ИСТИНА

Background: Three-dimensional structure of chromosomes displays diverse patterns across the tree of life, with compartments, contact domains and loops being quite universally observed. The Archaea remains understudied to this extent so far, despite being an intriguing area from the evolutionary perspective. Pioneering studies of chromatin structure of the archaeal kingdom based on high-throughput sequencing revealed considerable variability across the species and phyla at different levels of genome organization. Particularly, the chromosome architecture of Crenarchaeota, one of the hyperthermophilic phyla of Archaea, manifests diverse patterns across different orders. Objectives To describe the spatial organization of the hyperthermophilic crenarchaeon Thermofilum adornatus strain 1910bT chromosome. Methods The 3С-seq chromosome conformation capture approach was used. The chromosome contact map was reconstructed using Juicer (at maximum resolution of 2 Kbp). The A/B compartments calling was performed using cooltools. The insulation score was used to identify the chromosome interaction domains (CIDs). The whole-genome 3D reconstruction was conducted in 3DMax and LorDG. Chromosomal loops were called using Chromosight. To assess the transcriptional relation of the domains, we identified the predicted highly expressed genes (PHX) profile along with the GC-content and gene density, replication origins and the ORFs likely encoding SMC-like and histone-like proteins. Results On the contact map, we observed a curved secondary diagonal almost orthogonal to the main one. Noteworthy, the plaid patterns previously reported for the Sulfolobus species from the same Thermoproteales order were absent. Formal identification of the A/B compartments and whole-genome 3D reconstruction suggested that the chromosome can be divided into two domains, with the larger domain more enriched in CIDs. Interestingly, most PHX and predicted origins were located within the larger domain, suggesting that it could exhibit higher transcriptional activity. Further comparison of these domains with the whole-genome gene expression profiles will allow us to check whether they represent primitive expression-associated compartments. Exploration of 3D genomes in hyperthermophilic Archaea will shed light on the mechanisms of their adaptation to harsh environmental conditions and the evolution of the links between structural and functional organization in live organisms. This work was supported by the Russian Science Foundation [19-74-10092].