PhD defences at IPS2 during fall/winter 2022


Molecular basis of 3D chromatin organization in Arabidopsis and tomato during development and in response to heat stress

Keywords: Chromatin organization; Polycomb; H3K27me; HSFA1a; promoter-enhancer interactions

My thesis aimed to decipher the role of chromatin dynamics during plant development and response to the environment. I first worked on Arabidopsis to study the impact and involvement of H3K27me3- repressive covalent histone modification marks during plant development. Our results demonstrate that nuclear organization dynamics shape the transcriptional reprogramming, pointing at H3K27me3 as a key feature for the co-regulation of distant genes. I additionally worked on tomato to study the molecular basis of the re-organization of chromatin in response to an heat stress. Our findings elucidate the complexity of distal and proximal Regulatory Elements contact loop formation and reveal the key role of specific transcription factors in controlling transcriptional responses through the 3D reconfiguration of the chromatin structure.

Defense date: October 4, 2022

PhD supervisor: M. BENHAMED

Clément PICHOT

Identification and functional characterization of regulatory elements of genes controlling sex determinism in melon

Keywords: Cucumis melo L.; Flower; Regulatory element; Epigenomics

Flowering plants developed several biological strategies to increase genetic diversity and prevent self-fertilization. Through sex determination processes, unisexual flowers can develop on the same plant (monoecy) or on separate individuals (dioecy). In Cucumis melo, most flowers are male, with female flowers developing only on the first nodes of branches. The objective of my thesis was to study the cis- and trans-regulatory elements orchestrating the establishment of sexual programs. The proposed strategy was based on the analysis and integration of -omics data in bulk or at cellular resolution. Firstly, we assembled and annotated the melon genome. Secondly, we introduced the EgaCIP automated pipeline, a resource for analyzing -omics data using machine learning approaches. Finally, we developed the SAPTiCon automated pipeline, a resource for analyzing single cell/nucleus RNA-seq data.

Defense date: October 24, 2022

PhD supervisor: M. BENHAMED


Characterization of gene-proximal cis-regulatory sequences in plants

Keywords: cis-regulatory sequences; transcription; bioinformatics

Gene transcription is an essential process in the adaptive response of plants to environmental stresses. Cis-regulatory sequences are short DNA sequences that modulate the expression of target genes. Although numerous experimental and bioinformatic studies have advanced our knowledge of cis-regulatory sequences in the proximal regions of genes, their characterization still needs to be refined. In this context, this thesis summarizes the work done to better understand the structure and function of cis-regulatory sequences present in the gene-proximal regions by detecting short preferentially located DNA sequences in these regions. This thesis has characterized new putative cis-regulatory elements in plants and identified candidate sequences involved in the common stress response in Arabidopsis thaliana for which experimental validations have been initiated.

Defense date: December 14, 2022

PhD co-supervisors: M-L. MARTIN (IPS2) and S. COUSOL (IJPB)


PhD defences at IPS2 during fall/winter 2022