Romain KOSZUL, Institut Pasteur - Paris

Contact : Aurèle Piazza

Christophe Chapard1, Nathalie Bastié2, Léa Meneu1, Jacques Serizay1, Agnès Thierry1, Aurèle Piazza1, Frédéric Beckouët2, Julien Mozziconacci3, Romain Koszul1

1Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS UMR 3525, F-75015 Paris, France. 2LBME, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000, Toulouse, France. 3Muséum National d'Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université, 75005 Paris, France.

Advances in chromosome imaging and Hi-C approaches over the past decade have shown unequivocally that prokaryotic, archaeal, and eukaryotic chromosomes are not folded at random. The principles that govern the 3D organization of genomes, and its causal relationships with DNA processes such as transcription, repair or replication, are being actively studied. Converging evidence indicates that transcription, structural maintenance of chromosomes (SMC) ring-shaped protein complexes and heterochromatin play a major role in chromosome folding. In humans, SMC cohesin mediates chromatin loops that bring together distal regulatory elements and gene promoters. Similar cohesin-mediated loops compact the chromosome during metaphase of budding yeast mitosis (1). The cohesin ring organizes genomes by progressively expanding small DNA loops into larger structures, a ubiquitous process also called loop extrusion (2). Transcription and the deposition of DNA-binding proteins are involved in the positioning of loops, which can also be affected by discrete double-strand breaks (3,4). Recent in vitro single-molecule experiments suggest that loop expansion is mediated by Scc2-stimulated ATPase activity of cohesins.

We now provide a comprehensive overview of the roles of various cohesin regulators in the regulation of chromatin loop expansion in vivo. First, we demonstrate that Scc2 is essential for cohesin translocation, resulting in loop expansion (5). Acetylation of Smc3 during S phase counteracts this activity by stabilizing Pds5, which fine-tunes loop size and stability in G2. Then, we developed a transversal approach to address the limitations resulting from the complex nature of chromosomes, which exhibit an intertwined, multiscale network of structures. We study the behavior of large pseudo-random sequences using Mb long bacterial chromosomes cloned into the yeast genome, from which they have diverged for over 1.5 billion years. We characterized these chimeric genomes using RNA-seq, ChIP-seq, Hi-C, and engineering experiments supported by deep learning analysis to study the determinants of chromosome metabolism, and validate or identify the rules of chromosome folding regulation.

1.Dauban, L. et al. Regulation of Cohesin-Mediated Chromosome Folding by Eco1 and Other Partners. Mol. Cell 77, 1279–1293.e4 (2020).

2.Goloborodko, A. et al., Compaction and segregation of sister chromatids via active loop extrusion, eLife, e14864 (2016).

3.Piazza, A. et al. Cohesin regulates homology search during recombinational DNA repair. Nat. Cell Biol. 23, 1176–1186 (2021).

4.Arnould, C. et al. Loop extrusion as a mechanism for formation of DNA damage repair foci. Nature 590, 660–665 (2021).

5.Bastié, N., et al. Smc3 acetylation, Pds5 and Scc2 control the translocase activity that establishes cohesin-dependent chromatin loops. Nat. Struct. Mol. Bio. (2022) in press