Keywords: Archaea, DNA topoisomerases, 3C assay Internship Duration: 30/11/-1 - 30/11/-1
Head of the hosting team: Jacques Oberto
Website: Click here
Address of the host laboratory: Institut de Biologie Intégrative de la Cellule (I2BC) Team Biologie Cellulaire des Archées 1 Avenue de la Terasse, bat. 12 91190 Gif sur Yvette France
Supervisor: Tamara BastaE-mail: tamara.basta@i2bc.paris-saclay.fr Phone: +33618781473
Our group has a long-standing interest in Archaea, the third domain of life discovered in 1977 by Carl Woese. Compared to Bacterial and Eukaryotic organisms, much less is known about the basic molecular mechanisms that drive essential processes in archaeal cells. We are particularly interested to understand how hyperthermophilic archaea, that grow happily at temperatures above 80°C, preserve the integrity of their DNA. The intern will be involved in a collaborative project that aims to characterize chromosome sequence and structure dynamics, and associated molecular machineries, through the setup of state-of-the-art proteomics and genomics assays. Specifically, the intern will first adapt and apply multi-contact 3C assay recently developed by Noordermeer group (Ref.1) to measure cell-to-cell variation of 3D chromosome organization in the archaeon Thermococcus kodakarensis. Second, the intern will apply this assay to characterize the effect of loss and gain of DNA supercoiling (Ref. 2) on the genome organisation of T. kodakarensis. Throughout this project, the intern will learn to grow and manipulate T. kodakarensis in anaerobic conditions, acquire skills in next generation sequencing sample preparation and data analysis and will have to work in close collaboration with Noordermeer group and I2BC sequencing platform. We search for a highly motivated student with good communicational skills and interest in working with an “exotic” model organism. Previous experience in working with archaea will be a plus. We will provide friendly and supportive team environment and we encourage our interns to communicate in English.
Culturing of hyperthermophilic and anaerobic archaea Chromosome Conformation Capture (3C) assay Preparation of nanopore sequencing libraries Analysis of nanopore sequencing data
(1) Li-Hsin Chang, Sourav Ghosh, Andrea Papale, Mélanie Miranda, Vincent Piras, Jéril Degrouard, Mallory Poncelet, Nathan Lecouvreur, Sébastien Bloyer, Amélie Leforestier, David Holcman, Daan Noordermeer. A complex CTCF binding code defines TAD boundary structure and function. (2021) doi: https://doi.org/10.1101/2021.04.15.440007 (2) Villain P, da Cunha V, Villain E, Forterre P, Oberto J, Catchpole R, Basta T. The hyperthermophilic archaeon Thermococcus kodakarensis is resistant to pervasive negative supercoiling activity of DNA gyrase. Nucleic Acids Res. (2021) 49(21):12332-12347. doi: 10.1093/nar/gkab869.
