13 January – 13 March 2020
Dr Marco Di Stefano
Postdoctoral researcher at CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Carrer Baldiri i Reixac 4, 08028 Barcelona, Spain.
Dr Daniel Jost
Ecole Normale Superieure de Lyon, Laboratory of Biology and Modeling of the Cell, Parvis Rene Descartes 15, 69342, Lyon, France
Aim of the mission
In the plant Arabidopsis thaliana, several experimental studies have characterised the genome spatial organization. Imaging revealed that (i) chromosomes are organized in territories (Fransz et al. 2002) , (ii) the nucleolus generally localizes at the nuclear centre (Pontvianne et al. 2016) , (iii) telomeres cluster at the nucleolar periphery and (iv) centromeres are positioned at the nuclear periphery (Fransz et al. 2002; Fang and Spector 2005) . Complementarily, Hi-C experiments revealed the presence of specific interaction patterns: (i) strong inter- and intra-chromosome interactions between heterochromatic regions (Grob, Schmid, and Grossniklaus 2014; Feng et al. 2014) , and (ii) positive stripes of frequent interactions with neighboring chromatin regions enriched with H3K27me3, a histone modification associated with Polycomb repressive complexes (Wang et al. 2015) . In this STSM, we aim to perform theoretical studies to complement the experimental findings and try to unravel the mechanisms that are driving the genome organization. We will build coarse-grained genome-wide models of the A. thaliana nucleus and test to which extent the structure of the genome organization may be related to the epigenetic states of the chromatin. Specifically, we will explore the interplay of two mechanisms: topological restraints, controlling the entanglement of chromatin within the nuclear environment, and the attraction or repulsion between loci depending on their epigenetic state. We will, then, validate quantitatively our predictions against published experimental Hi-C and imaging data.
Fang, Yuda, and David L. Spector. 2005. Molecular Biology of the Cell . https://doi.org/ 10.1091/mbc.e05-08-0706 .
Feng, Suhua, Shawn J. Cokus, Veit Schubert, Jixian Zhai, Matteo Pellegrini, and Steven E. Jacobsen. 2014. Molecular Cell 55 (5): 694–707.
Fransz, Paul, J. Hans De Jong, Martin Lysak, Monica Ruffini Castiglione, and IngoSchubert. 2002. Proceedings of the National Academy of Sciences of the United States of America 99 (22): 14584–89.
Grob, Stefan, Marc W. Schmid, and Ueli Grossniklaus. 2014. Molecular Cell . https://doi.org/ 10.1016/j.molcel.2014.07.009 .
Pontvianne, Frédéric, Marie-Christine Carpentier, Nathalie Durut, Veronika Pavlištová, Karin Jaške, Šárka Schořová, Hugues Parrinello, et al. 2016. Cell Reports 16 (6): 1574–87.
Wang, Congmao, Chang Liu, Damian Roqueiro, Dominik Grimm, Rebecca Schwab, Claude Becker, Christa Lanz, and Detlef Weigel. 2015. Genome Research . https://doi.org/ 10.1101/gr.170332.113 .