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Histone arginine methylation keeps RUNX1 target genes in an intermediate state

Oncogene volume 32, pages 2565–2575 (2013)Cite this article

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Abstract

The coordinated recruitment of epigenetic regulators of gene expression by transcription factors such as RUNX1 (AML1, acute myeloid leukemia 1) is crucial for hematopoietic differentiation. Here, we identify protein arginine methyltransferase 6 (PRMT6) as a central functional component of a RUNX1 corepressor complex containing Sin3a and HDAC1 in human hematopoietic progenitor cells. PRMT6 is recruited by RUNX1 and mediates asymmetric histone H3 arginine-2 dimethylation (H3R2me2a) at megakaryocytic genes in progenitor cells. H3R2me2a keeps RUNX1 target genes in an intermediate state with concomitant H3K27me3 and H3K4me2 but not H3K4me3. Upon megakaryocytic differentiation PRMT6 binding is lost, the H3R2me2a mark decreases and a coactivator complex containing WDR5/MLL and p300/pCAF is recruited. This leads to an increase of H3K4me3 and H3K9ac, which result in augmented gene expression. Our results provide novel mechanistic insight into how RUNX1 activity in hematopoietic progenitor cells maintains differentiation genes in a suppressed state but poised for rapid transcriptional activation.

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References

  1. Orkin SH, Zon LI . Hematopoiesis: an evolving paradigm for stem cell biology. Cell 2008; 132: 631–644.

    Article  CAS  Google Scholar 

  2. Surani MA, Hayashi K, Hajkova P . Genetic and epigenetic regulators of pluripotency. Cell 2007; 128: 747–762.

    Article  CAS  Google Scholar 

  3. de Laat W, Klous P, Kooren J, Noordermeer D, Palstra RJ, Simonis M et al. Three-dimensional organization of gene expression in erythroid cells. Curr Topics Dev Biol 2008; 82: 117–139.

    Article  CAS  Google Scholar 

  4. Spivakov M, Fisher AG . Epigenetic signatures of stem-cell identity. Nat Rev 2007; 8: 263–271.

    Article  CAS  Google Scholar 

  5. Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 2006; 125: 315–326.

    Article  CAS  Google Scholar 

  6. Cui K, Zang C, Roh TY, Schones DE, Childs RW, Peng W et al. Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation. Cell stem cell 2009; 4: 80–93.

    Article  CAS  Google Scholar 

  7. Oguro H, Yuan J, Ichikawa H, Ikawa T, Yamazaki S, Kawamoto H et al. Poised lineage specification in multipotential hematopoietic stem and progenitor cells by the polycomb protein Bmi1. Cell stem cell 2010; 6: 279–286.

    Article  CAS  Google Scholar 

  8. Kirmizis A, Bartley SM, Kuzmichev A, Margueron R, Reinberg D, Green R et al. Silencing of human polycomb target genes is associated with methylation of histone H3 Lys 27. Genes Dev 2004; 18: 1592–1605.

    Article  CAS  Google Scholar 

  9. Azuara V, Perry P, Sauer S, Spivakov M, Jorgensen HF, John RM et al. Chromatin signatures of pluripotent cell lines. Nat Cell Biol 2006; 8: 532–538.

    Article  CAS  Google Scholar 

  10. Orford K, Kharchenko P, Lai W, Dao MC, Worhunsky DJ, Ferro A et al. Differential H3K4 methylation identifies developmentally poised hematopoietic genes. Dev Cell 2008; 14: 798–809.

    Article  CAS  Google Scholar 

  11. Okuda T, van Deursen J, Hiebert SW, Grosveld G, JR Downing . AML1 the target of multiple chromosomal translocations in human leukemia, is essential for normal fetal liver hematopoiesis. Cell 1996; 84: 321–330.

    Article  CAS  Google Scholar 

  12. Wang Q, Stacy T, Binder M, Marin-Padilla M, Sharpe AH, Speck NA . Disruption of the Cbfa2 gene causes necrosis and hemorrhaging in the central nervous system and blocks definitive hematopoiesis. Proc Natl Acad SciUSA 1996; 93: 3444–3449.

    Article  CAS  Google Scholar 

  13. Harada Y, Harada H . Molecular pathways mediating MDS/AML with focus on AML1/RUNX1 point mutations. J Cell Physiol 2009; 220: 16–20.

    Article  CAS  Google Scholar 

  14. Miyoshi H, Shimizu K, Kozu T, Maseki N, Kaneko Y, Ohki M . t(8;21) breakpoints on chromosome 21 in acute myeloid leukemia are clustered within a limited region of a single gene, AML1. Proc Natl Acad Sci USA 1991; 88: 10431–10434.

    Article  CAS  Google Scholar 

  15. Growney JD, Shigematsu H, Li Z, Lee BH, Adelsperger J, Rowan R et al. Loss of Runx1 perturbs adult hematopoiesis and is associated with a myeloproliferative phenotype. Blood 2005; 106: 494–504.

    Article  CAS  Google Scholar 

  16. Ichikawa M, Asai T, Saito T, Seo S, Yamazaki I, Yamagata T et al. AML-1 is required for megakaryocytic maturation and lymphocytic differentiation, but not for maintenance of hematopoietic stem cells in adult hematopoiesis. Nat Med 2004; 10: 299–304.

    Article  CAS  Google Scholar 

  17. Owen CJ, Toze CL, Koochin A, Forrest DL, Smith CA, Stevens JM et al. Five new pedigrees with inherited RUNX1 mutations causing familial platelet disorder with propensity to myeloid malignancy. Blood 2008; 112: 4639–4645.

    Article  CAS  Google Scholar 

  18. Song WJ, Sullivan MG, Legare RD, Hutchings S, Tan X, Kufrin D et al. Haploinsufficiency of CBFA2 causes familial thrombocytopenia with propensity to develop acute myelogenous leukaemia. Nat Genet 1999; 23: 166–175.

    Article  CAS  Google Scholar 

  19. Ben-Ami O, Pencovich N, Lotem J, Levanon D, Groner Y . A regulatory interplay between miR-27a and Runx1 during megakaryopoiesis. Proc Natl Acad Sci USA 2009; 106: 238–243.

    Article  CAS  Google Scholar 

  20. Elagib KE, Racke FK, Mogass M, Khetawat R, Delehanty LL, AN Goldfarb . RUNX1 and GATA-1 coexpression and cooperation in megakaryocytic differentiation. Blood 2003; 101: 4333–4341.

    Article  CAS  Google Scholar 

  21. Satoh Y, Matsumura I, Tanaka H, Ezoe S, Fukushima K, Tokunaga M et al. AML1/RUNX1 works as a negative regulator of c-Mpl in hematopoietic stem cells. J Biol Chem 2008; 283: 30045–30056.

    Article  CAS  Google Scholar 

  22. Pencovich N, Jaschek R, Tanay A, Groner Y . Dynamic combinatorial interactions of RUNX1 and cooperating partners regulates megakaryocytic differentiation in cell line models. Blood 2010; 117: e1–14.

    Article  Google Scholar 

  23. Zhao X, Jankovic V, Gural A, Huang G, Pardanani A, Menendez S et al. Methylation of RUNX1 by PRMT1 abrogates SIN3A binding and potentiates its transcriptional activity. Genes Dev 2008; 22: 640–653.

    Article  CAS  Google Scholar 

  24. Kitabayashi I, Yokoyama A, Shimizu K, Ohki M . Interaction and functional cooperation of the leukemia-associated factors AML1 and p300 in myeloid cell differentiation. EMBO J 1998; 17: 2994–3004.

    Article  CAS  Google Scholar 

  25. Wang L, Huang G, Zhao X, Hatlen MA, Vu L, Liu F et al. Post-translational modifications of Runx1 regulate its activity in the cell. Blood cells, molecules & diseases. Blood Cells Mol Dis 2009; 43: 30–34.

    Article  CAS  Google Scholar 

  26. Bedford MT, Clarke SG . Protein arginine methylation in mammals: who, what, and why. Mol Cell 2009; 33: 1–13.

    Article  CAS  Google Scholar 

  27. Shilatifard A . Molecular implementation and physiological roles for histone H3 lysine 4 (H3K4) methylation. Curr Opin Cell Biol 2008; 20: 341–348.

    Article  CAS  Google Scholar 

  28. Kirmizis A, Santos-Rosa H, Penkett CJ, Singer MA, Vermeulen M, Mann M et al. Arginine methylation at histone H3R2 controls deposition of H3K4 trimethylation. Nature 2007; 449: 928–932.

    Article  CAS  Google Scholar 

  29. Guccione E, Bassi C, Casadio F, Martinato F, Cesaroni M, Schuchlautz H et al. Methylation of histone H3R2 by PRMT6 and H3K4 by an MLL complex are mutually exclusive. Nature 2007; 449: 933–937.

    Article  CAS  Google Scholar 

  30. Iberg AN, Espejo A, Cheng D, Kim D, Michaud-Levesque J, Richard S et al. Arginine methylation of the histone H3 tail impedes effector binding. J Biol Chem 2008; 283: 3006–3010.

    Article  CAS  Google Scholar 

  31. Hyllus D, Stein C, Schnabel K, Schiltz E, Imhof A, Dou Y et al. PRMT6-mediated methylation of R2 in histone H3 antagonizes H3 K4 trimethylation. Genes Dev 2007; 21: 3369–3380.

    Article  CAS  Google Scholar 

  32. Xu G, Kanezaki R, Toki T, Watanabe S, Takahashi Y, Terui K et al. Physical association of the patient-specific GATA1 mutants with RUNX1 in acute megakaryoblastic leukemia accompanying Down syndrome. Leukemia 2006; 20: 1002–1008.

    Article  CAS  Google Scholar 

  33. Michaud-Levesque J, Richard S . Thrombospondin-1 is a transcriptional repression target of PRMT6. J Biol Chem 2009; 284: 21338–21346.

    Article  CAS  Google Scholar 

  34. Hoogenkamp M, Krysinska H, Ingram R, Huang G, Barlow R, Clarke D et al. The Pu.1 locus is differentially regulated at the level of chromatin structure and noncoding transcription by alternate mechanisms at distinct developmental stages of hematopoiesis. Mol Cell Biol 2007; 27: 7425–7438.

    Article  CAS  Google Scholar 

  35. Huang G, Zhang P, Hirai H, Elf S, Yan X, Chen Z et al. PU.1 is a major downstream target of AML1 (RUNX1) in adult mouse hematopoiesis. Nat Genet 2008; 40: 51–60.

    Article  CAS  Google Scholar 

  36. Wang W, Schwemmers S, Hexner EO, Pahl HL . AML1 is overexpressed in patients with myeloproliferative neoplasms and mediates JAK2V617F-independent overexpression of NF-E2. Blood 2010; 116: 254–246.

    Article  CAS  Google Scholar 

  37. Zhang X, Cheng X . Structure of the predominant protein arginine methyltransferase PRMT1 and analysis of its binding to substrate peptides. Structure 2003; 11: 509–520.

    Article  CAS  Google Scholar 

  38. Wilson NK, Calero-Nieto FJ, Ferreira R, Gottgens B . Transcriptional regulation of haematopoietic transcription factors. Stem Cell Res Ther 2011; 2: 6.

    Article  CAS  Google Scholar 

  39. Hannah R, Joshi A, Wilson NK, Kinston S, Gottgens B . A compendium of genome-wide hematopoietic transcription factor maps supports the identification of gene regulatory control mechanisms. Exp Hematol 2011; 39: 531–541.

    Article  CAS  Google Scholar 

  40. Kowenz-Leutz E, Pless O, Dittmar G, Knoblich M, Leutz A . Crosstalk between C/EBPbeta phosphorylation, arginine methylation, and SWI/SNF/Mediator implies an indexing transcription factor code. EMBO J 2010; 29: 1105–1115.

    Article  CAS  Google Scholar 

  41. Sims RJ, Reinberg D . Is there a code embedded in proteins that is based on post-translational modifications? Nat Rev Mol Cell Biol 2008; 9: 815–820.

    Article  CAS  Google Scholar 

  42. Murray-Zmijewski F, Slee EA, Lu X . A complex barcode underlies the heterogeneous response of p53 to stress. Nat Rev Mol Cell Biol 2008; 9: 702–712.

    Article  CAS  Google Scholar 

  43. O'Malley BW, Qin J, Lanz RB . Cracking the coregulator codes. Curr Opin Cell Biol 2008; 20: 310–315.

    Article  CAS  Google Scholar 

  44. Elagib KE, Goldfarb AN . Regulation of RUNX1 transcriptional function by GATA-1. Critical reviews in eukaryotic gene expression 2007; 17: 271–280.

    Article  CAS  Google Scholar 

  45. Goldfarb AN . Megakaryocytic programming by a transcriptional regulatory loop: a circle connecting RUNX1, GATA-1, and P-TEFb. J Cell Biochem 2009; 107: 377–382.

    Article  CAS  Google Scholar 

  46. Jiang H, Zhang F, Kurosu T, Peterlin BM . Runx1 binds positive transcription elongation factor b and represses transcriptional elongation by RNA polymerase II: possible mechanism of CD4 silencing. Mol Cell Biol 2005; 25: 10675–10683.

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  48. Ruthenburg AJ, Allis CD, Wysocka J . Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark. Mol Cell 2007; 25: 15–30.

    Article  CAS  Google Scholar 

  49. Yu M, Mazor T, Huang H, Huang HT, Kathrein KL, Woo AJ et al. Direct recruitment of polycomb repressive complex 1 to chromatin by core binding transcription factors. Mol Cell 2012; 45: 330–343.

    Article  CAS  Google Scholar 

  50. Lee TI, Jenner RG, Boyer LA, Guenther MG, Levine SS, Kumar RM et al. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 2006; 125: 301–313.

    Article  CAS  Google Scholar 

  51. Hammoud SS, Nix DA, Zhang H, Purwar J, Carrell DT, Cairns BR . Distinctive chromatin in human sperm packages genes for embryo development. Nature 2009; 460: 473–478.

    Article  CAS  Google Scholar 

  52. Hoogenkamp M, Lichtinger M, Krysinska H, Lancrin C, Clarke D, Williamson A et al. Early chromatin unfolding by RUNX1: a molecular explanation for differential requirements during specification versus maintenance of the hematopoietic gene expression program. Blood 2009; 114: 299–309.

    Article  CAS  Google Scholar 

  53. Balint BL, Szanto A, Madi A, Bauer UM, Gabor P, Benko S et al. Arginine methylation provides epigenetic transcription memory for retinoid-induced differentiation in myeloid cells. Mol Cell Biol 2005; 25: 5648–5663.

    Article  CAS  Google Scholar 

  54. Mahajan MC, Karmakar S, Newburger PE, Krause DS, Weissman SM . Dynamics of alpha-globin locus chromatin structure and gene expression during erythroid differentiation of human CD34(+) cells in culture. Exp Hematol 2009; 37: 1143–1156e3.

    Article  CAS  Google Scholar 

  55. Demaison C, Parsley K, Brouns G, Scherr M, Battmer K, Kinnon C et al. High-level transduction and gene expression in hematopoietic repopulating cells using a human immunodeficiency [correction of imunodeficiency] virus type 1-based lentiviral vector containing an internal spleen focus forming virus promoter. Hum Gene Ther 2002; 13: 803–813.

    Article  CAS  Google Scholar 

  56. Lausen J, Cho S, Liu S, Werner MH . The nuclear receptor co-repressor (N-CoR) utilizes repression domains I and III for interaction and co-repression with ETO. J Biol Chem 2004; 279: 49281–49288.

    Article  CAS  Google Scholar 

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Acknowledgements

We thank Reinhard Henschler of the Institute for Transfusion Medicine Frankfurt for providing hCD34+ cells. JL is supported by the LOEWE initiatives Onkogene Signaltransduktion Frankfurt (OSF), the LOEWE Center for Cell and Gene Therapy Frankfurt (CGT), Ministry of Higher Education, Research and the Arts of the state of Hessen (HMWK), III L 4-518/55.004 and III L 4-518/17004 and institutional funds of the Georg-Speyer-Haus. The Georg-Speyer-Haus is funded jointly by the German Federal Ministry of Health (BMG) and the HMWK. This project was supported by the Deutsche Forschungsgemeinschaft (SPP-1463, LA 1389/5-1).

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  1. Georg-Speyer-Haus, Institute for Biomedical Research, Frankfurt am Main, Germany

    J Herglotz, O N Kuvardina, S Kolodziej, A Kumar, H Hussong, M Grez & J Lausen

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  1. J Herglotz
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Herglotz, J., Kuvardina, O., Kolodziej, S. et al. Histone arginine methylation keeps RUNX1 target genes in an intermediate state. Oncogene 32, 2565–2575 (2013). https://doi.org/10.1038/onc.2012.274

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