New findings on genomic regulation mechanisms throughout evolution

The conservation of genome regulatory elements over long periods of evolution is not limited to vertebrates, as previously thought, but also in echinoderms (invertebrates). This is one of the most notable conclusions of a study published in the journal Nature Ecology & Evolution, which expands our knowledge of the mechanisms governing genomic regulation and biological evolution.

The main authors of the study are Marta S. Magri, Danila Voronov and Saoirse Foley, in a project led by the laboratories run by Ignacio Maeso, from the Faculty of Biology and the Biodiversity Research Institute at the University of Barcelona; Maria Ina Arnone, from the Stazione Zoologica Anton Dohrn (Italy); José Luis Gómez-Skarmeta, from the Andalusian Centre for Developmental Biology (CABD-CSIC-UPO); and Veronica Hinman, from the University of Florida (United States).

The study outlines a new scenario for understanding how genome regulation and chromatin organization influence the evolution of animal body plans. “Our study opens up new paths for understanding the biological and evolutionary significance of this extreme conservation, since for the first time we can compare these very ancient regulatory elements across different lineages, a scientific breakthrough that allows us to understand what properties they share,” says Ignacio Maeso, professor at the UB’s Department of Genetics, Microbiology and Statistics.

Gene regulation and evolutionary novelties in vertebrates

Echinoderms are a large group of invertebrates that includes sea urchins, starfish, sea cucumbers, ophiuroids, and sea lilies. They are the phylum closest to chordates — the group to which vertebrates belong — and have a unique phylogenetic position that allows for meaningful evolutionary comparisons between vertebrates and invertebrates.

For example, echinoderm larvae exhibit bilateral symmetry, while their adult forms have pentaradial symmetry, meaning that their body parts are arranged in five (or multiples of five) sections around a central axis. Animal morphology depends on the spatiotemporal control of gene expression — where, when, and which genes are activated in the body — which determines body plans in embryos and adults. But how are the genome and genes of each species regulated? How is chromatin folding, an essential element in gene regulation, controlled?

In this study, the sea urchin (Strongylocentrotus purpuratus) and the starfish (Patiria miniata) have been used as models to unravel the mysteries surrounding the evolution of echinoderms. To this end, the team has applied cutting-edge techniques to analyse 3D genomic organization — such as Hi-C and long-read sequencing — which have been little used in echinoderms to date.

The results reveal an extensive conservation of regulatory DNA elements across echinoderms and other animal groups. These highly conserved elements are most active during key stages of early development, suggesting that they control fundamental developmental programmes that have remained unchanged throughout animal evolution.

“It is impressive that, even across huge evolutionary distances, we see that developmentally relevant genes like FoxA and Tbx2/3 are conserved, and perhaps even more impressively, we see conservation of their regulatory regions. This makes the quest to understand gene regulation and its evolution even more fascinating and showcases how echinoderms are an indispensable tool to answer such questions”, says Maria Ina Arnone, from the Stazione Zoologica Anton Dohrn (Italy).

“This type of deep preservation may be a much more common phenomenon than we previously thought and is probably present in many more animal lineages,” notes Ignacio Maeso.

Furthermore, the study reveals that the CTCF protein — an essential factor in chromatin folding in vertebrates — does not play a crucial role in the organization of the 3D structure of chromatin in echinoderms, similar to what has been described in other invertebrates such as the fruit fly (Drosophila melanogaster).

“This discovery suggests that some of these mechanisms related to the function of CTCF in gene regulation could be evolutionary novelties in vertebrates. Furthermore, our study adds to other recent studies showing how the mechanisms responsible for the 3D organization of chromatin are more diverse than previously thought and that each animal lineage has evolved different types of strategies for folding its genome,” concludes the researcher.

Further information