Histone variants in archaea and the evolution of combinatorial chromatin complexity

Significance

Chromatin in eukaryotes is built around histone–DNA complexes, which act as platforms for the integration of regulatory information. Different layers of information are integrated in a combinatorial fashion, for example by exchanging core histones for variants with different properties. We show that histone variants also exist in archaea. In particular, we identify unique archaeal variants that act as capstones, preventing extension of histone–DNA complexes. Importantly, we show that some archaeal histone variants are ancient and have been maintained as distinct units for hundreds of millions of years. Our work suggests that complex combinatorial chromatin that uses histones as its building blocks exists outside eukaryotes and that the ancestor of eukaryotes might have already had complex chromatin.

Abstract

Nucleosomes in eukaryotes act as platforms for the dynamic integration of epigenetic information. Posttranslational modifications are reversibly added or removed and core histones exchanged for paralogous variants, in concert with changing demands on transcription and genome accessibility. Histones are also common in archaea. Their role in genome regulation, however, and the capacity of individual paralogs to assemble into histone–DNA complexes with distinct properties remain poorly understood. Here, we combine structural modeling with phylogenetic analysis to shed light on archaeal histone paralogs, their evolutionary history, and capacity to generate combinatorial chromatin states through hetero-oligomeric assembly. Focusing on the human commensal Methanosphaera stadtmanae as a model archaeal system, we show that the heteromeric complexes that can be assembled from its seven histone paralogs vary substantially in DNA binding affinity and tetramer stability. Using molecular dynamics simulations, we go on to identify unique paralogs in M. stadtmanae and Methanobrevibacter smithii that are characterized by unstable interfaces between dimers. We propose that these paralogs act as capstones that prevent stable tetramer formation and extension into longer oligomers characteristic of model archaeal histones. Importantly, we provide evidence from phylogeny and genome architecture that these capstones, as well as other paralogs in the Methanobacteriales, have been maintained for hundreds of millions of years following ancient duplication events. Taken together, our findings indicate that at least some archaeal histone paralogs have evolved to play distinct and conserved functional roles, reminiscent of eukaryotic histone variants. We conclude that combinatorially complex histone-based chromatin is not restricted to eukaryotes and likely predates their emergence.