Charting a dynamic DNA methylation landscape of the human genome (original) (raw)

Accession codes

Accessions

Gene Expression Omnibus

Data deposits

WGBS data are deposited at the Gene Expression Omnibus (see Supplementary Table 1 for the specific accession numbers). Supplementary Table 2 is available under GEO accession number GSE46644.

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Acknowledgements

We would like to thank K. Clement, P. Samavarchi-Tehrani, Z. Smith, M. Chan and R. Karnik for discussions and feedback. We would also like to thank F. Kelley, T. Durham, C. Epstein, N. Shoresh, G. Lauwers and the Massachusetts General Hospital tissue repository for assisting in sample and data management. E.D.R. is supported by the National Institutes of Health (NIH) Roadmap Epigenomics Project (ES017690). D.A.B. is supported by NIH grants P30AG10161, R01AG17917, R01AG15819 and R01AG36042. A.M. is supported by the Pew Charitable Trusts and is a New York Stem Cell Foundation, Robertson Investigator. This work was funded by NIH grants (U01ES017155 and P01GM099117) and The New York Stem Cell Foundation.

Author information

Author notes

  1. Fabian Müller
    Present address: Present address: Max Planck Institute for Informatics, 66123 Saarbrücken, Germany.,

Authors and Affiliations

  1. Broad Institute of MIT and Harvard, Cambridge, 02142, Massachusetts, USA
    Michael J. Ziller, Hongcang Gu, Julie Donaghey, Philip L. De Jager, Evan D. Rosen, Bradley E. Bernstein, Andreas Gnirke & Alexander Meissner
  2. Harvard Stem Cell Institute, Cambridge, 02138, Massachusetts, USA
    Michael J. Ziller, Julie Donaghey & Alexander Meissner
  3. Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, 02138, Massachusetts, USA
    Michael J. Ziller, Fabian Müller, Julie Donaghey & Alexander Meissner
  4. Division of Endocrinology, Beth Israel Deaconess Medical Center, Boston, 02215, Massachusetts, USA
    Linus T.-Y. Tsai & Evan D. Rosen
  5. Applied Bioinformatics, Center for Bioinformatics and Quantitative Biology Center, University of Tübingen, 72074 Tübingen, Germany,
    Oliver Kohlbacher
  6. Departments of Neurology and Psychiatry, Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Brigham and Women’s Hospital, 77 Avenue Louis Pasteur, NRB168, Boston, Massachusetts 02115, USA,
    Philip L. De Jager
  7. Rush Alzheimer’s Disease Center, Rush University Medical Center, 600 South Paulina Street, Chicago, Illinois 60612, USA,
    David A. Bennett
  8. Department of Pathology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA,
    Bradley E. Bernstein

Authors

  1. Michael J. Ziller
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  2. Hongcang Gu
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  3. Fabian Müller
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  4. Julie Donaghey
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  5. Linus T.-Y. Tsai
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  6. Oliver Kohlbacher
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  7. Philip L. De Jager
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  8. Evan D. Rosen
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  9. David A. Bennett
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  10. Bradley E. Bernstein
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  11. Andreas Gnirke
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  12. Alexander Meissner
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Contributions

M.J.Z. and A.M. conceived the study and interpreted the results. M.J.Z. designed the statistical framework, analysis strategy and analysed the data. H.G. performed in-house WGBS library production, F.M. contributed bioinformatics tools and J.D. performed cell culture experiments. L.T.-Y.T. and E.D.R. provided adipocyte nuclei for WGBS profiling, and P.L.D. and D.A.B. made adult brain and Alzheimer’s disease samples available. O.K. provided support on analysis strategy and statistical methods. B.E.B. and A.M. organized samples as part of the NIH Roadmap Epigenomics Project. H.G., A.G. and A.M. established the WGBS at the Broad Institute. A.M. supervised the project. M.Z. and A.M. wrote the paper with assistance from the other authors.

Corresponding author

Correspondence toAlexander Meissner.

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Competing interests

M.J.Z. and A.M. declare competing financial interests owing to the filing of a patent application on the selected regions.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-5, legends for Supplementary Tables 1-3 (see separate files for Supplementary Tables 1 and 3 and for Supplementary Table 2, see link in main paper), Supplementary Methods and additional references. (PDF 486 kb)

Supplementary Table 1

This file contains a summary of data sets, accession numbers and quality measures for all WGBS libraries use in this study. (XLSX 13 kb)

Supplementary Table 3

This file contains Motif enrichment results for cell type specific hypomethylated regions. (XLSX 240 kb)

Supplementary Data

This file contains the data associated with this paper. (ZIP 103 kb)

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Ziller, M., Gu, H., Müller, F. et al. Charting a dynamic DNA methylation landscape of the human genome.Nature 500, 477–481 (2013). https://doi.org/10.1038/nature12433

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