The genomes of all organisms throughout the tree of life are compacted and organized in chromatin by association of chromatin proteins. Eukaryotic genomes encode histones, which are assembled on the genome into octamers, yielding nucleosomes. Post-translational modifications of the histones, which occur mostly on their N-terminal tails, define the functional state of chromatin. Like eukaryotes, most archaeal genomes encode histones, which are believed to be involved in the compaction and organization of their genomes. Instead of discrete multimers, in vivo data suggest assembly of “nucleosomes” of variable size, consisting of multiples of dimers, which are able to induce repression of transcription. Based on these data and a model derived from X-ray crystallography, it was recently proposed that archaeal histones assemble on DNA into “endless” hypernucleosomes. In this review, we discuss the amino acid determinants of hypernucleosome formation and highlight differences with the canonical eukaryotic octamer. We identify archaeal histones differing from the consensus, which are expected to be unable to assemble into hypernucleosomes. Finally, we identify atypical archaeal histones with short N- or C-terminal extensions and C-terminal tails similar to the tails of eukaryotic histones, which are subject to post-translational modification. Based on the expected characteristics of these archaeal histones, we discuss possibilities of involvement of histones in archaeal transcription regulation.

Many archaea express histones, which organize the genome and play a key role in gene regulation. The structure and function of archaeal histone–DNA complexes remain however largely unclear. Recent studies show formation of hypernucleosomes consisting of DNA wrapped around an ‘endless’ histone-protein core. However, if and how such a hypernucleosome structure assembles on a long DNA substrate and which interactions provide for its stability, remains unclear. Here, we describe micromanipulation studies of complexes of the histones HMfA and HMfB with DNA. Our experiments show hypernucleosome assembly which results from cooperative binding of histones to DNA, facilitated by weak stacking interactions between neighboring histone dimers. Furthermore, rotational force spectroscopy demonstrates that the HMfB–DNA complex has a left-handed chirality, but that torque can drive it in a right-handed conformation. The structure of the hypernucleosome thus depends on stacking interactions, torque, and force. In vivo, such modulation of the archaeal hypernucleosome structure may play an important role in transcription regulation in response to environmental changes.

Remodelling chromatin structure is important for regulating gene expression, DNA replication and repair and other fundamental nuclear processes. The basic chromatin unit is the nucleosome. SWR1 is a multi-subunit complex, whose chromatin remodelling activity is associated with regulation of gene expression in heterochromatin regions of chromosomes in plants and mammals, and with the cellular response to DNA damage. In yeast, the simplest eukaryotic organism, the SWR1 complex is responsible for the ATP-dependent nucleosome remodelling by exchanging its canonical H2A histone with Htz1 variant (also known as H2A.Z in mammalian cells). In spite of a large number of genetic, biochemical and structural studies on SWR1, its detailed histone exchange mechanism remains largely unknown. To investigate the mechanism of histone exchange by SWR1, we have developed a single-molecule FRET assay, which monitors the interaction between individual nucleosomes and yeast SWR1 complexes in real time. The data show distinct dynamic behaviours in the presence or absence of ATP, or in the presence of non-hydrolysable ATP analogue. We hypothesize that the observed dynamics are important for the removal of canonical H2A histones or deposition of the histone variant Htz1. We anticipate that our data will help elucidate the molecular mechanism of histone exchange by SWR1.

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