Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Original Article
  • Published:

The NuRD complex cooperates with DNMTs to maintain silencing of key colorectal tumor suppressor genes

Oncogene volume 33, pages 2157–2168 (2014)Cite this article

Subjects

Abstract

Many tumor suppressor genes (TSGs) are silenced through synergistic layers of epigenetic regulation including abnormal DNA hypermethylation of promoter CpG islands, repressive chromatin modifications and enhanced nucleosome deposition over transcription start sites. The protein complexes responsible for silencing of many of such TSGs remain to be identified. Our previous work demonstrated that multiple silenced TSGs in colorectal cancer cells can be partially reactivated by DNA demethylation in cells disrupted for the DNA methyltransferases 1 and 3B (DNMT1 and 3B) or by DNMT inhibitors (DNMTi). Herein, we used proteomic and functional genetic approaches to identify additional proteins that cooperate with DNMTs in silencing these key silenced TSGs in colon cancer cells. We discovered that DNMTs and the core components of the NuRD (Mi-2/nucleosome remodeling and deacetylase) nucleosome remodeling complex, chromo domain helicase DNA-binding protein 4 (CHD4) and histone deacetylase 1 (HDAC1) occupy the promoters of several of these hypermethylated TSGs and physically and functionally interact to maintain their silencing. Consistent with this, we find an inverse relationship between expression of HDAC1 and 2 and these TSGs in a large panel of primary colorectal tumors. We demonstrate that DNMTs and NuRD cooperate to maintain the silencing of several negative regulators of the WNT and other signaling pathways. We find that depletion of CHD4 is synergistic with DNMT inhibition in reducing the viability of colon cancer cells in correlation with reactivation of TSGs, suggesting that their combined inhibition may be beneficial for the treatment of colon cancer. Since CHD4 has ATPase activity, our data identify CHD4 as a potentially novel drug target in cancer.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6

Similar content being viewed by others

References

  1. Ting AH, McGarvey KM, Baylin SB . The cancer epigenome—components and functional correlates. Genes Dev 2006; 20: 3215–3231.

    Article  CAS  PubMed  Google Scholar 

  2. Jones PA, Baylin SB . The epigenomics of cancer. Cell 2007; 128: 683–692.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Portela A, Esteller M . Epigenetic modifications and human disease. Nat Biotechnol 2010; 28: 1057–1068.

    Article  CAS  PubMed  Google Scholar 

  4. Chodavarapu RK, Feng S, Bernatavichute YV, Chen PY, Stroud H, Yu Y et al. Relationship between nucleosome positioning and DNA methylation. Nature 2010; 466: 388–392.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Choy JS, Wei S, Lee JY, Tan S, Chu S, Lee TH . DNA methylation increases nucleosome compaction and rigidity. J Am Chem Soc 2010; 132: 1782–1783.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Lin JC, Jeong S, Liang G, Takai D, Fatemi M, Tsai YC et al. Role of nucleosomal occupancy in the epigenetic silencing of the MLH1 CpG island. Cancer Cell 2007; 12: 432–444.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Bird A . DNA methylation patterns and epigenetic memory. Genes Dev 2002; 16: 6–21.

    Article  CAS  PubMed  Google Scholar 

  8. Nan X, Ng HH, Johnson CA, Laherty CD, Turner BM, Eisenman RN et al. Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 1998; 393: 386–389.

    Article  CAS  PubMed  Google Scholar 

  9. Lunyak VV, Burgess R, Prefontaine GG, Nelson C, Sze SH, Chenoweth J et al. Corepressor-dependent silencing of chromosomal regions encoding neuronal genes. Science 2002; 298: 1747–1752.

    Article  CAS  PubMed  Google Scholar 

  10. Hashimshony T, Zhang J, Keshet I, Bustin M, Cedar H . The role of DNA methylation in setting up chromatin structure during development. Nat Genet 2003; 34: 187–192.

    Article  CAS  PubMed  Google Scholar 

  11. Zhang Y, Ng HH, Erdjument-Bromage H, Tempst P, Bird A, Reinberg D . Analysis of the NuRD subunits reveals a histone deacetylase core complex and a connection with DNA methylation. Genes Dev 1999; 13: 1924–1935.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Lai AY, Wade PA . Cancer biology and NuRD: a multifaceted chromatin remodelling complex. Nat Rev Cancer 2011; 11: 588–596.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Wade PA, Gegonne A, Jones PL, Ballestar E, Aubry F, Wolffe AP . Mi-2 complex couples DNA methylation to chromatin remodelling and histone deacetylation. Nat Genet 1999; 23: 62–66.

    Article  CAS  PubMed  Google Scholar 

  14. Myant K, Stancheva I . LSH cooperates with DNA methyltransferases to repress transcription. Mol Cell Biol 2008; 28: 215–226.

    Article  CAS  PubMed  Google Scholar 

  15. Vire E, Brenner C, Deplus R, Blanchon L, Fraga M, Didelot C et al. The Polycomb group protein EZH2 directly controls DNA methylation. Nature 2006; 439: 871–874.

    Article  CAS  PubMed  Google Scholar 

  16. Mohammad HP, Cai Y, McGarvey KM, Easwaran H, Van Neste L, Ohm JE et al. Polycomb CBX7 promotes initiation of heritable repression of genes frequently silenced with cancer-specific DNA hypermethylation. Cancer Res 2009; 69: 6322–6330.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Di Croce L, Raker VA, Corsaro M, Fazi F, Fanelli M, Faretta M et al. Methyltransferase recruitment and DNA hypermethylation of target promoters by an oncogenic transcription factor. Science 2002; 295: 1079–1082.

    Article  CAS  PubMed  Google Scholar 

  18. Morey L, Brenner C, Fazi F, Villa R, Gutierrez A, Buschbeck M et al. MBD3, a component of the NuRD complex, facilitates chromatin alteration and deposition of epigenetic marks. Mol Cell Biol 2008; 28: 5912–5923.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Rhee I, Bachman KE, Park BH, Jair KW, Yen RW, Schuebel KE et al. DNMT1 and DNMT3b cooperate to silence genes in human cancer cells. Nature 2002; 416: 552–556.

    Article  CAS  PubMed  Google Scholar 

  20. Cameron EE, Bachman KE, Myohanen S, Herman JG, Baylin SB . Synergy of demethylation and histone deacetylase inhibition in the re-expression of genes silenced in cancer. Nat Genet 1999; 21: 103–107.

    Article  CAS  PubMed  Google Scholar 

  21. Suzuki H, Gabrielson E, Chen W, Anbazhagan R, van Engeland M, Weijenberg MP et al. A genomic screen for genes upregulated by demethylation and histone deacetylase inhibition in human colorectal cancer. Nat Genet 2002; 31: 141–149.

    Article  CAS  PubMed  Google Scholar 

  22. Suzuki H, Watkins DN, Jair KW, Schuebel KE, Markowitz SD, Chen WD et al. Epigenetic inactivation of SFRP genes allows constitutive WNT signaling in colorectal cancer. Nat Genet 2004; 36: 417–422.

    Article  CAS  PubMed  Google Scholar 

  23. Jurkin J, Zupkovitz G, Lagger S, Grausenburger R, Hagelkruys A, Kenner L et al. Distinct and redundant functions of histone deacetylases HDAC1 and HDAC2 in proliferation and tumorigenesis. Cell Cycle 2011; 10: 406–412.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Wilting RH, Yanover E, Heideman MR, Jacobs H, Horner J, van der Torre J et al. Overlapping functions of Hdac1 and Hdac2 in cell cycle regulation and haematopoiesis. EMBO J 2010; 29: 2586–2597.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Salazar R, Roepman P, Capella G, Moreno V, Simon I, Dreezen C et al. Gene expression signature to improve prognosis prediction of stage II and III colorectal cancer. J Clin Oncol 2011; 29: 17–24.

    Article  PubMed  Google Scholar 

  26. Weichert W, Roske A, Niesporek S, Noske A, Buckendahl AC, Dietel M et al. Class I histone deacetylase expression has independent prognostic impact in human colorectal cancer: specific role of class I histone deacetylases in vitro and in vivo. Clin Cancer Res 2008; 14: 1669–1677.

    Article  CAS  PubMed  Google Scholar 

  27. Weichert W . HDAC expression and clinical prognosis in human malignancies. Cancer Lett 2009; 280: 168–176.

    Article  CAS  PubMed  Google Scholar 

  28. Kouzarides T . Chromatin modifications and their function. Cell 2007; 128: 693–705.

    Article  CAS  PubMed  Google Scholar 

  29. Reale A, Matteis GD, Galleazzi G, Zampieri M, Caiafa P . Modulation of DNMT1 activity by ADP-ribose polymers. Oncogene 2005; 24: 13–19.

    Article  CAS  PubMed  Google Scholar 

  30. Chuang LS, Ian HI, Koh TW, Ng HH, Xu G, Li BF . Human DNA-(cytosine-5) methyltransferase-PCNA complex as a target for p21WAF1. Science 1997; 277: 1996–2000.

    Article  CAS  PubMed  Google Scholar 

  31. Esteve PO, Chin HG, Smallwood A, Feehery GR, Gangisetty O, Karpf AR et al. Direct interaction between DNMT1 and G9a coordinates DNA and histone methylation during replication. Genes Dev 2006; 20: 3089–3103.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Schuebel KE, Chen W, Cope L, Glockner SC, Suzuki H, Yi JM et al. Comparing the DNA hypermethylome with gene mutations in human colorectal cancer. PLoS Genet 2007; 3: 1709–1723.

    Article  CAS  PubMed  Google Scholar 

  33. Ying Y, Tao Q . Epigenetic disruption of the WNT/beta-catenin signaling pathway in human cancers. Epigenetics 2009; 4: 307–312.

    Article  CAS  PubMed  Google Scholar 

  34. Aleman A, Adrien L, Lopez-Serra L, Cordon-Cardo C, Esteller M, Belbin TJ et al. Identification of DNA hypermethylation of SOX9 in association with bladder cancer progression using CpG microarrays. Br J Cancer 2008; 98: 466–473.

    Article  CAS  PubMed  Google Scholar 

  35. Park M, Moon RT . The planar cell-polarity gene stbm regulates cell behaviour and cell fate in vertebrate embryos. Nat Cell Biol 2002; 4: 20–25.

    Article  CAS  PubMed  Google Scholar 

  36. Kaelin WG Jr . The concept of synthetic lethality in the context of anticancer therapy. Nat Rev Cancer 2005; 5: 689–698.

    Article  CAS  PubMed  Google Scholar 

  37. Piekarz RL, Frye R, Turner M, Wright JJ, Allen SL, Kirschbaum MH et al. Phase II multi-institutional trial of the histone deacetylase inhibitor romidepsin as monotherapy for patients with cutaneous T-cell lymphoma. J Clin Oncol 2009; 27: 5410–5417.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Kazantsev AG, Thompson LM . Therapeutic application of histone deacetylase inhibitors for central nervous system disorders. Nat Rev Drug Discov 2008; 7: 854–868.

    Article  CAS  PubMed  Google Scholar 

  39. Wozniak RJ, Klimecki WT, Lau SS, Feinstein Y, Futscher BW . 5-Aza-2'-deoxycytidine-mediated reductions in G9A histone methyltransferase and histone H3 K9 di-methylation levels are linked to tumor suppressor gene reactivation. Oncogene 2007; 26: 77–90.

    Article  CAS  PubMed  Google Scholar 

  40. Sansom OJ, Berger J, Bishop SM, Hendrich B, Bird A, Clarke AR . Deficiency of Mbd2 suppresses intestinal tumorigenesis. Nat Genet 2003; 34: 145–147.

    Article  CAS  PubMed  Google Scholar 

  41. Phesse TJ, Parry L, Reed KR, Ewan KB, Dale TC, Sansom OJ et al. Deficiency of Mbd2 attenuates Wnt signaling. Mol Cell Biol 2008; 28: 6094–6103.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Juttermann R, Li E, Jaenisch R . Toxicity of 5-aza-2'-deoxycytidine to mammalian cells is mediated primarily by covalent trapping of DNA methyltransferase rather than DNA demethylation. Proc Natl Acad Sci USA 1994; 91: 11797–11801.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Polo SE, Kaidi A, Baskcomb L, Galanty Y, Jackson SP . Regulation of DNA-damage responses and cell-cycle progression by the chromatin remodelling factor CHD4. EMBO J 2010; 29: 3130–3139.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Smeenk G, Wiegant WW, Vrolijk H, Solari AP, Pastink A, van Attikum H . The NuRD chromatin-remodeling complex regulates signaling and repair of DNA damage. J Cell Biol 2010; 190: 741–749.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Larsen DH, Poinsignon C, Gudjonsson T, Dinant C, Payne MR, Hari FJ et al. The chromatin-remodeling factor CHD4 coordinates signaling and repair after DNA damage. J Cell Biol 2010; 190: 731–740.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Huss M, Wieczorek H . Inhibitors of V-ATPases: old and new players. J Exp Biol 2009; 212 (Pt 3): 341–346.

    Article  CAS  PubMed  Google Scholar 

  47. Huang Y, Stewart TM, Wu Y, Baylin SB, Marton LJ, Perkins B et al. Novel oligoamine analogues inhibit lysine-specific demethylase 1 and induce reexpression of epigenetically silenced genes. Clin Cancer Res 2009; 15: 7217–7228.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Trapnell C, Pachter L, Salzberg SL . TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009; 25: 1105–1111.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Clements EG, Mohammad HP, Leadem BR, Easwaran H, Cai Y, Van Neste L et al. DNMT1 modulates gene expression without its catalytic activity partially through its interactions with histone-modifying enzymes. Nucleic Acids Res 2012; 40: 4334–4346.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Jin Q, Yu LR, Wang L, Zhang Z, Kasper LH, Lee JE et al. Distinct roles of GCN5/PCAF-mediated H3K9ac and CBP/p300-mediated H3K18/27ac in nuclear receptor transactivation. EMBO J 2011; 30: 249–262.

    Article  CAS  PubMed  Google Scholar 

  51. Yu LR, Zhu Z, Chan KC, Issaq HJ, Dimitrov DS, Veenstra TD . Improved titanium dioxide enrichment of phosphopeptides from HeLa cells and high confident phosphopeptide identification by cross-validation of MS/MS and MS/MS/MS spectra. J Proteome Res 2007; 6: 4150–4162.

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank JH Dannenberg for the gift of Hdac1 plasmids. We thank JH Dannenberg, P Kumar and members of the Bernards, Baylin laboratory for discussions and Kathy Bender and H. Liu for manuscript preparation. This work was supported by a grant from the Netherlands Organization for Scientific Research (NWO) to RB, and by grants ES011858 National Institute of Environmental Health Sciences (NIEHS) CA043318 National Cancer Institute (NCI) to SB. The views presented in this article do not necessarily reflect those of the US Food and Drug Administration.

Author information

Author notes

  1. Y Cai and E-J Geutjes: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, MD, USA

    Y Cai, W Wang, H Mohammad & S B Baylin

  2. Division of Molecular Carcinogenesis, Center for Biomedical Genetics and Cancer Genomics Centre, The Netherlands Cancer Institute, Amsterdam, The Netherlands

    E-J Geutjes, K de Lint, L Bruurs, J van Blijswijk & R Bernards

  3. Department of Research and Development, Agendia NV, Amsterdam, The Netherlands

    P Roepman

  4. Division of Systems Biology, Center of Excellence for Proteomics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA

    L-R Yu

  5. Central Microarray and Deep Sequencing Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands

    I de Rink

Authors
  1. Y Cai
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. E-J Geutjes
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. K de Lint
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. P Roepman
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. L Bruurs
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. L-R Yu
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. W Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. J van Blijswijk
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. H Mohammad
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. I de Rink
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. R Bernards
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. S B Baylin
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to R Bernards or S B Baylin.

Ethics declarations

Competing interests

The authors declare no conflict of interest.

Additional information

Supplementary Information accompanies this paper on the Oncogene website

Supplementary information

Rights and permissions

Reprints and permissions

About this article

Cite this article

Cai, Y., Geutjes, EJ., de Lint, K. et al. The NuRD complex cooperates with DNMTs to maintain silencing of key colorectal tumor suppressor genes. Oncogene 33, 2157–2168 (2014). https://doi.org/10.1038/onc.2013.178

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/onc.2013.178

Keywords

This article is cited by

Search

Advanced search

Quick links