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DNA-binding factors shape the mouse methylome at distal regulatory regions

A Corrigendum to this article was published on 25 April 2012

This article has been updated

Abstract

Methylation of cytosines is an essential epigenetic modification in mammalian genomes, yet the rules that govern methylation patterns remain largely elusive. To gain insights into this process, we generated base-pair-resolution mouse methylomes in stem cells and neuronal progenitors. Advanced quantitative analysis identified low-methylated regions (LMRs) with an average methylation of 30%. These represent CpG-poor distal regulatory regions as evidenced by location, DNase I hypersensitivity, presence of enhancer chromatin marks and enhancer activity in reporter assays. LMRs are occupied by DNA-binding factors and their binding is necessary and sufficient to create LMRs. A comparison of neuronal and stem-cell methylomes confirms this dependency, as cell-type-specific LMRs are occupied by cell-type-specific transcription factors. This study provides methylome references for the mouse and shows that DNA-binding factors locally influence DNA methylation, enabling the identification of active regulatory regions.

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Figure 1: Features of the mouse ES cell methylome.
Figure 2: General features of LMRs.
Figure 3: DNA binding is necessary and sufficient for LMR formation.
Figure 4: REST is required for LMR formation at its binding sites.
Figure 5: Methylation dynamics during differentiation.

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Primary accessions

Gene Expression Omnibus

Data deposits

Data sets generated for this study are available from GEO under accession GSE30206.

Change history

  • 25 April 2012

    Nature 480, 490–495 (2011) In the original version of this Article Erik van Nimwegen (Biozentrum of the University of Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, CH 4056 Basel, Switzerland) was inadvertently omitted from the author list. In the ‘Author contribution’ section the sentence beginning “Bioinformatic and statistical analyses.

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Acknowledgements

The authors thank A. Fernandez, C. Kohler, V. Petitjean and F. Staedtler (Novartis) and I. Nissen and C. Beisel (ETH-BSSE) for performing next generation sequencing experiments. R. Lister and J. Ecker for technical advice on BisSeq library generation. D. Schmitz for the pcDNA6-IRES-Blasticidin vector. D. Anderson for the REST antibody. H. Jørgensen for REST cds. L. Hoerner for help in Sanger bisulphite sequencing. M. Lorincz, N. Thomä and members of the Schübeler laboratory for feedback on the manuscript. R.M. is supported by an EMBO long-term postdoctoral fellowship. V.K.T. is supported by a Marie Curie International Incoming fellowship and an EMBO long-term postdoctoral fellowship. Research in the laboratory of D.S. is supported by the Novartis Research Foundation, the European Union (NoE “EpiGeneSys” FP7-HEALTH-2010-257082), the European Research Council (ERC EpiGePlas), the SNF Sinergia program and the Swiss initiative in Systems Biology (Cell Plasticity).

Author information

Authors and Affiliations

Authors

Contributions

Experiments were designed by R.M., F.L., A.S., V.K.T., E.J.O. and D.S. BisSeq, RNA-Seq and ChIP-seq experiments were conducted by R.M., A.S. and V.K.T. ChIP-seq data analysis was performed by M.B.S. and L.B. BS-PCR validation was performed by R.M., F.L. and C.W. Sequencing data processing was performed by D.G. and M.B.S. LMRs were first noticed by D.G. Bioinformatic and statistical analyses were conducted by M.B.S., L.B., R.I. and E.v.N. The manuscript was prepared by R.M., M.B.S., L.B. and D.S.

Corresponding author

Correspondence to Dirk Schübeler.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

The file contains Supplementary Figures 1-16 with legends, Supplementary Methods and additional references. The methods in this file were replaced on 25 April 2012. (PDF 16260 kb)

Supplementary Table 1

The table displays details of sequence datasets used in this study, and additional references (for external data sets only). (DOC 56 kb)

Supplementary Table 2

The table displays methylation segments identified in ES cells. (CSV 9880 kb)

Supplementary Table 3

The table displays Methylation segments identified in NP. A short description of each column is given at the top of the table. (CSV 7235 kb)

Supplementary Table 4

The table displays Genotype structure of the ES cell line used in the study. (CSV 29 kb)

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Stadler, M., Murr, R., Burger, L. et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 480, 490–495 (2011). https://doi.org/10.1038/nature10716

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