Thesis by Elise Jorge (GenPhyse, 2023-2025)

Comparative analysis of 3D genomics data

Thesis by Elise Jorge (GenPhyse, 2023-2025). This thesis, at the interface between statistics, molecular biology and functional genomics, seeks to develop a differential analysis method for Hi-C data to identify regions in the 3-D genome structure where modifications occur.

  • Accredited thesis 
  • Starting date : november 2023
  • Research unit :  GenPhySE (Genetics Physiology and Breeding Systems)
  • Thesis director : Sylvain Foissac (bioinformatique & génomique, GenPhySE, département GA)
  • Supervisors : Nathalie Vialaneix (statistique, MIAT, département MathNum)
  • Metaprogramme axis : axis 1 (Deciphering the functions of living matter at multiple scales: regulation and integration of biological processes) and axis 2 (Predicting phenotypes and their responses to changes in stress fields)

Summary :

The three-dimensional conformation of the genome has a major impact on its functioning, with important implications for fetal development, cell differentiation and disease development. Hi-C technology produces DNA sequencing data that aims to profile this three-dimensional conformation.

The objective of this thesis is :

  1. to develop a method for differential analysis of Hi-C data that can identify regions of modification in the 3D genomic structure
  2. to use this method to characterize differences between tissues or stages of gestation in data produced by targeted animal genome characterization projects (FR-AgENCODE pilot project of the international FAANG initiative, H2020 GENE-SWitCH project and data from the article (Marti-Marimon et al, 2021)).
Photo de Elise Jorge © INRAE

Contact :

 

(1) Maria Marti-Marimon, Nathalie Vialaneix, Yvette Lahbib Mansais, Matthias Zytnicki, Sylvie Camut, et al.. Major reorganization of chromosome conformation during muscle development in pig. Frontiers in Genetics, 2021, 12, pp.19 P. ⟨10.3389/fgene.2021.748239⟩⟨hal-03367056⟩

See also