Mots-Clés
transcription factors, DNA binding, modeling, genetic variants, plant domestication
Description
PhD Opportunity in Bioinformatics: Transcription factor DNA-binding models and their use to explore the genetic basis of plant domestication
Context
We are offering a PhD position within the Flo_Re (Floral Regulators) team at the Laboratoire de Physiologie Cellulaire et Végétale (LPCV), situated at the CEA Grenoble site. The Flo_Re team specializes in studying the developmental program leading to flower formation, with a specific focus on the function and evolutionary history of key regulators, predominantly transcription factors (TFs).
Objective
This project aims to enhance our understanding of transcription factors DNA binding modes and their variations across different families and classes 1. We will achieve this by developing and comparing TF binding site (TFBS) models using genomic data2,3, such as ChIP-seq and DAP-seq, which are available for numerous TFs in the model plant Arabidopsis thaliana.
Another key objective is to leverage these models and our knowledge of DNA-binding properties to gain insights into the molecular basis of plant domestication. Previous studies have shown that genetic changes during domestication primarily occur in regions that regulate the expression of unchanged coding sequences4. Notably, these changes often impact the DNA-binding sites of TFs. To explore this further, we will utilize our advanced TFBS models to annotate genetic variants associated with agronomic traits, starting with cabbage5.
Prerequisites
Proficiency in programming languages such as Bash, R, or Python.
Interest in plant biology.
Strong teamwork abilities.
Effective communication skills for presenting results and discussing challenges.
Prior experience in working with genome-wide sequence data is advantageous.
Practical Information
The PhD position is a 36-month contract starting from October 2023 or later.
You will be supervised by:
Romain BLANC-MATHIEU (CEA Researcher-Engineer)
François PARCY (CNRS Research Director and head of the Flo_Re team)
To apply, please send an email to romain.blancmathieu@cea.fr , including your CV and a brief description of your motivations.
References
1. Blanc-Mathieu, R., Dumas, R., Turchi, L., Lucas, J. & Parcy, F. Plant-TFClass: a structural classification for plant transcription factors. 2022.11.22.517060 Preprint at https://doi.org/10.1101/2022.11.22.517060 (2022).
2. Lai, X. et al. Building Transcription Factor Binding Site Models to Understand Gene Regulation in Plants. Mol. Plant 12, 743–763 (2019).
3. Lai, X. et al. The LEAFY floral regulator displays pioneer transcription factor properties. Mol. Plant 14, 829–837 (2021).
4. Swinnen, G., Goossens, A. & Pauwels, L. Lessons from Domestication: Targeting Cis-Regulatory Elements for Crop Improvement. Trends Plant Sci. 21, 506–515 (2016).
5. Guo, N. et al. Genome sequencing sheds light on the contribution of structural variants to Brassica oleracea diversification. BMC Biol. 19, 93 (2021).