Funded Interdisciplinary PhD Fellowship starting October 2025
Title : Capturing DNA Conformational Landscapes Through Laser Photo-modification and Next Generation Sequencing
The control of gene expression is a complex process in which the sequential sequence of DNA determines not only how it interacts with regulatory proteins, but also how it controls its own local and global structure. In other words, DNA compaction and topology control acces to the transcription machinery, thus dictating not only which genes are expressed, but also to what level. Numerous pathologies are associated with the dysfunction of this process and knowledge of the intricate mechanisms involved is essential for their treatment.
This project proposes a multidisciplinary approach based on ultra-rapid laser photo-modification of DNA and subsequent identification and quantification of the modifications using Next Generation Sequencing (Nanopore). Laser-induced photoactivation results in the formation of cyclobutane dimers between adjacent pyrimidines on a DNA chain. The probability of forming these structures is a function of the local structure of the DNA. By identifying and quantifying the occurrence of these dimers after a single (ns) irradiation one obtains, at one nucleotide resolution, an ’image’ of the local DNA trajectory; taken together over the whole DNA molecule, this provides a database of signal ‘photo-fingerprints’ that when linked with bespoke molecular dynamic models allow mapping of the local organisation of the DNA and thus the overall global topology of the whole polymer. Experiments in vitro on model plasmids have provided large databases of these photo-fingerprints.
The main goal of this project is to extend the in vitro analysis to develop a tool that is capable of characterising DNA in whole cells (prokaryote and eukaryote) and to obtain signature photo-fingerprints in various physiological contexts (supercoiling, chromatin compaction, transcription factors, cell growth phase…) that impact on transcription.
The methodology will combine 1) Analysis of various degrees of supercoiling (in a first instance this will be on model prokaryotic systems) on the photo-fingerprints obtained in transcription contexts, 2) The transition of the photo-modified DNA across the nanopore is associated with a very specific signal, this part of the project will be to fully analyse the nature of this signal and the effects of nearest neighbours of the pyrimidines on the probability of forming dimers. Ultimately this is related to the persistence length of the DNA and provides important knowledge of the local topology of the DNA, 3) Finally, based on the collated data, numerical modelling will be used in a predictive capacity to link specific photo-fingerprints with structural features of the DNA (bending, plectonemes, local melting…).
The candidate will ideally have a background in either biophysics and/or molecular biology or statistical physics with an interest in computational methods.
Competence in programming and data analysis (signal treatment, statistics...) is also required. Some knowledge of structural biology and physical chemistry would be a bonus. Experimental work will involve handling cells and DNA, DNA sequencing (nanopore), high energy lasers and pipetting robotics. Modelling will also require an aptitude for coding. The candidate will be co-directed by physicists and biologists who will ensure that they will receive adequate formation in all relevant subjects.
The funding for this Ph.D is already secured.
Laboratories involved:
Laboratoire Structure, Propriétés et Modélisation des Solides (SPMS; CentraleSupélec, CNRS), Yann Chalopin.
Computational Quantitative and Synthetic Biology (CQSB ; UMR 7238, Inserm 1284), Bianca Sclavi.
Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA), Ecole Normale Supérieure Paris-Saclay, M. Buckle.
Contact: yann.chalopin@centralesupelec.fr