PhD position: Single-cell elucidation of the evolution of an embryonic transcriptional programme
Posted by Patrick Lemaire, on 3 April 2018
Closing Date: 15 March 2021
The project:
Single-cell approaches are revolutionizing developmental biology. We can now trace in time the behavior of each cell in a live developing organism (1). In parallel, single-cell transcriptomics and genomics gives access to the transcriptional state of each cell (2). Combination of these two approaches promises to unravel how genomic information translates into individual cell behaviours.
We are harnessing these approaches to the embryos of ascidians (Tunicates, 3,4), a group of marine invertebrate chordates. These embryos develop with such stereotyped cell lineages that each cell of an embryo of one species has an exact homolog in all embryos of different, even distantly related, species. Contrasting with this extraordinary morphological conservation, the genomes of ascidians are widely divergent.
We are looking for a PhD student, who will study how the transcriptional program of homologous cells has evolved between distantly related tunicate species. She/He will focus on two classes of genes, those building the gene regulatory networks (GRN) driving development and the effector genes controlling cell behaviours through their action of cytoskeletal architecture.
The selected student will first establish single-cell RNA-seq for a range of developmental stages in 4 ascidians and 2 thaliaceans (a different class of tunicates, 5). From this dataset, She/He will analyse the level of conservation of the transcriptional programme across species, which could lead to a classification of genes/subnetworks according to their level of expression conservation. In a second step, she/he will select a few genes based on their pattern of expression conservation and their functional annotation and study their function in cell fate specification or embryonic morphogenesis using CRISPR/Cas9 technology.
The project is mostly experimental. Bioinformatics knowledge or a desire to acquire it will be a plus. More about the host group and institute can be found on the CRBM website: http://www.crbm.cnrs.fr/.
Collaborations with the Christiaen (NYU, New-York, USA), Zinzen (MDCC, Berlin, Germany) and Aerts (KU, Leuven, belgium) labs are foreseen.
2) Karaiskos N, Wahle P, Alles J, Boltengagen A, Ayoub S, Kipar C, Kocks C, Rajewsky N, Zinzen RP (2017) The Drosophila embryo at single-cell transcriptome resolution. Science. 358:194-199
3) Lemaire P. (2011) Evolutionary crossroads in developmental biology: the tunicates, Development, 138(11):2143-52.
4) Lemaire P. (2009) Unfolding a chordate developmental program, one cell at a time: Invariant cell lineages, short-range inductions and evolutionary plasticity in ascidians. Developmental Biology ;332(1):48-60.
5) Piette, J. and Lemaire, P. (2015) Thaliaceans, the neglected pelagic relatives of ascidians: a developmental and evolutionary enigma. The Quarterly Review of Biology. 90(2):117-145.
How to apply?
Interested candidates are encouraged to contact Patrick Lemaire (patrick.lemaire@crbm.cnrs.fr) directly prior any formal application to the Life Science doctoral school in Montpellier (Deadline for application May 18th 14:00, French time).
►Criteria to apply to the call
The contest for a doctoral contract is open to all candidates regardless of their nationality and institutions of graduation.
Twenty-four 3-year doctoral positions will be funded by the doctoral school
To be eligible, candidates must hold a Master’s degree (or diploma recognized as equivalent to a Master’s degree).
►Timeline for the 2018 campaign (All times are in Paris time zone.)
- 18th May 2018 at 14:00. Deadline for submission of applications
- 4th June: short listing of candidates
- 28th and 29th June 2018. Interviews of shortlisted applicants (video-conference for distant applicants should be possible)
►Application file
The doctoral school website is: http://www.adum.fr/as/ed/page.pl?site=cbs2&page=concoursed
Applications (single pdf file) should include the following documents:
- A cover letter and CV, including academic background and professional experience, in particular internships accomplished as part of the study program.
- Copies of diplomas. It is mandatory to hold a Masters degree by the beginning of the 2018/2019 academic year).
- Academic transcripts of all courses taken as part of university degrees *.
- At least two letters of recommendation. Referees are expected to explain how they have known the candidate, their frank evaluation of his/her capability and motivation to undertake a Ph.D., as well as of his/her creative and analytical skills. It is recommended that referee rank the student among all students they mentored (Top 5%, 10%, 20%).
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