PhD position OT-29020
PhD on chromosome folding dynamics during stem cell differentiation in bovine
31320 CASTANET TOLOSAN
INRAE presentation
The French National Research Institute for Agriculture, Food, and Environment (INRAE) is a major player in research and innovation. It is a community of 12,000 people with 272 research, experimental research, and support units located in 18 regional centres throughout France. Internationally, INRAE is among the top research organisations in the agricultural and food sciences, plant and animal sciences, as well as in ecology and environmental science. It is the world’s leading research organisation specialising in agriculture, food and the environment. INRAE’s goal is to be a key player in the transitions necessary to address major global challenges. Faced with a growing world population, climate change, resource scarcity, and declining biodiversity, the Institute has a major role to play in building solutions and supporting the necessary acceleration of agricultural, food and environmental transitions.
Work environment, missions and activities
You will be welcomed at the GenPhySE Joint Research Unit (https://genphyse.inrae.fr/) at the INRAE Occitanie-Toulouse Center, specifically within the GENOME3D team, which studies chromosome folding of animal genomes.
This PhD project aims to better understand the three-dimensional organization of animal genomes, and more specifically the dynamics and formation of nuclear compartments.
DNA, which carries genetic information, is folded within the cell nucleus. The genome is organized into two main nuclear compartments that are linked to gene expression and therefore potentially involved in the establishment of phenotypes. However, the causal relationship between nuclear compartments and gene expression remains unclear, and the molecular mechanisms that form and maintain nuclear compartments have not yet been elucidated.
In the first aim, we hypothesize that differences in nuclear compartmentalization between individuals during development play a role in the establishment of phenotypes. The variability of genome organization in wild-type bovine embryonic stem cells and those carrying mutations associated with a specific phenotype, the polled phenotype, will be studied during stem cell differentiation.
The second aim will study the molecular mechanisms underlying the formation of nuclear compartments. To this end, a nuclear compartment will be artificially created by recruiting a histone mark to a specific genomic region. The maintenance of the nuclear compartment will be studied throughout cell cycles and differentiation.
Overall, this research will deepen our understanding of the molecular mechanisms underlying the formation and maintenance of nuclear compartments, as well as provide greater insight into the role of nuclear compartmentalization in the establishment of phenotypes.
You will be in charge of:
- Cell culture experiments including bovine embryonic stem cell differentiation.
- Molecular biology experiments to study the chromatin (Hi-C, ChIP-seq, ATAC-seq, RNA-seq).
- Molecular cloning and cell culture experiments to create an artificial nuclear compartment.
- Bioinformatics analysis of the data you obtained.
This thesis is funded by the ANR JCJC DYNAMENT grant awarded to Anne-Laure Valton (https://anr.fr/Projet-ANR-25-CE20-3837)
Training and skills
Recommended training: Molecular Biology, Genomics, Genetics, Cell Biology
Knowledge required: A solid foundation in Molecular Biology and Genomics
Appreciated experience: Cell differentiation, cell culture, bioinformatic analysis of genomic data
Skills sought: If you have no experience in bioinformatics: a willingness to learn how to perform bioinformatics analysis of the data obtained in the project, strong writing and presentation skills for scientific results, and strong organizational skills.
INRAE's life quality
By joining our teams, you benefit from (depending on the type of contract and its duration):
- up to 30 days of annual leave + 15 days "Reduction of Working Time" (for a full time);
- parenting support: CESU childcare, leisure services;
- skills development systems: training, career advise;
- social support: advice and listening, social assistance and loans;
- holiday and leisure services: holiday vouchers, accommodation at preferential rates;
- sports and cultural activities;
- collective catering.
How to apply
I send my CV and my motivation letter
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