Evolution of DNA methylome diversity in eukaryotes

Our lab has participated in the special issue of the Journal of Molecular Biology: “Reading DNA modifications”. We contributed with a review: “Evolution of DNA methylome diversity in eukaryotes”. In this piece, we summarise a decade worth of insights obtained from whole genome bisulfite sequencing studies across eukaryotes. We speculate on the origins and functions of diverse DNA methylation patterns observed in different organisms and propose how such patterns might have evolved. This work expands our knowledge on the function and evolutionary origins of DNA methylation in plants, animals and fungi. The bonus was that our artwork (designed by Scot Nicholls) was selected for the cover of this special issue.

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Evolutionary conservation of DNA methylation loss during chordate development. Hourglass represents the developmental morphological divergence across species, where the mid-developmental phylotypic stage shows similar morphologies across distant taxa whereas early and late development are more prone to lineage specific forms.

Retention of paternal DNA methylome in the developing zebrafish germline

In mammals, DNA methylation undergoes two rounds of developmental remodelling; in primordial germ cells and in the pre-implantation embryo. However, it is currently unclear whether such DNA methylome reprogramming is more broadly conserved among vertebrates. This work led by Ksenia Skvortsova from our lab, published today in Nature Communications, demonstrates inheritance of the paternal methylation pattern in developing germ cells and absence of genome-wide reprogramming events. This study was published back to back with a similar study from the Hore lab (University of Otago).

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Functions and mechanisms of epigenetic inheritance in animals

Our review on inter- and transgenerational epigenetic inheritance in animals is just out in Nature Reviews Molecular Cell Biology. This is our take on trying to summarise a highly complex and polemic field on a few pages of text. This effort was led by Ksenia Skvortsova and our long term collaborator Nicola Iovino from the Max Planck Institute of Immunobiology and Epigenetics. For those who don’t feel like reading the whole piece, this is a two-sentence summary of the review: Briefly, epigenetic inheritance (EI) across generations is widespread in animals. There are excellent examples in flies and worms. In mammals EI that spans multiple generations is a rare event. Anamniotes that lack embryonic epigenome reprogramming might be useful models for EI.

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Amphioxus functional genomics and the origins of vertebrate gene regulation

This long-awaited study was published in Nature this week. As a part of a large international consortium, we generated a functional genomics resource for amphioxus (B. lanceolatum) comprising 96 datasets of RNA-seq, MethylC-seq, RRBS, CAGE-seq, ChIP-seq and ATAC-seq. Amphioxus (also known as “the lancelet”), is an invertebrate chordate that can help us resolve some of the earliest steps of vertebrate evolution. We uncovered that DNA methylation is removed from Amphioxus enhancers in a similar fashion as previously described in vertebrates. More about the study can be found at here.

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Germ line–inherited H3K27me3 restricts enhancer function during maternal-to-zygotic transition

Great to see this exciting collaboration led by the Iovino lab finally out in Science! Besides DNA itself, the parents provide a multitude of epigenetic information to the embryo. Here we show that the Polycomb repressive histone mark H3K27me3 is contributed maternally, to regulate the timing of zygotic genome activation in Drosophila. Preventing the propagation of maternally inherited H3K27me3 leads to precocious gene activation and, ultimately, embryo lethality.

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