Intricate mechanisms of gene regulation are critical for eukaryotes, particularly in multicellular organisms where diverse cell types arise from differential gene expression of a single genome. However, the evolution of gene regulatory pathways has been complex, involving recurrent simplifications or expansions tied to major evolutionary transitions. In our laboratory, we delve into the origins of DNA methylation in eukaryotes, its interplay with genome evolution and Giant Viruses, and the emergence of pluripotency factors in unicellular protists closely related to animals. We employ comparative and functional genomics in non-conventional model systems to address these questions, emphasizing the significance of broad taxonomic sampling for a comprehensive understanding of eukaryotic gene regulation.

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