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

by Schuster, Linda C , Bock, Christoph , Klughammer, Johanna , Seid, Charlotte A , Skjærven, Kaja Helvik , Hermann, Marcela , Lugo Ramos, Juan Sebastian , Datlinger, Paul , Liedvogel, Miriam , Nemc, Amelie , Evankow, Ann , Burger, Pamela A , Fortelny, Nikolaus , Bergthaler, Andreas , Romanovskaia, Daria , Distel, Martin , Kosack, Lindsay , Ergüner, Bekir , Schmidl, Christian , Kirchberger, Stefanie , Printz, Dieter , Kübber-Heiss, Anna , Keinath, Melissa C , Posautz, Annika , Distel, Daniel L , Thaller, Denise , Farlik, Matthias

in 631/114/2114 / 631/208/177 / 631/208/212/2304 / Animal species / Animals / Biological evolution / Comparative analysis / Conserved sequence / Datasets / Deoxyribonucleic acid / DNA / DNA - metabolism / DNA methylation / DNA Methylation - genetics / Epigenesis, Genetic / Epigenetics / Evolution / Gene mapping / Genome - genetics / Genomes / Humanities and Social Sciences / Invertebrates / Invertebrates - genetics / multidisciplinary / Nucleotide sequence / Organs / Regulatory mechanisms (biology) / Reptiles / Science / Science (multidisciplinary) / Species / Species comparisons / Vertebrates / Vertebrates - genetics / Vertebrates - metabolism

2023

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

2023

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

2023

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Journal Article

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

Schuster, Linda C,

Bock, Christoph,

Klughammer, Johanna,

Seid, Charlotte A,

Skjærven, Kaja Helvik,

Hermann, Marcela,

Lugo Ramos, Juan Sebastian,

Datlinger, Paul,

Liedvogel, Miriam,

Nemc, Amelie,

Evankow, Ann,

Burger, Pamela A,

Fortelny, Nikolaus,

Bergthaler, Andreas,

Romanovskaia, Daria,

Distel, Martin,

Kosack, Lindsay,

Ergüner, Bekir,

Schmidl, Christian,

Kirchberger, Stefanie,

Printz, Dieter,

Kübber-Heiss, Anna,

Keinath, Melissa C,

Posautz, Annika,

Distel, Daniel L,

Thaller, Denise,

Farlik, Matthias

2023

Overview

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.

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Publisher

Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio

Subject

/ Animals

/ Biological evolution

/ Comparative analysis