Euryarchaeal genomes are folded into SMC-dependent loops and domains, but lack transcription-mediated compartmentalization

Charlotte Cockram (1) , Agnès Thierry (1) , Aurore Gorlas (2) , Roxane Lestini (3) , Romain Koszul (1)

1 Régulation spatiale des Génomes - Spatial Regulation of Genomes
2 I2BC - Institut de Biologie Intégrative de la Cellule
3 LOB - Laboratoire d'Optique et Biosciences

Hi-C has become a routine method for probing the 3D organization of genomes. However, when applied to prokaryotes and archaea, the current protocols are expensive and limited in their resolution. We develop a cost-effective Hi-C protocol to explore chromosome conformations of these two kingdoms at the gene or operon level. We first validate it on E. coli and V. cholera, generating sub-kilobase-resolution contact maps, and then apply it to the euryarchaeota H. volcanii, Hbt. salinarum, and T. kodakaraensis. With a resolution of up to 1 kb, we explore the diversity of chromosome folding in this phylum. In contrast to crenarchaeota, these euryarchaeota lack (active/inactive) compartment-like structures. Instead, their genomes are composed of self-interacting domains and chromatin loops. In H. volcanii, these structures are regulated by transcription and the archaeal structural maintenance of chromosomes (SMC) protein, further supporting the ubiquitous role of these processes in shaping the higher-order organization of genomes.

Keywords: DNA loops; high-resolution; Hi-C; archaea; chromosome organization; SMC; transcription; bacteria; compartments; euryarchaeota

Domains: Genetics

Charlotte Cockram, Agnès Thierry, Aurore Gorlas, Roxane Lestini, Romain Koszul. Euryarchaeal genomes are folded into SMC-dependent loops and domains, but lack transcription-mediated compartmentalization. Molecular Cell, 2021, 81 (3), pp.459-472.e10. ⟨10.1016/j.molcel.2020.12.013⟩. ⟨hal-03379787⟩