A methylation-phosphorylation switch controls EZH2 stability and hematopoiesis

  1. Pengfei Guo
  2. Rebecca C Lim
  3. Keshari Rajawasam
  4. Tiffany Trinh
  5. Hong Sun
  6. Hui Zhang

  • Curated by eLife

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    eLife assessment

    This is a fundamental study describing a novel methylation event on EZH2 that regulates EZH2 protein stability and hematopoiesis. The methodologies are sound and the conclusions are largely supported by solid data. The work will be of interest to biomedical researchers in the field of cancer epigenetics.

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Abstract

The Polycomb Repressive Complex 2 (PRC2) methylates H3K27 to regulate development and cell fate by transcriptional silencing. Alteration of PRC2 is associated with various cancers. Here, we show that mouse Kdm1a deletion causes a dramatic reduction of PRC2 proteins, whereas mouse null mutation of L3mbtl3 or Dcaf5 results in PRC2 accumulation and increased H3K27 trimethylation. The catalytic subunit of PRC2, EZH2, is methylated at lysine 20 (K20), promoting EZH2 proteolysis by L3MBTL3 and the CLR4 DCAF5 ubiquitin ligase. KDM1A (LSD1) demethylates the methylated K20 to stabilize EZH2. K20 methylation is inhibited by AKT-mediated phosphorylation of serine 21 in EZH2. Mouse Ezh2 K20R/K20R mutants develop hepatosplenomegaly associated with high GFI1B expression, and Ezh2 K20R/K20R mutant bone marrows expand hematopoietic stem cells and downstream hematopoietic populations. Our studies reveal that EZH2 is regulated by methylation-dependent proteolysis, which is negatively controlled by AKT-mediated S21 phosphorylation to establish a methylation-phosphorylation switch to regulate the PRC2 activity and hematopoiesis.

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  1. Version published to 10.7554/elife.86168 on eLife
  2. eLife

    eLife assessment

    This is a fundamental study describing a novel methylation event on EZH2 that regulates EZH2 protein stability and hematopoiesis. The methodologies are sound and the conclusions are largely supported by solid data. The work will be of interest to biomedical researchers in the field of cancer epigenetics.

  3. eLife

    Reviewer #1 (Public Review):

    This study shows that SET7 and LSD1 regulate the dynamic methylation of EZH2 at K20, which is recognized by L3MBTL3 promoting protein degradation via the DCAF5-CRL4 E3 ubiquitin ligase. K20 methylation negatively regulates S21 phosphorylation and vice versa, modulating EZH2 functions. Mice harboring the K20 methylation-deficient mutant (K20R) exhibit hematopoietic defects. Overall, this is an interesting study elucidating a novel mechanism of EZH2 regulation. The methodologies are sound and the conclusions are largely supported by the data provided. However, there are some questions regarding the overall model and some contradictory results.

  4. eLife

    Reviewer #2 (Public Review):

    EZH2 is upregulated in most advanced cancers and has been investigated as a therapeutic target for many years. However, how EZH2 activity is regulated remains to be fully elucidated. In this study, Guo et al. provided a new mechanism for the regulation of EZH2. The authors demonstrated that the protein stability of EZH2 is dynamically regulated by lysine methylation-dependent proteolysis. Specifically, K20 of EZH2 is monomethylated by SET7 methyltransferase and demethylated by LSD1 demethylase. The methylated K20 is recognized by specific methyl-lysine reader L3MBTL3 to promote EZH2 for ubiquitin-dependent proteolysis by the CRL4DCAF5 ubiquitin E3 ligase complex, resulting in the dysregulation of EZH2/PRC2 activity and reduction of H3K27me3. The authors further found a methylation-phosphorylation switch existed in some cancer cells and this switch controls EZH2 stability and hematopoiesis.

    Overall, most conclusions of this paper are well-supported by the results presented, only some aspects of Figure 6 need to be extended. This work is of interest to biomedical researchers in the field of cancer epigenetics after minor revision.

  5. eLife

    Reviewer #3 (Public Review):

    In this study, the authors demonstrated a new mechanism by which the protein stability of EZH2 is regulated. This mechanism is multifaceted and yet the authors provided evidence for every step of regulation. EZH2 is monomethylated at K20 by SET7, which can be removed by LSD1 and recognized by L3MBTL3. L3MBTL3 recruits the ubiquitin E3 ligase CRLDCAF5 to EZH2 via methylation of K20, which results in polyubiquitylation and proteasomal degradation of the histone methyltransferase. Additionally, they found that AKT-mediated phosphorylation of EZH2 at S21 blocks monomethylation at K20 and vice versa. Finally, they demonstrated in the K20R GEMM model that stabilization of EZH2 protein leads to reactive hyperplasia and hematopoiesis. In general, this study reveals an interesting and novel mechanism underlying the regulation of the epigenetic mark H3K27me3 and the oncogenic function of EZH2. The authors have considered every aspect of the signaling pathway that regulates the protein stability of EZH2. The data was comprehensive, rigorous, and supportive of the conclusions they made. Their results may help explain some of the conflicting results that previous studies have reported.

    However, there are still some issues with the significance of the work and the quality of the data. The major issues are:
    1. The converged effect of EZH2 methylation and phosphorylation on H3K27me3 is unclear.
    2. How the methylation-phosphorylation switch of EZH2 determines the biological phenotypes they observed is not addressed.
    3. Some of the data in the manuscript is conflicting.

  6. Version published to 10.1101/2023.02.02.526767v1 on bioRxiv