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

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 Printz, Stefanie Kirchberger, Bekir Ergüner, Paul Datlinger, Nikolaus Fortelny, Christian Schmidl, Matthias Farlik, Kaja Skjærven, Andreas Bergthaler, Miriam Liedvogel, Denise Thaller, Pamela A. Burger, Marcela Hermann, Martin Distel, Daniel L. Distel, Anna Kübber-Heiss and Christoph Bock ()
Additional contact information
Johanna Klughammer: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
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
Miriam Liedvogel: Max Planck Institute for Evolutionary Biology
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

Nature Communications, 2023, vol. 14, issue 1, 1-23

Abstract: 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.

Date: 2023
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DOI: 10.1038/s41467-022-34828-y

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