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Genome-scale DNA methylation maps of pluripotent and differentiated cells

Abstract

DNA methylation is essential for normal development1,2,3 and has been implicated in many pathologies including cancer4,5. Our knowledge about the genome-wide distribution of DNA methylation, how it changes during cellular differentiation and how it relates to histone methylation and other chromatin modifications in mammals remains limited. Here we report the generation and analysis of genome-scale DNA methylation profiles at nucleotide resolution in mammalian cells. Using high-throughput reduced representation bisulphite sequencing6 and single-molecule-based sequencing, we generated DNA methylation maps covering most CpG islands, and a representative sampling of conserved non-coding elements, transposons and other genomic features, for mouse embryonic stem cells, embryonic-stem-cell-derived and primary neural cells, and eight other primary tissues. Several key findings emerge from the data. First, DNA methylation patterns are better correlated with histone methylation patterns than with the underlying genome sequence context. Second, methylation of CpGs are dynamic epigenetic marks that undergo extensive changes during cellular differentiation, particularly in regulatory regions outside of core promoters. Third, analysis of embryonic-stem-cell-derived and primary cells reveals that ‘weak’ CpG islands associated with a specific set of developmentally regulated genes undergo aberrant hypermethylation during extended proliferation in vitro, in a pattern reminiscent of that reported in some primary tumours. More generally, the results establish reduced representation bisulphite sequencing as a powerful technology for epigenetic profiling of cell populations relevant to developmental biology, cancer and regenerative medicine.

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Figure 1: CpG methylation levels in ES cells and NPCs for CpGs with ≥10-fold coverage.
Figure 2: Correlation between DNA and histone methylation.
Figure 3: Developmentally regulated de-methylation of highly conserved non-coding elements.
Figure 4: HCP hypermethylation of cultured cells.

Accession codes

Primary accessions

Gene Expression Omnibus

Data deposits

All primary sequencing data have been submitted to the NCBI GEO repository under accession numbers GSE11034 (RRBS), GSE11172 (ChIP-Seq) and GSE11483 (gene expression microarrays).

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Acknowledgements

We thank the staff of the Broad Institute Genome Sequencing Platform for assistance with data generation and B. Ramsahoye for the nearest neighbour analysis. This research was supported by funds from the National Human Genome Research Institute, the National Cancer Institute, and the Broad Institute of MIT and Harvard.

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Correspondence to Rudolf Jaenisch or Eric S. Lander.

Supplementary information

Supplementary Information 1

This file contains Supplementary Tables S1-S7 and Supplementary Figures S1-S9 with Legends. (PDF 11442 kb)

Supplementary Information 2

The file contains Supplementary Data S1. DNA and histone methylation states, and associated expression levels, for all analyzed high-CpG density promoters. (XLS 5606 kb)

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Meissner, A., Mikkelsen, T., Gu, H. et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454, 766–770 (2008). https://doi.org/10.1038/nature07107

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