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Impaired recruitment of the histone methyltransferase DOT1L contributes to the incomplete reactivation of tumor suppressor genes upon DNA demethylation

Oncogene volume 28, pages 4212–4224 (2009)Cite this article

Abstract

Understanding the mechanisms that link changes in DNA methylation with histone modifications is particularly relevant in the case of tumor suppressor genes that undergo transcriptional silencing in cancer cells in association with promoter CpG island hypermethylation. In this study, we show that two histone lysine methylation marks associated with active transcription, dimethylation of H3K79 (H3K79me2) and trimethylation of H3K4 (H3K4me3), are present in all the unmethylated promoters analysed, and both of them are lost when these promoters become hypermethylated. Most importantly, pharmacological and genetic interventions that cause DNA demethylation and partial recovery of gene transcription, result in the restoration of H3K4me3, but not of H3K79me2. We also show that DOT1L, the major H3K79 histone methyltransferase, is no longer recruited to the promoters that are demethylated after 5-aza-deoxycytidine treatment or genetic deletion of DNA methyltransferases. Knock-down and transfection experiments for DOT1L show that this enzyme has a direct role in maintaining the euchromatic and active status of these genes when unmethylated. These findings suggest that DNA demethylating interventions alone are not able to restore a complete euchromatic status and a full transcriptional reactivation of the epigenetically silenced tumor suppressor genes, and reinforce the necessity of targeting multiple elements of the epigenetics machinery for a successful treatment of malignancies.

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References

  • Akiyama Y, Watkins N, Suzuki H, Jair KW, van Engeland M, Esteller M et al. (2003). GATA-4 and GATA-5 transcription factor genes and potential downstream antitumor target genes are epigenetically silenced in colorectal and gastric cancer. Mol Cell Biol 23: 8429–8439.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ballestar E, Paz MF, Valle L, Wei S, Fraga MF, Espada J et al. (2003). Methyl-CpG binding proteins identify novel sites of epigenetic inactivation in human cancer. EMBO J 22: 6335–6345.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Berger SL . (2007). The complex language of chromatin regulation during transcription. Nature 447: 407–412.

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Costello JF, Fruhwald MC, Smiraglia DJ, Rush LJ, Robertson GP, Gao X et al. (2000). Aberrant CpG-island methylation has non-random and tumor-type specific patterns. Nat Genet 24: 132–138.

    Article  CAS  PubMed  Google Scholar 

  • Esteller M . (2008). Epigenetics in cancer. N Engl J Med 358: 1148–1159.

    Article  CAS  PubMed  Google Scholar 

  • Esteller M, Corn PG, Baylin SB, Herman JG . (2001). A gene hypermethylation profile of human cancer. Cancer Res 61: 3225–3229.

    CAS  PubMed  Google Scholar 

  • Fahrner JA, Eguchi S, Herman JG, Baylin SB . (2002). Dependence of histone modifications and gene expression on DNA hypermethylation in cancer. Cancer Res 62: 7213–7218.

    CAS  PubMed  Google Scholar 

  • Feng Q, Wang H, Ng HH, Erdjument-Bromage H, Tempst P, Struhl K et al. (2002). Methylation of H3.lysine 79 is mediated by a new family of HMTases without a SET domain. Curr Biol 12: 1052–1058.

    Article  CAS  PubMed  Google Scholar 

  • Garcia-Manero G . (2008). Demethylating agents in myeloid malignancies. Curr Opin Oncol 20: 705–710.

    Article  CAS  PubMed  Google Scholar 

  • Jones PA, Baylin SB . (2007). The epigenomics of cancer. Cell 128: 683.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kondo Y, Shen L, Issa JP . (2003). Critical role of histone methylation in tumor suppressor gene silencing in colorectal cancer. Mol Cell Biol 23: 206–215.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kouzarides T . (2007). Chromatin modifications and their function. Cell 128: 693–705.

    Article  CAS  PubMed  Google Scholar 

  • Lopez-Serra L, Esteller M . (2008). Proteins that bind methylated DNA and human cancer: reading the wrong words. Br J Cancer 98: 1881–1885.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • McGarvey KM, Fahrner JA, Greene E, Martens J, Jenuwein T, Baylin SB . (2006). Silenced tumor suppressor genes reactivated by DNA demethylation do not return to a fully euchromatic chromatin state. Cancer Res 66: 3541–3549.

    Article  CAS  PubMed  Google Scholar 

  • Milne TA, Martin ME, Brock HW, Slany RK, Hess JL . (2005). Leukemogenic MLL fusion proteins bind across a broad region of the Hoxa9 locus, promoting transcription and multiple histone modifications. Cancer Res 65: 11367–11374.

    Article  CAS  PubMed  Google Scholar 

  • Min J, Feng Q, Li Z, Zhang Y, Xu RM . (2003). Structure of the catalytic domain of human DOT1L, a non-SET domain nucleosomal histone methyltransferase. Cell 112: 711–723.

    Article  CAS  PubMed  Google Scholar 

  • Ng HH, Feng Q, Wang H, Erdjument-Bromage H, Tempst P, Zhang Y et al. (2002). Lysine methylation within the globular domain of histone H3 by Dot1 is important for telomeric silencing and Sir protein association. Genes Dev 16: 1518–1527.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nguyen CT, Weisenberger DJ, Velicescu M, Gonzales FA, Lin JC, Liang G et al. (2002). Histone H3-lysine 9 methylation is associated with aberrant gene silencing in cancer cells and is rapidly reversed by 5-aza-2′-deoxicytidine. Cancer Res 62: 6456–6461.

    CAS  PubMed  Google Scholar 

  • Okada Y, Feng Q, Lin Y, Jiang Q, Li Y, Coffield VM et al. (2005). hDOT1L links histone methylation to leukemogenesis. Cell 121: 167–178.

    Article  CAS  PubMed  Google Scholar 

  • Oki Y, Aoki E, Issa JP . (2007). Decitabine—bedside to bench. Crit Rev Oncol Hematol 61: 140–152.

    Article  PubMed  Google Scholar 

  • Paz MF, Fraga MF, Avila S, Guo M, Pollan M, Herman JG et al. (2003). A systematic profile of DNA methylation in human cancer cell lines. Cancer Res 63: 1114–1121.

    CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Simon JA, Lange CA . (2008). Roles of the EZH2 histone methyltransferase in cancer epigenetics. Mutat Res 647: 21–29.

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Turner BM . (2002). Cellular memory and the histone code. Cell 111: 285–291.

    Article  CAS  PubMed  Google Scholar 

  • van Leeuwen F, Gafken PR, Gottschling DE . (2002). Dot1p modulates silencing in yeast by methylation of the nucleosome core. Cell 109: 745–756.

    Article  CAS  PubMed  Google Scholar 

  • Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S et al. (2008). Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet 40: 897–903.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wysocka J, Swigut T, Milne TA, Dou Y, Zhang X, Burlingame AL et al. (2005). WDR5 associates with histone H3 methylated at K4 and is essential for H3 K4 methylation and vertebrate development. Cell 121: 859–872.

    Article  CAS  PubMed  Google Scholar 

  • Yoo CB, Jones PA . (2006). Epigenetic therapy of cancer: past, present and future. Nat Rev Drug Discov 5: 37–50.

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank Dr Yi Zhang for providing us with the hDOT1L expression vector for the transfection experiments. Supported by the European Union Grants FP7 CANCERDIP (HEALTH-F2-2007-200620) and SMARTER (LSHG-CT-2006-037415), the Health (FIS PI08 1345) and Education and Science (I+D+I MCYT08-03 and Consolider MEC09-05) Departments of the Spanish Government, the Health Department of the Catalan Government and the Spanish Association Against Cancer (AECC). FVJ is funded by FCT (Portuguese Foundation for Science and Technology) SFRH/BD/11757/2003. ME is an ICREA (Institució Catalana de Recerca i Estudis Avançats) Research Professor.

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Authors and Affiliations

  1. Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain

    F V Jacinto, E Ballestar & M Esteller

  2. Graduate Program in Areas of Basic and Applied Biology, University of Porto, Porto, Portugal

    F V Jacinto

  3. Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain

    M Esteller

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  1. F V Jacinto
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Correspondence to M Esteller.

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Supplementary Information accompanies the paper on the Oncogene website (http://www.nature.com/onc)

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Jacinto, F., Ballestar, E. & Esteller, M. Impaired recruitment of the histone methyltransferase DOT1L contributes to the incomplete reactivation of tumor suppressor genes upon DNA demethylation. Oncogene 28, 4212–4224 (2009). https://doi.org/10.1038/onc.2009.267

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