The Chromatin Landscape of the Histone-possessing Bacteria

Histone proteins have traditionally been thought to be restricted to eukaryotes and most archaea, with eukaryotic nucleosomal histones deriving from their archaeal ancestors. In contrast, bacteria lack histones as a rule. However, histone proteins have recently been identified in a few bacterial clades, most notably the phylum Bdellovibrionota, and these histones have been proposed to exhibit a range of divergent features compared with histones in archaea and eukaryotes. However, no functional genomic studies of the properties of Bdellovibrionota chromatin have been carried out. In this work, we map the landscape of chromatin accessibility, active transcription, and three-dimensional (3D) genome organization in a member of Bdellovibrionota (a strain). We find that, similar to what is observed in some archaea and in eukaryotes with compact genomes such as yeast, chromatin is characterized by preferential accessibility around promoter regions. Similar to eukaryotes, chromatin accessibility in positively correlates with gene expression. Mapping active transcription through single-strand DNA (ssDNA) profiling revealed that unlike in yeast, but similar to the state of mammalian and fly promoters, promoters exhibit very strong polymerase pausing. Finally, similar to that of other bacteria without histones, the genome exists in a 3D configuration organized by the parABS system along the axis defined by replication origin and termination regions. These results provide a foundation for understanding the chromatin biology of the unique Bdellovibrionota bacteria and the functional diversity in chromatin organization across the tree of life.