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Comparative analysis of genome-scale, base-resolution DNA methylation profiles across 580 animal species

Author

Listed:
  • Johanna Klughammer

    (CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
    Ludwig-Maximilians-Universität München)

  • Daria Romanovskaia

    (CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences)

  • Amelie Nemc

    (CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences)

  • Annika Posautz

    (University of Veterinary Medicine Vienna)

  • Charlotte A. Seid

    (Northeastern University Marine Science Center)

  • Linda C. Schuster

    (CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences)

  • Melissa C. Keinath

    (University of Kentucky)

  • Juan Sebastian Lugo Ramos

    (Max Planck Institute for Evolutionary Biology)

  • Lindsay Kosack

    (CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences)

  • Ann Evankow

    (Northeastern University Marine Science Center)

  • Dieter Printz

    (St. Anna Kinderkrebsforschung)

  • Stefanie Kirchberger

    (St. Anna Kinderkrebsforschung)

  • Bekir Ergüner

    (CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences)

  • Paul Datlinger

    (CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences)

  • Nikolaus Fortelny

    (CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences)

  • Christian Schmidl

    (CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences)

  • Matthias Farlik

    (CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences)

  • Kaja Skjærven

    (Institute of Marine Research (IMR))

  • Andreas Bergthaler

    (CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
    Medical University of Vienna, Center for Pathophysiology Infectiology and Immunology, Institute of Hygiene and Applied Immunology)

  • Miriam Liedvogel

    (Max Planck Institute for Evolutionary Biology
    Institute of Avian Research, An der Vogelwarte)

  • Denise Thaller

    (University of Veterinary Medicine Vienna)

  • Pamela A. Burger

    (University of Veterinary Medicine Vienna)

  • Marcela Hermann

    (Department of Medical Biochemistry)

  • Martin Distel

    (St. Anna Kinderkrebsforschung)

  • Daniel L. Distel

    (Northeastern University Marine Science Center)

  • Anna Kübber-Heiss

    (University of Veterinary Medicine Vienna)

  • Christoph Bock

    (CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
    Medical University of Vienna, Institute of Artificial Intelligence, Center for Medical Data Science)

Abstract

Methylation of cytosines is a prototypic epigenetic modification of the DNA. It has been implicated in various regulatory mechanisms across the animal kingdom and particularly in vertebrates. We mapped DNA methylation in 580 animal species (535 vertebrates, 45 invertebrates), resulting in 2443 genome-scale DNA methylation profiles of multiple organs. Bioinformatic analysis of this large dataset quantified the association of DNA methylation with the underlying genomic DNA sequence throughout vertebrate evolution. We observed a broadly conserved link with two major transitions—once in the first vertebrates and again with the emergence of reptiles. Cross-species comparisons focusing on individual organs supported a deeply conserved association of DNA methylation with tissue type, and cross-mapping analysis of DNA methylation at gene promoters revealed evolutionary changes for orthologous genes. In summary, this study establishes a large resource of vertebrate and invertebrate DNA methylomes, it showcases the power of reference-free epigenome analysis in species for which no reference genomes are available, and it contributes an epigenetic perspective to the study of vertebrate evolution.

Suggested Citation

  • 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.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-022-34828-y
    DOI: 10.1038/s41467-022-34828-y
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    References listed on IDEAS

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