The chromatin landscape of the euryarchaeonHaloferax volcanii

Abstract

Archaea, together with Bacteria, represent the two main divisions of life on Earth, with many of the defining characteristics of the more complex eukaryotes tracing their origin to evolutionary innovations first made in their archaeal ancestors. One of the most notable such features is nucleosomal chromatin, although archaeal histones and chromatin differ significantly from those of eukaryotes. Despite increased interest in archaeal histones in recent years, the properties of archaeal chromatin have been little studied using genomic tools. Here, we adapt the ATAC-seq assay to archaea and use it to map the accessible landscape of the genome of the euryarchaeote Haloferax volcanii. We integrate the resulting datasets with genome-wide maps of active transcription and single-stranded DNA (ssDNA) and find that while \textit{H. volcanii} promoters exist in a preferentially accessible state, modulation of transcriptional activity is not associated with changes in promoter accessibility, unlike the typical situation in eukaryotes. Applying orthogonal single-molecule footprinting methods, we quantify the absolute levels of physical protection of H. volcanii, and find that archaeal nucleosomal chromatin is similarly or only slightly more accessible, in aggregate, than that of eukaryotes. We also evaluate the degree of coordination of transcription within archaeal operons and make the unexpected observation that some CRISPR arrays are associated with highly prevalent ssDNA structures. These results provide a foundation for the future functional studies of archaeal chromatin.

The landscape of the histone-organized chromatin of Bdellovibrionota bacteria

“…Accessibility is centered around the promoter regions between genes (Figure 2B-E). We observe transcription start sites (TSS) scores (indicating the level of enrichment over promoter regions relative to flanking regions; see the Methods section and previous detailed discussions 43 ) in the 1.35-1.40 neighborhood, which is comparable to what we had previously found in the archaeon Haloferax volcanii 31 and (E) KAS-seq and ATAC-seq profiles around the ribosomal RNA locus of Bacteriovorax.…”

“…Previously we found no correlation between chromatin accessibility and transcriptional activity in the archaeon Haloferax volcanii 31 . In contrast, ATAC-seq signal both over promoter regions and gene bodies correlates positively with KAS signal, again over both promoter regions and gene bodies (Figure 4D).…”

“…We had previously observed promoter pausing using KAS-seq in the euryarchaeon Haloferax volcanii 31 . Bacteriovorax promoters are even more accentuated in KAS-seq profiles than in Haloferax -promoter KAS signal peaks at ∼12 RPM (Reads Per Million mapped reads) over Bacteriovorax promoters compared to a through at ∼10 RPM in intergenic space and ∼8 over gene bodies (Figure 3B-D); in Haloferax these values are ∼11, ∼10 and ∼8 RPM, respectively 31 .…”

“…These observations pose a long list of tantalizing questions about the physical organization of the genomes of these histone-possessing bacteria, about the relationship between chromatin structure and gene expression, and about how such features compare to those of archaea. However, while archaea have received some experimental attention in the past decade [28][29][30][31] , these properties have not been assayed so far with functional genomic tools in the bacterial clades that have histones.…”

DNA-bridging by an archaeal histone variant via a unique tetramerisation interface

“…While this relationship is not necessarily causal, it is consistent with histones regulating transcription in M. jannaschii via competition for promoter access. While the deletion of the nonessential histone gene in H. salinarum leads to genome-wide, significant but subtle changes in gene expression 14 , recent ATAC-seq data for H. volcanii rather point to an accessible promoter state independent of the transcription level of the gene 52 and in line with chromatin reconstitution experiments in T. kodakarensis 9 . The call is still out whether histones in the archaea primarily function as genome compactors or gene expression regulators.…”