Mapping and Regulation of Allele-Specific Genes During Piglet Development

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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 join the REGLISS team (Regulatory Genomics for Animal Species) at INRAE’s GenPhySE laboratory (UMR 1388), whose primary focus is the regulation of gene expression through the analysis of “-omics” data associated with biological variations of interest. The team consists of 5 researchers and 2 engineers and technicians, and welcomes interns and doctoral students (2 theses in progress).

For this internship, the work will focus primarily on genes exhibiting monoallelic expression, either allele-specific or parent-specific. Using unique samples and datasets obtained as part of the ANR STEM4PIGS and COLOCATION projects, derived from embryonic stem cells (ESCs) and fetuses at two stages of development, you will study the dynamics of these genes of interest during fetal development in piglets.

The internship will therefore focus on the analysis of RNA-seq data from approximately 90 ESC lines and 110 placentas, all derived from reciprocal crosses between the Large White and Meishan breeds. These datasets allow us to study gene expression as well as the parental origin of expression through the identification of genetic variants—primarily SNPs—located within the transcripts. For this reason, it is necessary to combine these data with genomic data from each individual and its parents in order to identify the parental origin of the genetic variants present in each individual and to distinguish genes exhibiting allele-specific expression from those exhibiting monoallelic expression of parental origin.

The goal of the internship is to identify genes that are allele-specific or subject to parental imprinting, and then to analyze their variation across different tissues and stages of gestation. The internship will also involve characterizing the gene networks involved and their associated biological functions.

Training and skills

 Recommended training: Master 2

Knowledge required: 

- Knowledge of omics data (genomics, transcriptomics, epigenomics)

- Ability to work on a computing cluster and in R using tools such as RMarkdown

- Ability to conduct a literature review of computational tools

- Knowledge of version control tools (GitHub)

- Interest in developing reusable and interoperable analysis pipelines

- Attention to detail, independence, organizational skills, and a passion for teamwork

How to apply

I send my CV and my motivation letter