PhD Fellowship in Developmental Biology

Analysis of the regulatory landscapes associated with Nodal and BMP signaling by Assays for Transposase Accessible Chromatin (ATAC-Seq)

A three-year PhD position supported by the French Foundation for Medical Research (FRM) is available  to work in the group Gene regulatory networks, axis specification and morphogenesis of the sea urchin embryo at the Institute of Biology Valrose in Nice.
The area of research will concern the analysis of transcriptional regulation downstream of Nodal and BMP2/4 signalling in the sea urchin embryo (see Lapraz F, Haillot E, and Lepage,T – 2015 – A deuterostome origin of the Spemann organiser suggested by Nodal and ADMPs functions in Echinoderms; Nature communications and Molina MD, Quirin M, Haillot E, De Crozé N, Range R, Rouel M, Jimenez F, Amrouche R, Chessel A, Lepage T- MAPK and GSK3/ß-TRCP-mediated degradation of the maternal Ets domain transcriptional repressor Yan/Tel controls the spatial expression of nodal in the sea urchin embryo- PLOS genetics  2018 Sep 17;14(9).

Project description:

The Nodal and BMP members of the TGF-beta family of morphogens play key roles during embryonic development and homeostasis but how cells read these gradients of morphogens and how they interpret them at the level of the promoter sequence of the target genes is not well understood.  Our laboratory has recently generated data of chromatin accessibility in wild type embryos at different developmental stages and following over-activation or inhibition of the Nodal and BMP2/4 pathways by ATAC-seq. In addition, we have recently obtained a high-quality genome assembly for the Mediterranean sea urchin Paracentrotus lividus. The availability of these resources as well as the availability of the genome sequence of several sea urchins offers a unique opportunity to investigate the architecture  and the logic of activation of the cis-regulatory modules of Nodal and BMP2/4 target genes.
The postdoctoral project will aim at integrating the results of these ATAC-seq data in the analysis of the dorsal-ventral gene regulatory network of the sea urchin embryo. In particular, the project will focus on identifying,  annotating and validating the cis-regulatory modules of the Nodal and BMP2/4 target genes and on  exploring the regulatory landscapes associated with Nodal and BMP signaling.  Another goal will be to search for conserved motifs within the CRMs of Nodal and BMP target genes and to identify the transcription factors that bind to these conserved motifs. This project offers a unique opportunity to investigate how the Nodal and BMP morphogen gradients are decoded at the level of the cis regulatory modules of their target genes and how chromatin accessibility is modulated during the process of cell fate specification and determination.


Preferably, candidates should have obtained their master degree recently. They should have a training in bioinformatics  and an understanding of  the questions related to cell signalling, cell fate specification  and transcriptional regulation. Both national and international candidates are encouraged to apply. Interested candidates should send a Curriculum Vitae, a summary of research interests and goals and contact information for two referees.

Please apply via :

Starting: The starting date is at the earliest on November 2018

Dr Thierry Lepage :                       Research team webpage