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Goals and candidate profile
The thesis topic is to understand the role of chromatin structure and modifications in the spatiotemporal dynamics of genome replication in the yeast S. cerevisiae. This multidisciplinary project will rely on molecular biology, bioinformatics, and physico-mathematical analysis. Ideally, the candidate will have an interdisciplinary profile combining a training in these three domains. Monodisciplinary profiles of good level are also acceptable. According to his/her competences and interests, the candidate will contribute to the experiments, to signal analysis and artificial intelligence and/or to mathematical modelling. Prior experience with nanopore sequencing will be appreciated but is not a prerequisite. Please go to http://bit.ly/2PbwJlb to officially apply.
Detailed description of the research project
The general goal of the laboratory is to understand the spatiotemporal program of genome replication of eukaryotic cells. This program ensures the faithful transmission of genetic information at each cell division. Its perturbations are implicated in cancer and other diseases. Understanding this program requires to determine the position, efficiency and activation time of replication origins, the speed of replication fork progression, and the cell-to-cell variability of these parameters, along the whole genome.
DNA replication takes place in the context of chromatin. Nucleosomes, formed by the wrapping of 147 bp of DNA around histone octamers, restrict the access of replication proteins to DNA. During replication, nucleosomes are disassembled to allow the recruitment and progression of the replication machinery and reassembled in the wake of the replication fork. The affinity of DNA to nucleosomes can therefore affect both origin firing and fork progression. Many reversible modifications of the histones (acetylation, methylation, etc.) can modify this affinity or facilitate the recruitment of specific regulatory factors. However, we still know little about the role of histone modifications in DNA replication regulation.
We recently developed in the yeast S. cerevisiae a revolutionary method to map DNA replication at the single molecule level at high throughput, based on nucleotide analog incorporation during replication and detection by nanopore sequencing. This approach allows to simultaneously obtain the replicative status and the nucleotide sequence of long (10 kb - 1,000 kb) DNA molecules, and thus to quantify replication initiation, elongation and termination, molecule by molecule, over the whole genome.
This thesis project will take advantage of this novel methodology to understand the role of specific histone modifications in replication fork propagation in S. cerevisiae. Besides biological experiments, relying on specific mutant strains deficient in chromatin regulators and modifiers, or carrying point-mutated histone alleles, the project will necessitate the development of novel bioinformatic, machine learning and mathematical modelling tools for analysis of nanopore sequencing signals. The results will allow to determine the rate of origin activation and the distribution of replication fork speeds genome-wide, in the mutant and wild-type strains, and the effect of these mutations on genome stability. The methodology will then be applied to the human genome.
1. Hennion M, Arbona JM, Cruaud C, Proux F, Le Tallec B, Novikova E, Engelen S, Lemainque A, Audit B, Hyrien O (2018) Mapping DNA replication with nanopore sequencing. BioRxiv, Sep 25, 2018, doi: 10.1101/426858.
2. Petryk N, Kahli M, d'Aubenton-Carafa Y, Jaszczyszyn Y, Shen Y, Sylvain M, Thermes C, Chen CL, Hyrien O (2016) Replication landscape of the human genome. Nature Comm., 7, 10208. doi: 10.1038/ncomms10208.
3. Bar-Ziv R, Voichek Y, Barkai N. (2016) Chromatin dynamics during DNA replication. Genome Res. Sep;26(9):1245-56. doi: 10.1101/gr.201244.115.
Research will be conducted at the Institut de Biologie de l'Ecole Normale Supérieure (IBENS; https://www.ibens.ens.fr/), in the heart of the Latin quarter in Paris, a top scientific and intellectual environnement. Brief visits to collaborating teams in Lyon and Tel-Aviv are to be planned (2-3 per year). The doctoral contract will be managed by the Centre National de la Recherche Scientifique (CNRS), the main scientific research agency in France. The successful candidate shall be enrolled on a PhD program of the CdV doctoral school.
The candidate must have a Master and/or degree in engineering at the time of recruitment. Applications must include a detailed CV; at least two references (people who may be contacted); a one-page cover letter; a one-page résumé of laboratory internships; grades for the Master or the engineering degree. Informal enquiries can be sent to email@example.com. To officially apply please go to http://bit.ly/2PbwJlb.