Dear colleagues, 

Thank you for bringing this offer to the attention of potential PhD candidates. Montpellier is a fantastic city for combining systems biology and evo-devo approaches. Candidates should directly contact me with a CV and a letter of motivation before applying to the University of Montpellier doctoral school in health science and the EpigenMed international PhD program.

Best wishes, 

Patrick

PhD project on the evolutionary plasticity of the architecture of ascidian developmental Gene Regulatory Networks

Tunicate team, CRBM, CNRS, Montpellier, France
Our group is studying the evolution of the embryonic development of ascidians, a clade of invertebrate chordates closely related to vertebrates. For this, we are comparing the embryonic development of two species from different genera, Ciona intestinalis and Phallusia mammillata. These two animals diverged over 300 million years ago, yet they develop with the same invariant cell lineages and very similar morphologies (1). This exceptional conservation of morphogenetic programs contrasts with rapid genome divergence. The Ciona and Phallusia genomes are so divergent that non-coding sequences of orthologous genes can no longer be aligned. Ascidians thus provide a unique opportunity to understand how a morphogenetic program can be conserved over long periods of time in spite of extreme genome sequence drift.

The proposed project will focus on the evolution in Phallusia of the early developmental Gene Regulatory Network (GRN) that, in Ciona, leads to the specification of most tissue fates by the onset of gastrulation (2). We will first test the impact of genome sequence divergence on the expression profiles of the transcription factors and signaling ligands of this network. This will reveal whether homologous cells in early Ciona and Phallusia embryos share common regulatory states (i. e.  express the same combinations of transcription factors) and cell signaling events. We will then explore the conservation of the regulatory links between transcription factors and signaling ligands. For this, existing ChIP-seq data in both species and other cis-regulatory signatures (3) will be combined to identify the cis-regulatory sequences driving the expression of these transcription factors in both species. We will test whether cis-regulatory activity is conserved in cross-species transgenic experiments, and study how conservation/divergence of activity relates to the evolution of their sequences. Overall, this project will thus explore the level of regulatory network plasticity that is compatible with morphological stability over long periods of time.

Applicants with suitable qualifications should contact before March 10 the PhD supervisors, Patrick Lemaire ([log in to unmask]) and Jacques Piette ([log in to unmask]) with a CV, a letter of motivation, and the names of two referees. Candidates with a biology degree and some computational skills, or the desire to acquire them, will be given preference. A good command of English is expected. Knowledge of French is not required. The 3-year position is funded by the health science doctoral school of the University of Montpellier (ecole-doctorale-CBS2.igh.cnrs.fr) and the Epigenmed International PhD program (www.epigenmed.fr). Deadline for application to the doctoral program is March 15, 2013. 

References:  1) Lemaire, P. Evolutionary crossroads in developmental biology: the tunicates. Development 138, 2143–2152 (2011). 2) Imai, K. S., Levine, M., Satoh, N. & Satou, Y. Regulatory blueprint for a chordate embryo. Science 312, 1183–1187 (2006). 3) Khoueiry, P., Rothbächer, U. Frangulian, E. Daian, F. Roure, A. Dubchak, I. and Lemaire, P. (2010) A cis-regulatory signature in ascidians and flies, independent of transcription factor binding sites. Current Biology, 20(9):792-802.

Patrick Lemaire
CRBM
1919 Route de Mende
34293 MONTPELLIER Cédex
http://www.aniseed.cnrs.fr/lemaire/
email: [log in to unmask]