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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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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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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Integrated supplementary information
Supplementary Figure 2 The chromatin context for the minority of sequences that escape de novo methylation in homozygous ES cells is not notably different compared to those sequences that are methylated.
Errors in ChIP-seq data or other factors may be involved.
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Supplementary Figures 1 and 2, and Supplementary Table 1. (PDF 136 kb)
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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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DOI: https://doi.org/10.1038/ng.3272
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