DNA methylation reprogramming in marsupial embryos is restricted to the extraembryonic lineage

Angeloni, A.; Hammond, J. M.; Peters, T. J.; Reis, A. L. M.; Kemp, L.; Amos, T.; Gamaarachchi, H.; Humphries, S.; Wilmott, L. A.; Pal, S.; Masamsetti, V. P.; Weatherstone, M.; Ip, K. C. K.; Pazaky, K.; Steel, A.; Lyons, R.; Walters, E. D.; Liu, N.; Tam, P.; Polo, J. M.; Waters, P. D.; Clark, S. J.; Richards, L. J.; Smith, A. D.; Lee, H.; Deveson, I. W.; Griffith, O. W.; Skvortsova, K.

doi:10.1101/2025.11.09.686659

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bioRxiv · 10.1101/2025.11.09.686659

DNA methylation reprogramming in marsupial embryos is restricted to the extraembryonic lineage

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Abstract

DNA methylation (5mC) is an epigenetic mark that plays a critical role in defining cell fate. Following fertilisation, DNA methylation inherited from gametes must be reprogrammed to establish totipotency and enable the parental-to-zygotic transition. To accomplish this, non-mammalian vertebrates such as zebrafish and medaka subtly reprogram maternal 5mC profiles while maintaining high methylation levels throughout embryogenesis. In contrast, eutherian mammals such as mouse and human undergo global 5mC erasure in both embryonic and extraembryonic lineages. However, while embryonic 5mC is rapidly re-established to high levels upon implantation, the trophectoderm, which gives rise to the placenta, displays sustained and conserved DNA hypomethylation, suggesting that this drastic 5mC erasure may be functionally linked to complex placentation in mammals. To clarify whether extensive post-fertilisation 5mC erasure co-evolved with placentation, we explored embryonic methylation dynamics in marsupials, a lineage of therian mammals with a short-lived placenta. We produced a near complete telomere-to-telomere (T2T) genome and generated detailed epigenome maps of embryonic development for an Australian marsupial, the fat-tailed dunnart (Sminthopsis crassicaudata). We found the dunnart embryo exhibits genome wide DNA demethylation at the blastocyst stage, but these changes occur in the trophectoderm only, suggesting that 5mC erasure in the placenta is an ancestral state in therian mammals. Furthermore, the T2T-level dunnart genome assembly enabled identification of sex chromosomes, uncovering extensive hypomethylation of the paternally-inherited inactive X chromosome in females and revealing the previously unannotated master regulator of X chromosome inactivation, lncRNA Rsx. Our data indicate that while the use of genome-wide 5mC erasure differs between eutherian and marsupial lineages, 5mC erasure in extraembryonic tissue is ancestral to therian mammals and may be necessary to support placental development. HIGHLIGHTSO_LIFirst embryonic DNA methylation maps in an Australian marsupial C_LIO_LIExtensive global erasure of DNA methylation in the trophectoderm C_LIO_LIMaintenance of high DNA methylation in the embryonic lineage C_LIO_LIHypomethylated paternal X chromosome with methylated escapee genes C_LI

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Angeloni, A., Hammond, J. M., Peters, T. J., Reis, A. L. M., Kemp, L., Amos, T., Gamaarachchi, H., Humphries, S., Wilmott, L. A., Pal, S., Masamsetti, V. P., Weatherstone, M., Ip, K. C. K., Pazaky, K., Steel, A., Lyons, R., Walters, E. D., Liu, N., Tam, P., Polo, J. M., Waters, P. D., Clark, S. J., Richards, L. J., Smith, A. D., Lee, H., Deveson, I. W., Griffith, O. W., Skvortsova, K.. 2025-11-11. DNA methylation reprogramming in marsupial embryos is restricted to the extraembryonic lineage. https://doi.org/10.1101/2025.11.09.686659

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