An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)

  1. Vardhman Rakyan1,9,
  2. Thomas Down2,
  3. Natalie Thorne3,
  4. Paul Flicek4,
  5. Eugene Kulesha5,
  6. Stefan Graf5,
  7. Eleni Tomazou6,
  8. Liselotte Backdahl7,
  9. Nathan Johnson5,
  10. Marils Herberth8,
  11. Kevin Howe3,
  12. David Jackson6,
  13. Marcos Miretti6,
  14. Heike Fiegler6,
  15. John Marioni3,
  16. Ewan Birney5,
  17. Tim Hubbard6,
  18. Nigel Carter6,
  19. Simon Tavare3, and
  20. Stephan Beck7
  1. 1 Institute of Cell and Molecular Science;
  2. 2 Gurdon Institute;
  3. 3 CRI;
  4. 4 European Bioinformatics Institute;
  5. 5 EBI;
  6. 6 Sanger Institute;
  7. 7 UCL;
  8. 8 University of Cambridge

Abstract

We report a novel resource (methylation profiles of DNA, mPod) for human genome-wide tissue-specific DNA methylation profiles. mPod consists of three fully integrated parts, genome-wide DNA methylation reference profiles of 13 normal somatic tissues, placenta, sperm and an immortalized cell line, a visualization tool that has been integrated with the Ensembl genome browser and a new algorithm for the analysis of immunoprecipitation-based DNA methylation profiles. We demonstrate the utility of our resource by identifying the first comprehensive genome-wide set of tissue-specific differentially methylated regions (tDMRs) that may play a role in cellular identity and the regulation of tissue-specific genome function. We also discuss the implications of our findings with respect to the regulatory potential of regions with varied CpG density, gene expression, transcription factor motifs, gene ontology and correlation with other epigenetic marks such as histone modifications.

Footnotes

    • Received February 13, 2008.
    • Accepted June 15, 2008.

  • This manuscript is Open Access.

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  1. Published in Advance June 24, 2008, doi: 10.1101/gr.077479.108 Genome Res. gr.077479.108 Copyright © 2008, Cold Spring Harbor Laboratory Press

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