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Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger

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Abstract

Histone H3 lysine 4 methylation (H3K4me) has been proposed as a critical component in regulating gene expression, epigenetic states, and cellular identities1. The biological meaning of H3K4me is interpreted by conserved modules including plant homeodomain (PHD) fingers that recognize varied H3K4me states1,2. The dysregulation of PHD fingers has been implicated in several human diseases, including cancers and immune or neurological disorders3. Here we report that fusing an H3K4-trimethylation (H3K4me3)-binding PHD finger, such as the carboxy-terminal PHD finger of PHF23 or JARID1A (also known as KDM5A or RBBP2), to a common fusion partner nucleoporin-98 (NUP98) as identified in human leukaemias4,5, generated potent oncoproteins that arrested haematopoietic differentiation and induced acute myeloid leukaemia in murine models. In these processes, a PHD finger that specifically recognizes H3K4me3/2 marks was essential for leukaemogenesis. Mutations in PHD fingers that abrogated H3K4me3 binding also abolished leukaemic transformation. NUP98–PHD fusion prevented the differentiation-associated removal of H3K4me3 at many loci encoding lineage-specific transcription factors (Hox(s), Gata3, Meis1, Eya1 and Pbx1), and enforced their active gene transcription in murine haematopoietic stem/progenitor cells. Mechanistically, NUP98–PHD fusions act as ‘chromatin boundary factors’, dominating over polycomb-mediated gene silencing to ‘lock’ developmentally critical loci into an active chromatin state (H3K4me3 with induced histone acetylation), a state that defined leukaemia stem cells. Collectively, our studies represent, to our knowledge, the first report that deregulation of the PHD finger, an ‘effector’ of specific histone modification, perturbs the epigenetic dynamics on developmentally critical loci, catastrophizes cellular fate decision-making, and even causes oncogenesis during mammalian development.

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Figure 1: The PHD finger-containing NUP98–JARID1A fusion isoform (NJL), but not that lacking the PHD finger (NJS), confers leukaemogenic potentials to haematopoietic stem/progenitor cells.
Figure 2: JARID1A-PHD3, an essential motif for NJL-mediated leukaemia, specifically recognizes H3K4me3/2 marks.
Figure 3: NUP98–JARID1A enforced high H3K4me3 and active transcription associated with developmentally critical loci such as Hox.
Figure 4: The H3K4me3/2 engagement by NUP98–JARID1A perturbs the epigenetic state of developmentally critical loci during haematopoiesis.

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Accession codes

Primary accessions

Protein Data Bank

Data deposits

The structural coordinates of JARID1A-PHD3 in the H3-bound or free state have been submitted to the Protein Data Bank under accessions 3GL6, 2KGG and 2KGI, and the chemical shift assignment of NMR structures to BioMagResBank under accessions 16209 and 16210.

Change history

  • 11 June 2009

    In Fig. 1e, the x-axis label was changed from 'Cd115 (c-Kit)' to 'Cd117 (c-Kit)'.

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Acknowledgements

We thank L. Baker, P. Chi, A. Ruthenberg and A. Xiao for critical reading and help in manuscript preparation, C. Hughes for antibodies, and other Allis laboratory members for their advice. We are extremely grateful to M. Kamps and S. Rafii for shared plasmids and expert advice. Thanks to E. Coutavas, W. Chen, E. Ezhkova and the R. Roeder laboratory for help on cell and animal work. G.G.W. is supported by a Leukemia & Lymphoma Society Fellow award and a Choh-Hao Li Memorial Fund Scholar award; H.L.D. is supported by a predoctoral Boehringer Ingelheim Foundation fellowship; This research was supported by the National Institutes of Health (NIH) grant and funds of Rockefeller University to C.D.A., funds of Abby Rockefeller Mauze Trust and the Dewitt Wallace and Maloris Foundations to D.J.P., US Department of Defense CDMRP grant to J.-L.L., and a joint Starr Foundation Cancer Consortium grant.

Author Contributions G.G.W. and C.D.A. designed the study. G.G.W. performed most of the cellular and molecular experiments, and wrote the paper; J.S. performed protein preparation, NMR structure determination and crystallization; Z.W. performed crystallographic analyses; H.L.D. and G.G.W. did the immunostaining; F.C. participated in plasmid/protein preparation; H.L. performed isothermal titration calorimetry measurement; G.G.W. and J.-L.L. performed animal studies; D.J.P. and C.D.A. supervised the structural and functional aspects of the project, respectively, and helped with manuscript preparation.

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Correspondence to C. David Allis.

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Wang, G., Song, J., Wang, Z. et al. Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger. Nature 459, 847–851 (2009). https://doi.org/10.1038/nature08036

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