The NIH Roadmap Epigenomics Mapping Consortium

Journal name:
Nature Biotechnology
Volume:
28,
Pages:
1045–1048
Year published:
DOI:
doi:10.1038/nbt1010-1045
Published online

The NIH Roadmap Epigenomics Mapping Consortium aims to produce a public resource of epigenomic maps for stem cells and primary ex vivo tissues selected to represent the normal counterparts of tissues and organ systems frequently involved in human disease.

At a glance

Figures

  1. Layers of genome organization.
    Figure 1: Layers of genome organization.

    Genome function and cellular phenotypes are influenced by DNA methylation and the protein-DNA complex known as chromatin. In mammals, DNA methylation occurs on cytosine bases, primarily in the context of CpG dinucleotides. Accessible chromatin that is hypersensitive to DNase I digestion marks promoters and functional elements bound by transcription factors or other regulatory proteins. Histone modifications, associated proteins such as Polycomb repressors and noncoding RNAs constitute an additional layer of chromatin structure that affects genome function in a context-dependent manner.

  2. Portal for the NIH Roadmap Epigenomics Mapping Consortium.
    Figure 2: Portal for the NIH Roadmap Epigenomics Mapping Consortium.

    A public portal (http://www.roadmapepigenomics.org/) provides general information about the consortium and its participants, along with links to experimental protocols, consortium data and interfaces for visualizing epigenomic maps.

References

  1. Altshuler, D., Daly, M.J. & Lander, E.S. Science 322, 881888 (2008).
  2. Bird, A. Nature 447, 396398 (2007).
  3. Feinberg, A.P. Nature 447, 433440 (2007).
  4. Jaenisch, R. & Bird, A. Nat. Genet. 33 Suppl, 245254 (2003).
  5. Jones, P.A. & Baylin, S.B. Cell 128, 683692 (2007).
  6. Kouzarides, T. Cell 128, 693705 (2007).
  7. Bernstein, B.E., Meissner, A. & Lander, E.S. Cell 128, 669681 (2007).
  8. Fraser, P. & Bickmore, W. Nature 447, 413417 (2007).
  9. Zaratiegui, M., Irvine, D.V. & Martienssen, R.A. Cell 128, 763776 (2007).
  10. Schwartz, Y.B. & Pirrotta, V. Nat. Rev. Genet. 8, 922 (2007).
  11. Grewal, S.I. & Moazed, D. Science 301, 798802 (2003).
  12. Henikoff, S. Nat. Rev. Genet. 9, 1526 (2008).
  13. Jirtle, R.L. & Skinner, M.K. Nat. Rev. Genet. 8, 253262 (2007).
  14. Hess, J.L. Crit. Rev. Eukaryot. Gene Expr. 14, 235254 (2004).
  15. Hansen, R.S. et al. Proc. Natl. Acad. Sci. USA 96, 1441214417 (1999).
  16. Dalgliesh, G.L. et al. Nature 463, 360363 (2010).
  17. Batty, N., Malouf, G. G. & Issa, J. P. Cancer Lett. 280, 192200 (2009).
  18. Birney, E. et al. Nature 447, 799816 (2007).
  19. Heintzman, N.D. et al. Nature 459, 108112 (2009).
  20. Eckhardt, F. et al. Nat. Genet. 38, 13781385 (2006).
  21. Meissner, A. et al. Nature 454, 766770 (2008).
  22. Cokus, S.J. et al. Nature 452, 215219 (2008).
  23. Barski, A. et al. Cell 129, 823837 (2007).
  24. Hesselberth, J.R. et al. Nat. Methods 6, 283289 (2009).
  25. Mikkelsen, T.S. et al. Nature 448, 553560 (2007).
  26. Lister, R. et al. Nature 462, 315322 (2009).
  27. Toronto International Data Release Workshop Authors Nature 461, 168170 (2009).
  28. Suzuki, M.M. & Bird, A. Nat. Rev. Genet. 9, 465476 (2008).
  29. Satterlee, J. Nat. Biotechnol. 28, 10391044 (2010).
  30. Frazer, K.A. et al. Nature 449, 851861 (2007).

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Author information

Affiliations

  1. Bradley E. Bernstein, Alexander Meissner, Manolis Kellis, Eric S. Lander and Tarjei S. Mikkelsen are at the Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.

  2. Bradley E. Bernstein is also at the Howard Hughes Medical Institute, Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.

  3. Alexander Meissner is in the Department of Stem Cell and Regenerative Biology at Harvard University, Cambridge, Massachusetts, USA.

  4. John A. Stamatoyannopoulos is in the Departments of Genome Sciences and Medicine, University of Washington School of Medicine, Seattle, Washington, USA.

  5. Joseph F. Costello is in the Department of Neurosurgery, University of California at San Francisco, San Francisco, California, USA.

  6. Bing Ren is at the Ludwig Institute for Cancer Research, University of California San Diego School of Medicine, La Jolla, California, USA.

  7. Aleksandar Milosavljevic and Arthur L. Beaudet are in the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.

  8. Marco A. Marra and Martin Hirst are at the Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.

  9. Joseph R. Ecker is in the Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, California, USA.

  10. Peggy J. Farnham is at the Genome Center, University of California at Davis, Davis, California, USA.

  11. James A. Thomson is at the University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA.

Competing financial interests

The authors declare no competing financial interests.

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