Epigenetic gatekeeping enables genome-scale horizontal gene transfer in eukaryotic cells

Horizontal gene transfer drives rapid evolutionary innovation, yet well-substantiated cases are largely confined to prokaryotes. Eukaryote-to-eukaryote transfer remains exceptionally rare, and direct genome-scale demonstrations are absent. Here, inspired by endosymbiotic genome acquisition, we show that mammalian cells can initiate genome-scale horizontal gene transfer through phagocytic uptake of intact algal cells, albeit at a much lower frequency than cell fusion. Live-cell imaging captures the early nuclear appearance of transferred algal DNA after fusion, while genome sequencing and cytogenetic analyses reveal stable retention of chromosome-scale algal DNA in mammalian cells. Hybrid cells maintain more than 16 Mb of algal DNA, including intact chromosomes, as telomere-linked structures that persist for 95 generations without selection. Transferred algal DNA shows a progressive increase in DNA methylation together with enrichment of repressive histone modifications, forming heterochromatic domains that physically associate with host chromosomes. Notably, mammalian cells deficient in a de novo DNA methyltransferase show reduced stable establishment and retention of transferred algal DNA, supporting a gatekeeping role for DNA methylation in the stable accommodation of foreign genomes. Our findings reveal an epigenetic mechanism that contributes to the stable accommodation of large-scale foreign DNA between distantly related eukaryotes.