The roots of animal epigenetic regulation: insights from sponge epigenomes

Theme: Evolution & Adaptation

Primary Supervisor:

Alexandre de Mendoza Soler

School of Biological and Behavioural Sciences, QMUL

Alexandre de Mendoza Soler's Profile Picture

Secondary Supervisor:

Ferdinand Marletaz

Genetics, Evolution and Environment, UCL

Ferdinand Marletaz's Profile Picture

Project Description:

Sponges are believed to be sister group to the rest of animals, which makes them the perfect model system to understand early animal evolution. Importantly, features shared between sponges and other animal phyla were likely present in the last common ancestor of all animals, thus giving crucial insight into the origins of multicellularity. Furthermore, sponges play an important role in today’s marine and freshwater ecosystems, providing critical filtering capacities as well as niches to bacteria and other organisms.
In this project we want to understand what the roles of DNA methylation in sponges are. DNA methylation is a heritable epigenetic mark involved in gene regulation that can mediate long-term transcriptional responses to environmental change. However, most of our knowledge regarding DNA methylation stems from mammalian systems, known to have quite divergent methylation patterns to those of invertebrates. Thus, it is currently very difficult to extrapolate how DNA methylation affects gene regulation in important invertebrate linages. We will take advantage of the recently sequenced Ephydatia muelleri genome to investigate the role of DNA methylation in this freshwater sponge. Unlike most sponges, Ephydatia can be grown in laboratory conditions, and is therefore experimentally tractable. We would use demethylating drugs to understand the transcriptional effects of methylation loss, profiling a battery of genomic techniques (transcriptome, methylome and open chromatin analysis). We would perform these experiments under various environmental conditions, to address the importance of DNA methylation to environmental perturbations and transcriptional adaptation.
During the project we will use a combination of cutting edge epigenomic techniques and bioinformatic analysis required for this type of large-scale genomic datasets, building on the world-class expertise at the de Mendoza laboratory.

Policy Impact of Research:

Since oceans are changing at ever increasing speed due to human-derived perturbations, it is believed that selection on the current genetic variation might not be sufficient for animals to cope with rapid environmental changes. Therefore, we need to understand how epigenetic changes might be involved in transcriptional plasticity, which can contribute to adaptation in shorter timescales. Lessons derived from sponge epigenomes will reveal deeply conserved mechanisms in animal evolution and will l

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