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Genome-scale DNA methylation maps of pluripotent and differentiated cells

Author

Listed:
  • Alexander Meissner

    (Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Harvard University, Cambridge, Massachusetts 02138, USA)

  • Tarjei S. Mikkelsen

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA)

  • Hongcang Gu

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA)

  • Marius Wernig

    (Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA)

  • Jacob Hanna

    (Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA)

  • Andrey Sivachenko

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA)

  • Xiaolan Zhang

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA)

  • Bradley E. Bernstein

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Molecular Pathology Unit and Center for Cancer Research, MGH, Charlestown, Massachusetts 02129, USA
    Harvard Medical School, Boston, Massachusetts 02115, USA)

  • Chad Nusbaum

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA)

  • David B. Jaffe

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA)

  • Andreas Gnirke

    (Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA)

  • Rudolf Jaenisch

    (Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA)

  • Eric S. Lander

    (Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Harvard Medical School, Boston, Massachusetts 02114, USA)

Abstract

DNA methylation mapped DNA methylation, an important mechanism of epigenetic modification that produces different patterns of gene expression from a single DNA sequence, is vital to normal development and its malfunction can cause cancer and other abnormalities. A map of DNA methylation in embryonic stem cells, and in various cell types derived from them, has now been produced at nucleotide resolution using high-throughput bisulphite sequencing combined with single molecule-based sequencing. The map reveals specific sites in the genome where methylation changes as cells develop, for instance when embryonic stem cells mature into nerve cells. More generally, the methodology will be of value for the epigenetic profiling of cell populations relevant to developmental biology, cancer and regenerative medicine.

Suggested Citation

  • Alexander Meissner & Tarjei S. Mikkelsen & Hongcang Gu & Marius Wernig & Jacob Hanna & Andrey Sivachenko & Xiaolan Zhang & Bradley E. Bernstein & Chad Nusbaum & David B. Jaffe & Andreas Gnirke & Rudol, 2008. "Genome-scale DNA methylation maps of pluripotent and differentiated cells," Nature, Nature, vol. 454(7205), pages 766-770, August.
    • Handle: RePEc:nat:nature:v:454:y:2008:i:7205:d:10.1038_nature07107
    DOI: 10.1038/nature07107
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    Citations

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    Cited by:

    1. Jinling Zhang & Xuebin Zhu & Yuhong Li & Lingyan Zhu & Shiming Li & Guoying Zheng & Qi Ren & Yonghong Xiao & Fumin Feng, 2016. "Correlation of CpG Island Methylation of the Cytochrome P450 2E1/2D6 Genes with Liver Injury Induced by Anti-Tuberculosis Drugs: A Nested Case-Control Study," IJERPH, MDPI, vol. 13(8), pages 1-9, August.
    2. Sun Shuying & Yu Xiaoqing, 2016. "HMM-Fisher: identifying differential methylation using a hidden Markov model and Fisher’s exact test," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 15(1), pages 55-67, March.
    3. Sandhya Malla & Kanchan Kumari & Carlos A. García-Prieto & Jonatan Caroli & Anna Nordin & Trinh T. T. Phan & Devi Prasad Bhattarai & Carlos Martinez-Gamero & Eshagh Dorafshan & Stephanie Stransky & Da, 2024. "The scaffolding function of LSD1 controls DNA methylation in mouse ESCs," Nature Communications, Nature, vol. 15(1), pages 1-24, December.
    4. Yu Xiaoqing & Sun Shuying, 2016. "HMM-DM: identifying differentially methylated regions using a hidden Markov model," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 15(1), pages 69-81, March.
    5. Johanna Klughammer & Daria Romanovskaia & Amelie Nemc & Annika Posautz & Charlotte A. Seid & Linda C. Schuster & Melissa C. Keinath & Juan Sebastian Lugo Ramos & Lindsay Kosack & Ann Evankow & Dieter , 2023. "Comparative analysis of genome-scale, base-resolution DNA methylation profiles across 580 animal species," Nature Communications, Nature, vol. 14(1), pages 1-23, December.
    6. Amir D. Hay & Noah J. Kessler & Daniel Gebert & Nozomi Takahashi & Hugo Tavares & Felipe K. Teixeira & Anne C. Ferguson-Smith, 2023. "Epigenetic inheritance is unfaithful at intermediately methylated CpG sites," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    7. Jincheol Park & Shili Lin, 2018. "Detection of Differentially Methylated Regions Using Bayesian Curve Credible Bands," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 10(1), pages 20-40, April.
    8. Yurika Matsui & Mohamed Nadhir Djekidel & Katherine Lindsay & Parimal Samir & Nina Connolly & Gang Wu & Xiaoyang Yang & Yiping Fan & Beisi Xu & Jamy C. Peng, 2023. "SNIP1 and PRC2 coordinate cell fates of neural progenitors during brain development," Nature Communications, Nature, vol. 14(1), pages 1-18, December.

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