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Human body epigenome maps reveal noncanonical DNA methylation variation

Author

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  • Matthew D. Schultz

    (Bioinformatics Program, University of California
    Genomic Analysis Laboratory, The Salk Institute for Biological Studies
    †Present addresses: Human Longevity Inc., La Jolla, California 92121, USA (M.D.S.); Discovery Science, Janssen Pharmaceutical of Johnson & Johnson, La Jolla, California 92121, USA (J.W.W.))

  • Yupeng He

    (Bioinformatics Program, University of California
    Genomic Analysis Laboratory, The Salk Institute for Biological Studies)

  • John W. Whitaker

    (University of California
    †Present addresses: Human Longevity Inc., La Jolla, California 92121, USA (M.D.S.); Discovery Science, Janssen Pharmaceutical of Johnson & Johnson, La Jolla, California 92121, USA (J.W.W.))

  • Manoj Hariharan

    (Genomic Analysis Laboratory, The Salk Institute for Biological Studies)

  • Eran A. Mukamel

    (Computational Neurobiology Laboratory, The Salk Institute for Biological Studies
    University of California)

  • Danny Leung

    (Ludwig Institute for Cancer Research)

  • Nisha Rajagopal

    (Ludwig Institute for Cancer Research)

  • Joseph R. Nery

    (Genomic Analysis Laboratory, The Salk Institute for Biological Studies)

  • Mark A. Urich

    (Genomic Analysis Laboratory, The Salk Institute for Biological Studies)

  • Huaming Chen

    (Genomic Analysis Laboratory, The Salk Institute for Biological Studies)

  • Shin Lin

    (Stanford University)

  • Yiing Lin

    (Washington University School of Medicine)

  • Inkyung Jung

    (Ludwig Institute for Cancer Research)

  • Anthony D. Schmitt

    (Ludwig Institute for Cancer Research)

  • Siddarth Selvaraj

    (Bioinformatics Program, University of California)

  • Bing Ren

    (Ludwig Institute for Cancer Research
    University of California, San Diego School of Medicine, Institute of Genomic Medicine)

  • Terrence J. Sejnowski

    (Computational Neurobiology Laboratory, The Salk Institute for Biological Studies
    University of California at San Diego
    Howard Hughes Medical Institute, The Salk Institute for Biological Studies)

  • Wei Wang

    (University of California
    University of California)

  • Joseph R. Ecker

    (Genomic Analysis Laboratory, The Salk Institute for Biological Studies
    Howard Hughes Medical Institute, The Salk Institute for Biological Studies)

Abstract

As part of the Epigenome Roadmap Project, genome-wide maps of DNA methylation and transcriptomes together with genomic DNA sequencing of 18 different primary human tissue types from 4 individuals are presented; analysis reveals widespread differential methylation of CG sites between tissues, and the presence of non-CG methylation in adult tissues.

Suggested Citation

  • Matthew D. Schultz & Yupeng He & John W. Whitaker & Manoj Hariharan & Eran A. Mukamel & Danny Leung & Nisha Rajagopal & Joseph R. Nery & Mark A. Urich & Huaming Chen & Shin Lin & Yiing Lin & Inkyung J, 2015. "Human body epigenome maps reveal noncanonical DNA methylation variation," Nature, Nature, vol. 523(7559), pages 212-216, July.
    • Handle: RePEc:nat:nature:v:523:y:2015:i:7559:d:10.1038_nature14465
    DOI: 10.1038/nature14465
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    Citations

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    Cited by:

    1. Jamie L. Endicott & Paula A. Nolte & Hui Shen & Peter W. Laird, 2022. "Cell division drives DNA methylation loss in late-replicating domains in primary human cells," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    2. Qiang Zhang & Sai Ma & Zhengzhi Liu & Bohan Zhu & Zirui Zhou & Gaoshan Li & J. Javier Meana & Javier González-Maeso & Chang Lu, 2023. "Droplet-based bisulfite sequencing for high-throughput profiling of single-cell DNA methylomes," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    3. Victoria L. Sork & Shawn J. Cokus & Sorel T. Fitz-Gibbon & Aleksey V. Zimin & Daniela Puiu & Jesse A. Garcia & Paul F. Gugger & Claudia L. Henriquez & Ying Zhen & Kirk E. Lohmueller & Matteo Pellegrin, 2022. "High-quality genome and methylomes illustrate features underlying evolutionary success of oaks," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    4. Liam McAllan & Damir Baranasic & Sergio Villicaña & Scarlett Brown & Weihua Zhang & Benjamin Lehne & Marco Adamo & Andrew Jenkinson & Mohamed Elkalaawy & Borzoueh Mohammadi & Majid Hashemi & Nadia Fer, 2023. "Integrative genomic analyses in adipocytes implicate DNA methylation in human obesity and diabetes," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
    5. Hagar Taman & Christopher G Fenton & Endre Anderssen & Jon Florholmen & Ruth H Paulssen, 2021. "DNA hypo-methylation facilitates anti-inflammatory responses in severe ulcerative colitis," PLOS ONE, Public Library of Science, vol. 16(4), pages 1-17, April.
    6. Iryna Ivasyk & Leonora Olivos-Cisneros & Stephany Valdés-Rodríguez & Marie Droual & Hosung Jang & Robert J. Schmitz & Daniel J. C. Kronauer, 2023. "DNMT1 mutant ants develop normally but have disrupted oogenesis," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    7. Yinwen Zhang & Hosung Jang & Rui Xiao & Ioanna Kakoulidou & Robert S. Piecyk & Frank Johannes & Robert J. Schmitz, 2021. "Heterochromatin is a quantitative trait associated with spontaneous epiallele formation," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    8. Andrea L Liebl & Jeff S Wesner & Andrew F Russell & Aaron W Schrey, 2021. "Methylation patterns at fledging predict delayed dispersal in a cooperatively breeding bird," PLOS ONE, Public Library of Science, vol. 16(6), pages 1-13, June.
    9. Min-Rui-Xuan Xu & Zhen-Yang Liao & Jordan R. Brock & Kang Du & Guo-Yin Li & Zhi-Qiang Chen & Ying-Hao Wang & Zhong-Nan Gao & Gaurav Agarwal & Kevin H-C Wei & Feng Shao & Shuai Pang & Adrian E. Platts , 2023. "Maternal dominance contributes to subgenome differentiation in allopolyploid fishes," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    10. 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.

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