Research teams

Epigenetic Natural Variation

VarEpi 7 members

2026 PhD project proposal: Investigating inter-individual epigenetic variability in Arabidopsis thaliana

 
In animals and humans, some regions of the genome have a highly variable level of DNA methylation between individuals, independently of the DNA sequence. Variable methylation regions (VMRs) are distributed non-randomly in the regulatory regions of genes whose functions are associated with developmental plasticity. The degree of methylation of part of the VMRs is thought to be determined during the early stages of embryonic development, prior to differentiation, and could therefore be a missing link in the mechanisms of memory of early exposures known to contribute to the developmental origins of health and disease. In plants, epigenetic variability is strongly structured by geography and climate and contributes to short- and medium-term evolutionary processes. However, the degree of inter-individual variation has never been studied directly, meaning that this potential mechanism for memorising early exposures remains unexplored in plants.

The aim of the thesis project is to highlight VMRs in the model plant Arabidopsis by studying the leaf methylome of a large number of isogenic individuals grown under homogeneous conditions. An in-depth characterisation of VMRs (methylation context, genomic distribution, function of associated genes, etc.) will be carried out. Using two stress protocols applied during the seed stage and to developping seedlings, the project will aim to investigate the influence of the early environment on the methylation status of VMRs. The relationship between VMRs and gene expression and chromatin structure will be investigated using genome-wide approaches. The PhD student will have access to a collection of mutants, ecotypes and epigenetic recombinant lines (epiRIL) to explore the status of VMRs using targeted approaches. Epigenome editing may be used to validate the function of VMRs of interest. Finally, the transmission or non-transmission of methylation status will be studied in the offspring in order to assess the stochastic or heritable nature of the phenomenon.
 


_____________________________________________________________________________________________________________________

Ingénieur d'Etude - Saclay Plant Sciences - Position now Open

One position (Ingénieur d’Étude, 18 months) in bioinformatics/biostatistics (M/F)

The Saclay Plant Sciences network (SPS) gathers around 55 research teams specialized in plant sciences belonging to 5 institutes in the Saclay area (south west of Paris) and represents about 700 people. The current research activities of the SPS partners concern the genetic, molecular and cellular mechanisms that control plant physiology and development, as well as their interactions with fluctuating biotic or abiotic environments. These studies extend from the gene to the entire plant, and use the concepts and tools of biochemistry, biophysics, imaging, molecular biology, genetics, cell biology, modelling and bioinformatics. Data analysis and research in bioinformatics and bio-statistics is currently carried out by 25 permanent bio-informaticians and statisticians in the 5 institutes.

SPS is recruiting one bioinformatician “Ingénieur.e de Recherche” to participate and manage the SPS-Bioinformatics Analysis and Research Support (SPS-BARS), a bioinformatics service composed of 3 bioinformaticians (including the IR) that provides support activities to the SPS research community and takes over the increasing requests for the analysis of biological data. The recruited engineer will be allocated for a large part of her/his time to Research Units to work on specific projects. These projects are validated by the SPS bioinformatics committee which is composed of bioinformaticians and biologists from SPS. Teaching missions (academic and/or professional education) may also be requested.

Tasks and responsibilities

The main mission is to provide support to Research Units for the bioinformatics and/or biostatistics analysis of their data. This support includes:
- advising and guiding the implementation of methods and tools for the analysis of biological data,
- maintaining an active bibliographic survey and evaluating published tools and methods,
- developing, when necessary, new analytical methods and tools,
- analyzing data in collaboration with the Units,
- ensuring the transfer of tools and expertise to the Units,
- delivering training courses in bioinformatics and biostatistics,
- maintaining the methods and tools developed by the Units, and ensuring their integration into core software solutions like Snakemake or Nextflow.

The additional mission will be the management of the SPS-BARS through
- the daily interactions and supervision of the other engineers of the service,
- the organization of the SPS bioinformatics calls and training sessions,
- the interactions with the SPS bioinformatics committee.

Job profile

Several needs have been identified and some of the following skills are expected:
- Analysis of HTS data (variant calling, genome assembly, differential expression, epigenomics...),
- Analysis of metabolomic data,
- Analysis of proteomic data,
- Analysis of imaging data,
- Data integration

Duration:
Funds are available for 18 months.

Salary:
The engineer will be recruited by INRAE. Depending on the previous experience, the gross salary will range from 2300€ to 2900€ for the IR position (net salary between 1900€ and 2400€).

Candidate profile and conditions

The candidate is expected to have a PhD or an engineer degree in bioinformatics, statistics, applied mathematics or a related field. Teaching experience in bioinformatics/biostatistics will be appreciated.

SPS is committed to foster gender equality, so female candidates are encouraged to apply.

To apply

Applications (cover letter, detailed CV and 2 reference letters) should be sent to etienne.delannoy[at]inrae.fr and nicolas.bouche[at]inrae.fr.

Epigenetic Natural Variation

Leader:

Nicolas Bouché
Contact us
Back