Dynamic and heterogeneous DNA methylation in pluripotent cells — ASN Events
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  2. Poster Session 1
  3. Dynamic and heterogeneous DNA methylation in pluripotent cells

Dynamic and heterogeneous DNA methylation in pluripotent cells (#125)

Heather J Lee 1 2 , Steffen Rulands 3 4 5 6 , Stephen J Clark 1 , Christof Angermueller 7 , Sebastien A Smallwood 1 8 , Felix Krueger 9 , Gavin Kelsey 1 , Oliver Stegle 7 , Benjamin D Simons 3 4 5 , Wolf Reik 1 2 6 10
  1. Epigenetics Programme, Babraham Institute, Cambridge, UK
  2. Sanger Institute, Cambridge, UK
  3. Cavendish Laboratory, University of Cambridge, Cambridge, UK
  4. Gurdon Institute, University of Cambridge, Cambridge, UK
  5. Stem Cell Institute, University of Cambridge, Cambridge, UK
  6. Department of Physiology, University of Cambridge, Cambridge, UK
  7. European Bioinformatics Institute, European Molecular Biology Laboratory, Cambridge, UK
  8. Fredrich Miescher Institute for Biomedical Research, Basel, Switzerland
  9. Bioinformatics Group, Babraham Institute, Cambridge, UK
  10. Centre for Trophoblast Research, University of Cambridge, Cambridge, UK

Pluripotent mouse embryonic stem cells (ESCs) display dynamic heterogeneity characterised by stochastic switching between discrete transcriptional states. Using single-cell bisulphite sequencing (scBS-seq)1, we have recently demonstrated that DNA methylation is also heterogeneous in ESCs. Furthermore, we have observed dynamic regulation of this epigenetic mark using Nanog-GFP ESCs. To further investigate the dynamic relationship between transcriptional and epigenetic heterogeneity in ESCs, we employed scBS-seq and parallel single-cell methylome and transcriptome sequencing (scM&T-seq)2. Variance in DNA methylation is specifically increased at enhancers in primed ESCs, suggesting that epigenetic dynamics at distal regulatory elements may contribute to transcriptional heterogeneity in these cells. DNA methylation heterogeneity at enhancers is manifest as a continuous spectrum, rather discrete states, and is restricted to the 'more pluripotent' transcriptional state within primed ESCs, demonstrating a qualitative difference between transcriptional and epigenetic heterogeneity. We previously postulated that DNA methylation heterogeneity could be generated by rapid turnover of cytosine modifications when Dnmt3 and Tet enzymes are co-expressed3. Accordingly, DNA methylation heterogeneity at enhancers was not observed in naïve ESCs or in differentiating embryoid bodies that lack co-expression of these enzymes. Furthermore, depletion of either Dnmt3 or Tet enzymes in primed ESCs abolished DNA methylation heterogeneity at enhancers. Using biophysical modelling we argue that the non-linear action of Dnmt3 and Tet enzymes may generate oscillatory dynamics in DNA methylation. Consistently, we observe coordinated oscillations in DNA methylation at enhancers during the transition from naïve to primed pluripotency in vitro. Analysis of scM&T-seq data from E5.5 mouse epiblast suggests that DNA methylation may also oscillate in vivo. This represents an unprecedented level of dynamic epigenetic regulation during development.

  1. Smallwood, Lee, et al. (2014) Nat Methods 11:817-20.
  2. Angermueller, Clark, Lee, Macaulay, et al. (2016) Nat Methods 13:229-32.
  3. Lee, Hore, et al. (2014) Cell Stem Cell 14:710-9.
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