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Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues

Abstract

DNA methylation has been comprehensively profiled in normal and cancer cells, but the dynamics that form, maintain and reprogram differentially methylated regions remain enigmatic. Here, we show that methylation patterns within populations of cells from individual somatic tissues are heterogeneous and polymorphic. Using in vitro evolution of immortalized fibroblasts for over 300 generations, we track the dynamics of polymorphic methylation at regions developing significant differential methylation on average. The data indicate that changes in population-averaged methylation occur through a stochastic process that generates a stream of local and uncorrelated methylation aberrations. Despite the stochastic nature of the process, nearly deterministic epigenetic remodeling emerges on average at loci that lose or gain resistance to methylation accumulation. Changes in the susceptibility to methylation accumulation are correlated with changes in histone modification and CTCF occupancy. Characterizing epigenomic polymorphism within cell populations is therefore critical to understanding methylation dynamics in normal and cancer cells.

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Figure 1: Epipolymorphism.
Figure 2: Differentially methylated loci are epipolymorphic.
Figure 3: Extensive average differential methylation during fibroblast evolution in vitro.
Figure 4: Hypermethylation is a parallel, stochastic and gradual evolutionary process.
Figure 5: Spatial constraints canalize hypermethylation patterns.
Figure 6: H3K4me3, CTCF binding and H3K27me3 are anticorrelated with DNA methylation kinetics.

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Acknowledgements

We thank the members of the Tanay group for discussions. Research in the Tanay laboratory was supported by grants from the Israel Science Foundation (grant 1372/08), the European Commission Framework Programme 7 Network of Excellence EPIGENESYS and the BLUEPRINT European Union consortium. Research in the Rotter laboratory was supported by a Center of Excellence grant from the Flight Attendant Medical Research Institute (FAMRI). E.N.G.-Y. is a fellow of the Talpiot Medical Leadership Program at the Sheba Medical Center.

Author information

Authors and Affiliations

Authors

Contributions

G.L., E.N.G.-Y., V.R. and A.T. designed the experiments. G.L. and Z.M. performed bisulfite and immunoprecipitation experiments with help from E.N.G.-Y. and A.Z. G.L., N.M.C., A.B. and A.T. analyzed the data. G.L. extracted RNA and conducted tissue culture with help from A.M., R.B. and N.G. S.H.-S. and D.A.Z. performed high-throughput sequencing and assisted with protocol adaptations. G.L. and A.T. wrote the manuscript.

Corresponding author

Correspondence to Amos Tanay.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–20 and Supplementary Note (PDF 6604 kb)

Supplementary Table 1

Names of samples analyzed in this study, as well statistics on the number of mapped reads and the number of adequately covered 4-mers. (XLS 29 kb)

Supplementary Table 2

Names of amplicons assayed using Deep-BIS, as well as statistics on the length and genomic coordinates of primers, genomic sequence, amplicon length, number of CpGs, CpG content, and behavior in the MeDIP-seq data. (XLS 50 kb)

Supplementary Table 3

Names of amplicons assayed using ChIP-Deep-BIS, as well as statistics on the length and genomic coordinates of primers, genomic sequence, amplicon length, number of CpGs, CpG content, and amplicon class, indicating whether regions are imprinted, repeat sequences, or reside on chromosome X. The length of the original amplicon is indicated for those amplicons that represent approximately half of a larger amplicon, designed by introducing internal primers in order to generate smaller amplicons more likely to amplify sonicated material. (XLS 42 kb)

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Landan, G., Cohen, N., Mukamel, Z. et al. Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues. Nat Genet 44, 1207–1214 (2012). https://doi.org/10.1038/ng.2442

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