Regulatory principles of echinoderm metamorphosis

While some animals develop directly from embryos into their adult forms, others present an intermediate larval stage. The metamorphosis of the larva into the adult form can be more or less dramatic, and, in the case of echinoderms, involve a drastic change in body symmetry from a bilateral larva into a pentaradial adult (five-way symmetry). The adult first grows as a set of cells, the 'rudiment' that grows within the larva and finally everts from it. While this process relies on the same development genes as embryonic development, these genes are mobilised by an alternative developmental program encoded in the genome. I want to understand how these two regulatory programs that control development from egg to larva and from larva to pentaradial adult can coexist in the same genome.
Genes are controlled by regulatory elements, segments of DNA that are bound by specialised proteins called transcription factors. I want to determine what are the regulatory elements in the genome that control the metamorphosis of the larval into an adult with an alternative body symmetry and which transcription factors play the most important role in mobilising these elements. We will use sequencing-based technologies, such as single-cell transcriptomics and computational analyses to find this out. We will then use transgenic sea urchin larvae carrying a gene encoding for a fluorescent protein under the control of such promoters to monitor where these regulatory elements are active.
Echinoderm genomes are quite plastic, which means gene order can change and some have postulated that this could have played a key role in rewiring gene regulation. To test this idea, we will evaluate the genomic changes that took place in different echinoderm lineages. Then, as regulatory elements are embedded in loops of DNA known as three-dimensional chromatin compartments, we will see if these are affected during metamorphosis, and finally build an integrative model of rudiment development. We expect to uncover the new regulatory route that has made possible the evolution of a new body plan in these mesmerising organisms.

While some animals develop directly from embryos into their adult forms, others present an intermediate larval stage. The metamorphosis of the larva into the adult form can be more or less drastic, and, in the case of echinoderms, involve a change in body symmetry from a bilateral larva into a pentaradial adult (five-way symmetry). The adult first grows as a set of cells, the 'rudiment' that grows within the larva and finally everts from it. While this process relies on the same development genes as embryonic development, these genes are mobilised by an alternative developmental program encoded in the genome. I want to understand how these two regulatory programs (the embryonic and metamorphosis ones) can coexist in the genome and be successively activated, by better understanding the regulatory architecture of echinoderm genomes. To do this, I first want to characterise the regulatory elements involved in rudiment development, identify the key transcription factors responsible for the initiation of the rudiment development and functionally assess their role. Then, I plan to experimentally survey the activation pattern of rudiment specific elements using a reporter approach and dissect their combinatorial and respective role in establishing a pentaradial bodyplan. Finally, I will investigate how the genome plasticity of echinoderms has reshaped their regulatory architecture by combining comparative genomics with HiC to characterise three-dimensional chromatin domains controlling rudiment regulation. We expect to uncover the new regulatory route that has made possible the evolution of a new bodyplan in these mesmerising organisms.