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Integrative Biology of Marine Organisms
UMR 7232

Research projects

AnimalCellulose (2021-2023)



Tunicates are characterized by a unique feature: they are the only animals that produce cellulose. This capacity, restricted to plants, fungi and bacteria, has appeared through the acquisition of a cellulose synthase gene by horizontal transfer. Cellulose is key in ascidians since it is the major component of the tunic, an acellular exoskeleton-like structure secreted by the epidermis that surrounds the animal both in the adult and in the tadpole larva. The goal of our project is to use the knowledge on molecular patterning of the epidermis during embryogenesis as an entry point to uncover mechanisms controlling tunic production and 3D morphogenesis by extracellular material.
This project is financed by Sorbonne Université within the frame of the Emergence program.


AscidianDiversity (2020-2021)



Our team belonging to a marine station, we ambition to establish novel ascidian species as models for experimental molecular embryology. We aim at comparing, with the reference species Ciona intestinalis, the cellular and molecular mechanisms regulating embryonic development. We are working at generating resources (transcriptomes, genomes...), methods (in situ hybridization, electroporation...), and data (expression patterns, cis-regulatory elements activity...) for several local species. This project is supported by the CNRS (INSB) in the frame of the Diversity of Biological Mechanisms call.



VentralPNS (2018-2021)



While vertebrate peripheral nervous system (PNS) exclusively arises from dorsal structures (neural crest and placodes), a large part of invertebrate chordate (ascidians and amphioxus) PNS originates from the ventral ectoderm. BMP signals induce a neurogenic field from which sensory neurons are selected by Notch signaling. This ventral PNS (vPNS) likely corresponds to an ancestral chordate structure that may have been lost in vertebrates or shifted dorsally to form placodes/neural crest, possibly via co-option of ancestral specification mechanisms. Our project aims at exploring functionally the ventral PNS using both groups of invertebrate chordates as references. We will perform a thorough side-by-side comparison to 1) identify vPNS genes, 2) define their hierarchy and transcriptional regulation, 3) determine whether their mode of regulation is conserved and 4) probe the existence of vertebrate counterparts for either a vPNS territory, vPNS neurons or vPNS gene regulatory networks.

This ANR funded project is a collaboration with two other teams from the BIOM:

- Group E1 Evolution and Development of Chordates led by Hector ESCRIVA and Stéphanie BERTRAND (amphioxus)

- Group E3 Development and evolution of vertebrates led by Sylvie MAZAN (catshark and lamprey)


ChorMedFin (2012-2015)



Ciona larval tail epidermis is characterized by a crystal-like cellular organization of only 8 rows of cells, each endowed with a specific expression profile. We have uncovered key events that establish this patterning and control the formation of two derivatives along the midlines: the peripheral nervous system (composed of epidermal sensory neurons) and the median fin. This latter structure is a fascinating case of morphogenesis without cells. The tunic surrounding the larva is formed by the secretion of extracellular material (including cellulose) extending along the ventral and dorsal midlines to form the fin blades. We have proposed that the tail epidermal neurons and the fin may have common origins with vertebrate structures, the neural crest and/or placodes and the median fin, respectively.

In order to get insights into the formation and evolutionary history of the median fin and peripheral nervous system in chordates, we propose to:

1) Reconstruct the GRN in Ciona. Regulatory interactions among the members of the network (around 30 genes) and their functions will be determined using gain- and loss-of-function experiments (by electroporation and morpholinos injection). In order to discriminate between direct and indirect interactions, functional cis-regulatory DNA responsible for the specific expression of each factor of the network will be identified. To accelerate the definition of minimal functional elements, we will search for clusters of binding sites for the relevant interacting transcription factors in conserved non-coding genomic DNA (between the two sequenced Ciona genomes). The predicted DNA fragments from both Ciona species will be tested in C. intestinalis.

2) Describe the development of the equivalent structures and uncover their specification in other basal chordates. Species at gradually increasing phylogenetic distances for which genome has been sequenced have been selected (an ascidian Phallusia mammillata, a basal tunicate Oikopleura dioica and the amphioxus Branchiostoma lanceolatum). A cellular and molecular description will be performed and will allow assessing the involvement of signaling pathways (FGF, BMP, Nodal and Notch) shown to be important in Ciona, using pharmacological inhibitors and recombinant proteins.

3) Test GRN conservation. First, the expression patterns of the key players identified in the Ciona network will be determined in these basal chordates. Then, the cis-regulatory elements controlling conserved expression patterns will be tentatively predicted in these species using the regulatory logic learned in Ciona. Finally, cross-species enhancer activity will be used to evaluate the conservation of the transcriptional logic.

The  ChorMedFin (Chordates Median Fin: Gene regulatory networks controlling median fin formation in basal chordates) project has been funded by the ANR.



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