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PhD position available in Raphaël Pantier's lab

PhD project:
Interplay between transcription factors and genome architecture in embryonic stem cellss

Abstract :
Transcription factors are key molecular determinants of cellular identity during development
and in human diseases. They interpret our genome via recognition of specific DNA sequences,
resulting in target genes being switched ‘on’ or ‘off’. Our recent research revealed a new type
of gene regulation based on sensing of A/T nucleotide content (Pantier et al, 2021). In
particular, the transcription factor SALL4 binds to short AT-rich motifs on the genome, and its
function is essential for stem cell identity in vitro and embryonic development in vivo.

In this PhD project, you will exploit state-of-the-art genomics techniques in genetically
engineered mouse embryonic stem cells to dissect the molecular function of SALL4: regulation
of transcription via long range enhancer-promoter looping (1), regulation of 3D genome
structure via modulation of lamina-associated domains (2). These investigations will help us
better understand how transcription factors interact across different genomic scales in order to
control cell identity.

Reference
IGBMC / PhD-Pantier

Contract type
PHD

Publication date
07/22/2026

We are seeking a highly motivated and enthusiastic individual to join our research group at IGBMC. Our overall aim is to better understand how cellular identity is determined at the molecular level, using embryonic stem cells as a model system. We combine genetic engineering, genomics, biochemical and cellular assays to dissect the function of important transcriptional and epigenetic regulators both in physiological and pathological conditions.

In this PhD project, you will exploit state-of-the-art genomics techniques to dissect the molecular function of the transcription factor SALL4 in embryonic stem cells: regulation of transcription via long range enhancer-promoter looping (1), regulation of 3D genome structure via modulation of lamina-associated domains (2). These investigations will help us better understand how SALL4 controls embryonic development, and how this protein is de-regulated in developmental disorders and aggressive cancers. More generally, this work will clarify how transcription factors interact across different genomic scales to regulate cell identity. Additional information regarding the PhD project is available here:https://amethis3.unistra.fr/amethis-client/prd/consulter/offre/1125

 

You will benefit from a supportive and collaborative work environment to carry out your research. The Institute of Genetics Molecular and Cellular Biology (IGBMC) includes a diverse and international scientific community and hosts a large range of state-of-the-art facilities including genomics, bioinformatics, proteomics, microscopy, flow cytometry and cell culture.

 

Relevant publications:

  1. Chhatbar et al., bioRxiv (2025): https://doi.org/10.1101/2025.11.14.688441
  2. Giuliani et al., bioRxiv (2025): https://doi.org/10.1101/2025.10.27.684836
  3. Pantier et al., Mol Cell (2021): https://doi.org/10.1016/j.molcel.2020.11.046

 

Keywords: stem cells, transcription, genome architecture, transcription factors, SALL4, CRISPR/Cas9 engineering, next-generation sequencing

Application procedures

The PhD position is fully funded (3 years) and available from October 2026.

Please send a complete application including CV (1), cover letter (2), and contact details of at least one referee (3) by email to Raphaël Pantier (pantierr@igbmc.fr). Candidates can also contact the laboratory for additional information regarding the research project.

Related to :

Profil

- Recently obtained Master degree in genomics, molecular biology or other relevant discipline.

- Strong motivation to work in the field of gene regulation and chromatin biology.

- Good handling of standard molecular biology techniques.

- Prior experience in generating or analysing genomics data would be desirable, but not mandatory.

- English language proficiency (B2 or higher).