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FBXL10 protects Polycomb-bound genes from hypermethylation

Nature Genetics volume 47, pages 479–485 (2015)Cite this article

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Abstract

Nearly all CpG-dense promoters are occupied by the multidomain chromosomal protein FBXL10. We show here that complete inactivation of the Fbxl10 gene leads to dense de novo methylation only of promoters that are co-occupied by both FBXL10 and Polycomb repressive complexes; this methylation results in pervasive defects in embryonic development and the death of homozygous Fbxl10-mutant embryos at midgestation. Deletion of key components of Polycomb repressive complexes 1 and 2 did not lead to ectopic genomic methylation. These results indicate that FBXL10 protects Polycomb-occupied promoters against ectopic de novo methylation. To our knowledge, FBXL10 is the first reported factor whose loss leads to a gain in genomic DNA methylation.

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Figure 1: Structure and domain organization of the FBXL10 gene and protein, and characterization of the gene-trap truncation allele.
Figure 2: Retention of ES cell characteristics and pluripotency of Fbxl10T/T ES cells.
Figure 3: DNA hypermethylation in Fbxl10T/T ES cells.
Figure 4: Effect of the de novo methylation induced by ablation of FBXL10 on gene expression.
Figure 5: Rescue of methylation and transcriptional phenotypes by restoration of FBXL10-2 expression.
Figure 6: Chromatin context of DNA sequences prone to hypermethylation in Fbxl10T/T ES cells.
Figure 7: Effect of removal of FBXL10 on RING1B distribution and lack of de novo methylation after genetic ablation of core components of PRC1 and PRC2.

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Acknowledgements

We thank I. Okamoto, R. Margueron and E. Heard (Institut Curie) for Ezh2−/− mutant ES cells, L. Di Croce (Centre for Genomic Regulation (CRG) and Pompeu Fabra University (UPF)) for DNA from Eed−/− and Ring1b−/− ES cells, K. Anderson and O. Yarychkivska for comments on the manuscript and V. Bardwell (University of Minnesota, Minneapolis) for her gift of antiserum to FBXL10. This study was supported by grants from the US National Institutes of Health to J.R.E. and T.H.B. and by a grant from the US Department of Defense to J.R.E. M.B. was supported in part by the Phillippe Foundation.

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Authors and Affiliations

  1. Department of Genetics and Development, College of Physicians and Surgeons of Columbia University, New York, New York, USA

    Mathieu Boulard & Timothy H Bestor

  2. Department of Medicine, Center for Pharmacogenomics, Washington University School of Medicine, St. Louis, Missouri, USA

    John R Edwards

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  1. Mathieu Boulard
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M.B., J.R.E. and T.H.B. designed the study, analyzed the data and wrote the manuscript. M.B. performed the experiments. J.R.E. analyzed RRBS, ChIP-seq and RNA-seq data.

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Correspondence to Timothy H Bestor.

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Boulard, M., Edwards, J. & Bestor, T. FBXL10 protects Polycomb-bound genes from hypermethylation. Nat Genet 47, 479–485 (2015). https://doi.org/10.1038/ng.3272

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