    Figure 3: Overexpression of SUV39H1 inhibits p53-dependent apoptosis.

    (a) Western blot analysis of B5/589 cells overexpressing SUV39H1 and treated with Nutlin3a. The dotted line in the figure divides the vector from SUV39H1 bands. The discontinuity in the bands of the first three westerns is due to deletion of irrelevant lanes in this gel. (b) ChIP analysis showing H3K9me3 occupancy on p53 target promoters in B5/589 cells overexpressing SUV39H1 and treated with MI-219 for 24 h. The target sequences were detected by qrtPCR analysis of eluted DNA. The relative H3K9me3 occupancy over the percent input is shown as a bar diagram. Acetylcholine receptor (AChR) is used as a negative control. (c) qrtPCR of B5/589 cells overexpressing SUV39H1 and treated with 0 μM, 5 μM or 10 μM of MI-219. (d) ChIP analysis showing p53 occupancy on its target promoters in B5/589 cells overexpressing SUV39H1 and treated with MI-219 for 24 h. The target sequences were detected by qrtPCR analysis of eluted DNA. The relative p53 promoter occupancy over the percent input is shown as a bar diagram. (e) Propidium iodide staining of HCT116 cells overexpressing SUV39H1 and treated with increasing doses of etoposide. The percentage of cells undergoing apoptosis (less than 2N content of DNA) is shown as a line diagram. All error bars represent s.e.m. of representative experiments done in triplicate.

  4. Silencing of SUV39H1 causes p21-dependent, but p53-independent, cell cycle arrest.
    Figure 4: Silencing of SUV39H1 causes p21-dependent, but p53-independent, cell cycle arrest.

    (a) qrtPCR of HCT116 WT cells stably transduced with inducible sh-SUV39H1 and cultured in the presence of doxycycline for the indicated time points. (b) ChIP analysis showing H3K9me3 occupancy on p53 target promoters in HCT116 WT cells stably transduced with inducible sh-SUV39H1 and cultured in the presence of doxycycline for the indicated time points. The target sequences were detected by qrtPCR analysis of eluted DNA. The relative H3K9me3 occupancy over the percent input is shown as a bar diagram. (c) Western blot analysis of HCT116 WT cells stably transduced with inducible sh-SUV39H1. Day 0, 1, 2 and 3 represent time after doxycycline addition into the medium. (d) Colony formation assay in HCT116 WT cells stably transduced with sh-SUV39H1. The cells were grown in the absence or presence of doxycycline. The colonies formed after 9 d were counted and are shown as a bar diagram. (e) Propidium iodide staining in HCT116 p53 WT, HCT116 p53−/− and HCT116 p21−/− cells stably transduced with inducible sh-SUV39H1. Day 0, 1, 2 and 3 represent time after addition of doxycycline into the medium. A bar diagram for each cell line showing the percentage of cells in S phase is also shown on the right. All error bars represent s.e.m. of representative experiments done in triplicate.

  5. Pre-silencing of SUV39H1 cooperates with chemotherapy-induced apoptosis in a p53-dependent manner.
    Figure 5: Pre-silencing of SUV39H1 cooperates with chemotherapy-induced apoptosis in a p53-dependent manner.

    (a) Propidium iodide (PI) staining in HCT116 p53 WT and HCT116 p53−/− cells stably transduced with sh-SUV39H1. The cells were pre-silenced for SUV39H1 by growing cells in the presence of doxycycline for two days followed by treatment with increasing doses of etoposide. The percentage of cells showing less than a 2N content of DNA (apoptosis) in each condition is shown in the table (see Supplementary Fig. 7 for actual FACS graphs). (b) Real-time analysis of HCT116 WT cells stably transduced with inducible sh-SUV39H1 and cultured in the presence of doxycycline for two days followed by treatment with MI-219. (c) Western blot analysis of HCT116 WT cells stably transduced with sh-SUV39H1 and treated with 0 μM, 5 μM, 10 μM or 20 μM of etoposide for 48 h. The cells were either untreated or pre-treated with doxycycline for two days before treating with etoposide. (d) ChIP analysis in HCT116 WT cells stably expressing sh-SUV39H1 showing p53 occupancy on its target promoters. The cells were either untreated or treated with doxycycline for two days, followed by MI-219 treatment for 24 h. The target sequences were detected by qrtPCR analysis of eluted DNA. The relative p53 promoter occupancy over the percent input is shown in the form of bar diagram. Acetylcholine receptor (AChR) was used as a negative control. Error bars represent s.e.m. of representative experiments done in triplicate. (e) Schematic diagram illustrating the role of SUV39H1 in p53-induced apoptosis. SUV39H1 is the HMTase that adds the H3K9me3 repressive chromatin mark on p53 target promoters, which keeps them in a closed chromatin conformation. Activation of p53 downregulates SUV39H1 expression, which in turn leads to a decrease in the H3K9me3 epigenetic mark on p53 target promoters. This results in a more open chromatin conformation that allows a higher level of p53 recruitment, leading to increased transcription of target genes and resulting in enhanced apoptosis.

References

  1. Jenuwein, T. & Allis, C.D. Translating the histone code. Science 293, 10741080 (2001).
  2. Mandinova, A. & Lee, S.W. The p53 pathway as a target in cancer therapeutics: obstacles and promise. Sci. Transl. Med. 3, 64rv1 (2011).
  3. Vousden, K.H. & Prives, C. Blinded by the light: the growing complexity of p53. Cell 137, 413431 (2009).
  4. Vazquez, A., Bond, E.E., Levine, A.J. & Bond, G.L. The genetics of the p53 pathway, apoptosis and cancer therapy. Nat. Rev. Drug Discov. 7, 979987 (2008).
  5. Liu, L. et al. p53 sites acetylated in vitro by PCAF and p300 are acetylated in vivo in response to DNA damage. Mol. Cell. Biol. 19, 12021209 (1999).
  6. Vaziri, H. et al. hSIR2(SIRT1) functions as an NAD-dependent p53 deacetylase. Cell 107, 149159 (2001).
  7. Dai, C. & Gu, W. p53 post-translational modification: deregulated in tumorigenesis. Trends Mol. Med. 16, 528536 (2010).
  8. Brooks, C.L. & Gu, W. The impact of acetylation and deacetylation on the p53 pathway. Protein Cell 2, 456462 (2011).
  9. Drost, J. et al. BRD7 is a candidate tumour suppressor gene required for p53 function. Nat. Cell Biol. 12, 380389 (2010).
  10. Lee, D. et al. SWI/SNF complex interacts with tumor suppressor p53 and is necessary for the activation of p53-mediated transcription. J. Biol. Chem. 277, 2233022337 (2002).
  11. Naidu, S.R., Love, I.M., Imbalzano, A.N., Grossman, S.R. & Androphy, E.J. The SWI/SNF chromatin remodeling subunit BRG1 is a critical regulator of p53 necessary for proliferation of malignant cells. Oncogene 28, 24922501 (2009).
  12. Groth, A., Rocha, W., Verreault, A. & Almouzni, G. Chromatin challenges during DNA replication and repair. Cell 128, 721733 (2007).
  13. Jaskelioff, M. & Peterson, C.L. Chromatin and transcription: histones continue to make their marks. Nat. Cell Biol. 5, 395399 (2003).
  14. Khorasanizadeh, S. The nucleosome: from genomic organization to genomic regulation. Cell 116, 259272 (2004).
  15. Schneider, R. & Grosschedl, R. Dynamics and interplay of nuclear architecture, genome organization, and gene expression. Genes Dev. 21, 30273043 (2007).
  16. Rubbi, C.P. & Milner, J. p53 is a chromatin accessibility factor for nucleotide excision repair of DNA damage. EMBO J. 22, 975986 (2003).
  17. Allison, S.J. & Milner, J. Loss of p53 has site-specific effects on histone H3 modification, including serine 10 phosphorylation important for maintenance of ploidy. Cancer Res. 63, 66746679 (2003).
  18. Jacobs, S.A. et al. Specificity of the HP1 chromo domain for the methylated N-terminus of histone H3. EMBO J. 20, 52325241 (2001).
  19. Sims, R.J. III, Nishioka, K. & Reinberg, D. Histone lysine methylation: a signature for chromatin function. Trends Genet. 19, 629639 (2003).
  20. Rice, J.C. et al. Histone methyltransferases direct different degrees of methylation to define distinct chromatin domains. Mol. Cell 12, 15911598 (2003).
  21. Sugrue, M.M., Shin, D.Y., Lee, S.W. & Aaronson, S.A. Wild-type p53 triggers a rapid senescence program in human tumor cells lacking functional p53. Proc. Natl. Acad. Sci. USA 94, 96489653 (1997).
  22. Ide, T. et al. GAMT, a p53-inducible modulator of apoptosis, is critical for the adaptive response to nutrient stress. Mol. Cell 36, 379392 (2009).
  23. Muñoz-Fontela, C. et al. Transcriptional role of p53 in interferon-mediated antiviral immunity. J. Exp. Med. 205, 19291938 (2008).
  24. Fodor, B.D., Shukeir, N., Reuter, G. & Jenuwein, T. Mammalian Su(var) genes in chromatin control. Annu. Rev. Cell Dev. Biol. 26, 471501 (2010).
  25. Lehnertz, B. et al. Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin. Curr. Biol. 13, 11921200 (2003).
  26. El-Deiry, W.S. et al. WAF1, a potential mediator of p53 tumor suppression. Cell 75, 817825 (1993).
  27. Contente, A., Dittmer, A., Koch, M.C., Roth, J. & Dobbelstein, M. A polymorphic microsatellite that mediates induction of PIG3 by p53. Nat. Genet. 30, 315320 (2002).
  28. Marine, J.C. & Lozano, G. Mdm2-mediated ubiquitylation: p53 and beyond. Cell Death Differ. 17, 93102 (2010).
  29. Mirza, A. et al. Human survivin is negatively regulated by wild-type p53 and participates in p53-dependent apoptotic pathway. Oncogene 21, 26132622 (2002).
  30. Hoffman, W.H., Biade, S., Zilfou, J.T., Chen, J. & Murphy, M. Transcriptional repression of the anti-apoptotic survivin gene by wild type p53. J. Biol. Chem. 277, 32473257 (2002).
  31. Johnsen, J.I. et al. p53-mediated negative regulation of stathmin/Op18 expression is associated with G2/M cell-cycle arrest. Int. J. Cancer 88, 685691 (2000).
  32. Krause, K. et al. Expression of the cell cycle phosphatase cdc25C is down-regulated by the tumor suppressor protein p53 but not by p73. Biochem. Biophys. Res. Commun. 284, 743750 (2001).
  33. Badie, C., Itzhaki, J.E., Sullivan, M.J., Carpenter, A.J. & Porter, A.C. Repression of CDK1 and other genes with CDE and CHR promoter elements during DNA damage-induced G2/M arrest in human cells. Mol. Cell. Biol. 20, 23582366 (2000).
  34. Innocente, S.A., Abrahamson, J.L., Cogswell, J.P. & Lee, J.M. p53 regulates a G2 checkpoint through cyclin B1. Proc. Natl. Acad. Sci. USA 96, 21472152 (1999).
  35. Löhr, K., Moritz, C., Contente, A. & Dobbelstein, M. p21/CDKN1A mediates negative regulation of transcription by p53. J. Biol. Chem. 278, 3250732516 (2003).
  36. Bosch-Presegué, L. et al. Stabilization of Suv39H1 by SirT1 is part of oxidative stress response and ensures genome protection. Mol. Cell 42, 210223 (2011).
  37. Roberts, C.W. & Orkin, S.H. The SWI/SNF complex–chromatin and cancer. Nat. Rev. Cancer 4, 133142 (2004).
  38. O'Carroll, D. et al. Isolation and characterization of Suv39h2, a second histone H3 methyltransferase gene that displays testis-specific expression. Mol. Cell. Biol. 20, 94239433 (2000).
  39. Waldman, T., Lengauer, C., Kinzler, K.W. & Vogelstein, B. Uncoupling of S phase and mitosis induced by anticancer agents in cells lacking p21. Nature 381, 713716 (1996).
  40. Cherrier, T. et al. p21WAF1 gene promoter is epigenetically silenced by CTIP2 and SUV39H1. Oncogene 28, 33803389 (2009).
  41. Pommier, Y., Leo, E., Zhang, H. & Marchand, C. DNA topoisomerases and their poisoning by anticancer and antibacterial drugs. Chem. Biol. 17, 421433 (2010).
  42. Fu, Y. et al. Medicinal chemistry of paclitaxel and its analogues. Curr. Med. Chem. 16, 39663985 (2009).
  43. Peters, A.H. et al. Loss of the Suv39h histone methyltransferases impairs mammalian heterochromatin and genome stability. Cell 107, 323337 (2001).
  44. Kondo, Y. et al. Downregulation of histone H3 lysine 9 methyltransferase G9a induces centrosome disruption and chromosome instability in cancer cells. PLoS ONE 3, e2037 (2008).
  45. Berk, A.J. Recent lessons in gene expression, cell cycle control, and cell biology from adenovirus. Oncogene 24, 76737685 (2005).
  46. Soria, C., Estermann, F.E., Espantman, K.C. & O'Shea, C.C. Heterochromatin silencing of p53 target genes by a small viral protein. Nature 466, 10761081 (2010).
  47. Chen, L. et al. MDM2 recruitment of lysine methyltransferases regulates p53 transcriptional output. EMBO J. 29, 25382552 (2010).
  48. Cross, B. et al. Inhibition of p53 DNA binding function by the MDM2 protein acidic domain. J. Biol. Chem. 286, 1601816029 (2011).
  49. Chi, P., Allis, C.D. & Wang, G.G. Covalent histone modifications–miswritten, misinterpreted and mis-erased in human cancers. Nat. Rev. Cancer 10, 457469 (2010).
  50. Ellis, L., Atadja, P.W. & Johnstone, R.W. Epigenetics in cancer: targeting chromatin modifications. Mol. Cancer Ther. 8, 14091420 (2009).
  51. Hake, S.B., Xiao, A. & Allis, C.D. Linking the epigenetic 'language' of covalent histone modifications to cancer. Br. J. Cancer 90, 761769 (2004).
  52. Ozdağ, H. et al. Differential expression of selected histone modifier genes in human solid cancers. BMC Genomics 7, 90 (2006).
  53. Godar, S. et al. Growth-inhibitory and tumor-suppressive functions of p53 depend on its repression of CD44 expression. Cell 134, 6273 (2008).
  54. Zhou, B.P. et al. HER-2/neu induces p53 ubiquitination via Akt-mediated MDM2 phosphorylation. Nat. Cell Biol. 3, 973982 (2001).
  55. Fang, L. et al. p21Waf1/Cip1/Sdi1 induces permanent growth arrest with markers of replicative senescence in human tumor cells lacking functional p53. Oncogene 18, 27892797 (1999).
  56. Bunz, F. et al. Requirement for p53 and p21 to sustain G2 arrest after DNA damage. Science 282, 14971501 (1998).
  57. Shangary, S. et al. Temporal activation of p53 by a specific MDM2 inhibitor is selectively toxic to tumors and leads to complete tumor growth inhibition. Proc. Natl. Acad. Sci. USA 105, 39333938 (2008).
  58. Vassilev, L.T. et al. In vivo activation of the p53 pathway by small-molecule antagonists of MDM2. Science 303, 844848 (2004).
  59. Mungamuri, S.K., Yang, X., Thor, A.D. & Somasundaram, K. Survival signaling by Notch1: mammalian target of rapamycin (mTOR)-dependent inhibition of p53. Cancer Res. 66, 47154724 (2006).
  60. Schaniel, C. et al. Smarcc1/Baf155 couples self-renewal gene repression with changes in chromatin structure in mouse embryonic stem cells. Stem Cells 27, 29792991 (2009).

Download references

Author information

Affiliations

  1. Department of Oncological Sciences, Mount Sinai School of Medicine, New York, New York, USA.

    • Sathish Kumar Mungamuri,
    • Erica Kay Benson &
    • Stuart A Aaronson
  2. University of Michigan Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, USA.

    • Shaomeng Wang
  3. Institute for Cancer Genetics, Department of Pathology and Cell Biology, College of Physicians and Surgeons of Columbia University, New York, New York, USA.

    • Wei Gu
  4. Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, USA.

    • Sam W Lee

Contributions

S.K.M. and S.A.A. planned the project. S.K.M. conducted all the experiments, with participation by E.K.B. S.W. provided the MI-219 MDM2 inhibitor. S.A.A. supervised the study, along with S.W.L. and W.G. S.K.M. and S.A.A. wrote the paper.

Competing financial interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to:

Author details

Supplementary information

PDF files

  1. Supplementary Text and Figures (3M)

    Supplementary Figures 1–8 and Supplementary Table 1

Additional data