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Lineage-specific functions of TET1 in the postimplantation mouse embryo

Nature Genetics volume 49, pages 10611072 (2017) | Download Citation

Abstract

The mammalian TET enzymes catalyze DNA demethylation. While they have been intensely studied as major epigenetic regulators, little is known about their physiological roles and the extent of functional redundancy following embryo implantation. Here we define non-redundant roles for TET1 at an early postimplantation stage of the mouse embryo, when its paralogs Tet2 and Tet3 are not detectably expressed. TET1 regulates numerous genes defining differentiation programs in the epiblast and extraembryonic ectoderm. In epiblast cells, TET1 demethylates gene promoters via hydroxymethylation and maintains telomere stability. Surprisingly, TET1 represses a majority of epiblast target genes independently of methylation changes, in part through regulation of the gene encoding the transcriptional repressor JMJD8. Dysregulated gene expression in the absence of TET1 causes embryonic defects, which are partially penetrant in an inbred strain but fully lethal in non-inbred mice. Collectively, our study highlights an interplay between the catalytic and non-catalytic activities of TET1 that is essential for normal development.

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Acknowledgements

We thank G. Daley and A. Yabuuchi (Harvard Medical School) for generating the Tet1 GT mouse. SMARTer RNA–seq and amplicon sequencing were performed by K. Coeck at the VIB Nucleomics Core (KU Leuven) under the expert guidance of P. Verhasselt, R. Janky, W. Van Delm and S. Derveaux. WGBS and oxWGBS were performed at Novogene, and data were analyzed by Y.S. Li. We also thank L. Vermeire and L. Umans for technical guidance in mouse embryo manipulation and protocols for WISH, and H. Zhao for help with bioinformatic analyses. We are grateful for suggestions from M. Wilkinson and C. Verfaillie in the critique of this manuscript. This work was supported by Fonds voor Wetenschappelijk Onderzoek (FWO) Research Foundation–Flanders grants G.0C56.13N and G.0632.13N, Ministerie van de Vlaamse Gemeenschap and Marie Curie Career Integration grant PCIG-GA-2012-321658 (K.P.K.), US NIH grant R35 CA210043 (A.R.) and ERC Consolidator Grant award CHAMELEON 617595 (D.L.).

Author information

Author notes

    • Rita Khoueiry
    •  & Abhishek Sohni

    These authors contributed equally to this work.

Affiliations

  1. KU Leuven Department of Development and Regeneration, Stem Cell Institute Leuven, Leuven, Belgium.

    • Rita Khoueiry
    • , Abhishek Sohni
    • , Xinlong Luo
    • , Joris Vande Velde
    • , Michela Bartoccetti
    •  & Kian Peng Koh
  2. VIB Center for Cancer Biology, Laboratory for Translational Genetics, Leuven, Belgium.

    • Bernard Thienpont
    • , Bram Boeckx
    •  & Diether Lambrechts
  3. KU Leuven Department of Human Genetics, Laboratory for Translational Genetics, Leuven, Belgium.

    • Bernard Thienpont
    • , Bram Boeckx
    •  & Diether Lambrechts
  4. VIB Center for the Biology of Disease, Leuven, Belgium.

    • An Zwijsen
  5. KU Leuven Department of Human Genetics, Leuven, Belgium.

    • An Zwijsen
  6. La Jolla Institute for Allergy and Immunology, La Jolla, California, USA.

    • Anjana Rao

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Contributions

R.K. performed all experiments involving mouse embryo dissection and manipulation, derivation of ESC lines, cell culture, cellular flux assays and amplicon sequencing analysis. A.S. performed RNA–seq analysis, Flow-FISH and luciferase reporter assays and generated TET1 and JMJD8 rescue cell lines. B.T. performed MeDIP, hMeDIP, mass spectrometry and integrative ChIP–seq with WGBS analysis. X.L. performed TET1 and ΔN-JMJD8 ChIP–qPCR and ChIP–seq analysis. J.V.V. performed dot blot analysis, ELISA and confocal microscopy. M.B. contributed X-gal staining of embryos and assisted in derivation of ESC lines. B.B. contributed IPA analysis. A.Z. contributed expertise on mouse dissection and WISH assays. A.R. contributed the Tet1 GT mouse strain. D.L. provided next-generation sequencing expertise and support. R.K. and A.S. wrote the methods and prepared all figures. K.P.K. conceived the study, directed the research and wrote the manuscript with assistance from all co-authors.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Kian Peng Koh.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–11 and Supplementary Note.

Excel files

  1. 1.

    Supplementary Table 1

    Differential expression analysis of epiblast (Epi) samples by DESeq2.

  2. 2.

    Supplementary Table 2

    RPKM values of gene expression in all Epi and ExE samples.

  3. 3.

    Supplementary Table 3

    Differential expression analysis of ExE samples by DESeq2.

  4. 4.

    Supplementary Table 4

    List of differentially expressed genes in Tet1 KO ExE involved in mitochondrial oxidative phosphorylation.

  5. 5.

    Supplementary Table 5

    Differentially methylated regions in Tet1 KO EpiLC12 versus wt EpiLC15.

  6. 6.

    Supplementary Table 6

    Differential expression analysis of EpiLC samples by DESeq2.

  7. 7.

    Supplementary Table 7

    RPKM values of gene expression in all EpiLC samples.

  8. 8.

    Supplementary Table 8

    List of primers.

Text files

  1. 1.

    Supplementary Data 1

    BED file of WGBS DMRs with gain of methylation in EpiLC KO12 compared to EpiLC wt15.

  2. 2.

    Supplementary Data 2

    BED file of WGBS DMRs with loss of methylation in EpiLC KO12 compared to EpiLC wt15.

  3. 3.

    Supplementary Data 3

    BED file of oxWGBS DMRs with gain of methylation in EpiLC KO12 compared to EpiLC wt15.

  4. 4.

    Supplementary Data 4

    BED file of oxWGBS DMRs with loss of methylation in EpiLC KO12 compared to EpiLC wt15.

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https://doi.org/10.1038/ng.3868

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