PhD (M/F) Genome organisation and stability

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PhD (M/F) Genome organisation and stability

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Job description

Offer DescriptionScientific environment
The PhD project will be carried out under the supervision of Dr Vincent Vanoosthuyse at the Laboratoire de Biologie et Modélisation de la Cellule (LBMC). This PhD project is funded as part of a scientific consortium led by Philippe Pasero (IGH, Montpellier, France), a pioneer in the study of the impact of DNA:RNA hybrids on DNA replication and genome stability. The consortium also involves Chunlong Chen’s team at the Institut Curie in Paris, which specialises in the spatio-temporal analysis of replication programmes.The LBMC is a leading research institution dedicated to the study of the fundamental mechanisms of cellular biology. We combine experimental approaches in molecular, cellular and genetic biology with mathematical and computer modelling methods to understand the complex processes that regulate cell function.Located on the Monod campus of the ENS-Lyon, the LBMC brings together 115 researchers in 17 research teams. This advantageous location gives us privileged access to all the resources and infrastructures we need to carry out our research missions. In particular, we benefit from cutting-edge expertise in RNA sequencing techniques, as well as access to flow cytometry (SFR Biosciences) and sequencing (IGFL) platforms.
The LBMC offers a dynamic, high-performance working environment. It is home to several teams interested in the organisation and stability of chromosomes during the cell cycle, which facilitates high-quality scientific exchanges. Finally, the LBMC team and Bioinformatics Hub will provide dedicated training and support for the analysis of NGS data.Scientific question and Project
Two fundamental steps underlie the accurate transmission of the genome to daughter cells during the cell-cycle: (i) the faithful replication of DNA in S phase and (ii) the spectacular, condensin-driven reorganisation of sister-chromatids in the following mitosis, which is required for their accurate segregation to daughter cells in anaphase. Although these two essential steps are sometimes separated by several hours, they can influence each other. In particular, problems arising during DNA replication (known as DNA replication stress) can impact condensin function and the structuration and integrity of chromosomes in the following mitosis (for example, see PMID: 32966795). Such chromosome abnormalities in mitosis can contribute to aneuploidy, a hallmark of cancer. How DNA replication stress impinges on the condensin-driven assembly of chromosomes at the next mitosis remains largely unclear and is an important focus of our research.DNA replication stress is characterised by the slowing down of replication forks and their frequent reversal and/or collapse, which increases the likelihood of deleterious DNA damage. Whatever its origin, replication stress often leads to chromosome fragility in metaphase and to chromosome segregation defects in anaphase (such as anaphase bridges or micronuclei for example). Strikingly these collective hallmarks of replication stress can be largely alleviated by the over-expression of RNase H1, a highly conserved enzyme that degrades the RNA moiety of RNA:DNA hybrids. This observation suggests that replication stress disrupts the metabolism of RNA:DNA hybrids in a way that is sufficient to overwhelm the cellular machinery and to trigger a wide range of chromosome abnormalities that can persist until the following mitosis. The population of stress-induced RNA:DNA hybrids with such a strong genome-destabilising impact has not yet been conclusively identified. It is also unclear whether such RNA:DNA hybrids are merely a toxic by-product of DNA&RNA transactions at stressed replication forks that needs to be quickly removed or whether they are a necessary, albeit short-lived, intermediate in a genome-stabilising process. A major objective of our research is to identify and characterise these stress-induced RNA:DNA hybrids and to decipher how they impact chromosome integrity.A better understanding of the genome-destabilising impact of RNA:DNA hybrids requires new tools to quickly manipulate RNA:DNA hybrids in live cells. We have developed an innovative strategy to map and quickly manipulate RNA:DNA hybrids in live human cells. We use Virus-Like Particles to deliver a panel of ready-made regulators and sensors of RNA:DNA hybrids directly into live cells. Our results show that such delivery happens under four hours at physiologically-relevant levels and is quick enough to be compatible with the manipulation and mapping of RNA:DNA hybrids in specific phases of the cell-cycle. The aim of this PhD project is to use these new innovative tools on synchronous populations of human cells in culture to identify and characterise the population of genome-destabilising RNA:DNA hybrids that is triggered upon replication stress in S phase.Techniques used
A wide range of techniques will be used throughout the project: cell culture, cell sorting (FACS), production of Virus-Like Particles, Immunofluorescence and live imaging, Proximity Ligation Assays (PLA), Cut&Tag, DNA:RNA Immunoprecipitation (DRIP), etc… The candidate will be expected to analyse their own NGS data using routine bioinformatics approaches. For this, both the team and the in-house ‘Bioinformatics Hub’ at the LBMC will provide dedicated teaching and support.Where to apply WebsiteRequirementsResearch Field Biological sciences Education Level PhD or equivalentLanguages FRENCH Level BasicResearch Field Biological sciences » Biology Years of Research Experience NoneAdditional InformationAdditional commentsOur little extras :
– A stimulating working environment in close contact with research staff
– 44 days’ holiday / RTT per year
– Partial reimbursement of transport tickets is possible under certain conditions + sustainable mobility package
– A site accessible by public transport
– Financial contribution to health insurance costs
– Access to the CNRS Economic and Social Action Committee after 6 months’ service
– The CNRS is committed to professional equality through a network of correspondents and equal opportunities correspondents. Website for additional job detailsWork Location(s)Number of offers available 1 Company/Institute Laboratoire de Biologie et Modélisation de la Cellule Country France City LYON 07 GeofieldContact CityLYON 07 WebsiteSTATUS: EXPIREDShare this page

Expected salary

Location

Lyon

Job date

Sat, 15 Jun 2024 00:10:25 GMT

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