KDM6B interacts with TFDP1 to activate P53 signalling in regulating mouse palatogenesis

Abstract

Epigenetic regulation plays extensive roles in diseases and development. Disruption of epigenetic regulation not only increases the risk of cancer, but can also cause various developmental defects. However, the question of how epigenetic changes lead to tissue-specific responses during neural crest fate determination and differentiation remains understudied. Using palatogenesis as a model, we reveal the functional significance of Kdm6b, a H3K27me3 demethylase, in regulating mouse embryonic development. Our study shows that Kdm6b plays an essential role in cranial neural crest development, and loss of Kdm6b disturbs P53 pathway-mediated activity, leading to complete cleft palate along with cell proliferation and differentiation defects in mice. Furthermore, activity of H3K27me3 on the promoter of Trp53 is antagonistically controlled by Kdm6b, and Ezh2 in cranial neural crest cells. More importantly, without Kdm6b, the transcription factor TFDP1, which normally binds to the promoter of Trp53, cannot activate Trp53 expression in palatal mesenchymal cells. Furthermore, the function of Kdm6b in activating Trp53 in these cells cannot be compensated for by the closely related histone demethylase Kdm6a. Collectively, our results highlight the important role of the epigenetic regulator KDM6B and how it specifically interacts with TFDP1 to achieve its functional specificity in regulating Trp53 expression, and further provide mechanistic insights into the epigenetic regulatory network during organogenesis.

Data availability

Sequencing data have been deposited in GEO under accession code GSE175383.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Tingwei Guo

    Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
    Competing interests
    No competing interests declared.
  2. Xia Han

    Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
    Competing interests
    No competing interests declared.
  3. Jinzhi He

    Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
    Competing interests
    No competing interests declared.
  4. Jifan Feng

    Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9944-2604
  5. Junjun Jing

    Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5745-5207
  6. Eva Janečková

    Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
    Competing interests
    No competing interests declared.
  7. Jie Lei

    Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
    Competing interests
    No competing interests declared.
  8. Thach-Vu Ho

    Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6293-4739
  9. Jian Xu

    Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
    Competing interests
    Jian Xu, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8162-889X
  10. Yang Chai

    Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
    For correspondence
    ychai@usc.edu
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2477-7247

Funding

National Institutes of Health (R01 DE012711)

  • Yang Chai

National Institutes of Health (R01 DE022503)

  • Yang Chai

National Institutes of Health (U01 DE028729)

  • Yang Chai

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Marianne E Bronner, California Institute of Technology, United States

Ethics

Animal experimentation: All mouse studies were conducted with protocols approved by the Department of Animal Resources and the Institutional Animal Care and Use Committee (IACUC) of the University of Southern California (Protocols 9320 and 20299).

Version history

  1. Received: October 9, 2021
  2. Preprint posted: October 14, 2021 (view preprint)
  3. Accepted: February 24, 2022
  4. Accepted Manuscript published: February 25, 2022 (version 1)
  5. Version of Record published: April 13, 2022 (version 2)

Copyright

© 2022, Guo et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 1,826
    views
  • 294
    downloads
  • 9
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Tingwei Guo
  2. Xia Han
  3. Jinzhi He
  4. Jifan Feng
  5. Junjun Jing
  6. Eva Janečková
  7. Jie Lei
  8. Thach-Vu Ho
  9. Jian Xu
  10. Yang Chai
(2022)
KDM6B interacts with TFDP1 to activate P53 signalling in regulating mouse palatogenesis
eLife 11:e74595.
https://doi.org/10.7554/eLife.74595

Share this article

https://doi.org/10.7554/eLife.74595

Further reading

    1. Developmental Biology
    Amandine Jarysta, Abigail LD Tadenev ... Basile Tarchini
    Research Article

    Inhibitory G alpha (GNAI or Gαi) proteins are critical for the polarized morphogenesis of sensory hair cells and for hearing. The extent and nature of their actual contributions remains unclear, however, as previous studies did not investigate all GNAI proteins and included non-physiological approaches. Pertussis toxin can downregulate functionally redundant GNAI1, GNAI2, GNAI3, and GNAO proteins, but may also induce unrelated defects. Here, we directly and systematically determine the role(s) of each individual GNAI protein in mouse auditory hair cells. GNAI2 and GNAI3 are similarly polarized at the hair cell apex with their binding partner G protein signaling modulator 2 (GPSM2), whereas GNAI1 and GNAO are not detected. In Gnai3 mutants, GNAI2 progressively fails to fully occupy the sub-cellular compartments where GNAI3 is missing. In contrast, GNAI3 can fully compensate for the loss of GNAI2 and is essential for hair bundle morphogenesis and auditory function. Simultaneous inactivation of Gnai2 and Gnai3 recapitulates for the first time two distinct types of defects only observed so far with pertussis toxin: (1) a delay or failure of the basal body to migrate off-center in prospective hair cells, and (2) a reversal in the orientation of some hair cell types. We conclude that GNAI proteins are critical for hair cells to break planar symmetry and to orient properly before GNAI2/3 regulate hair bundle morphogenesis with GPSM2.

    1. Computational and Systems Biology
    2. Developmental Biology
    Gang Xue, Xiaoyi Zhang ... Zhiyuan Li
    Research Article

    Organisms utilize gene regulatory networks (GRN) to make fate decisions, but the regulatory mechanisms of transcription factors (TF) in GRNs are exceedingly intricate. A longstanding question in this field is how these tangled interactions synergistically contribute to decision-making procedures. To comprehensively understand the role of regulatory logic in cell fate decisions, we constructed a logic-incorporated GRN model and examined its behavior under two distinct driving forces (noise-driven and signal-driven). Under the noise-driven mode, we distilled the relationship among fate bias, regulatory logic, and noise profile. Under the signal-driven mode, we bridged regulatory logic and progression-accuracy trade-off, and uncovered distinctive trajectories of reprogramming influenced by logic motifs. In differentiation, we characterized a special logic-dependent priming stage by the solution landscape. Finally, we applied our findings to decipher three biological instances: hematopoiesis, embryogenesis, and trans-differentiation. Orthogonal to the classical analysis of expression profile, we harnessed noise patterns to construct the GRN corresponding to fate transition. Our work presents a generalizable framework for top-down fate-decision studies and a practical approach to the taxonomy of cell fate decisions.