Chromatin and gene regulation in archaea

Abstract

The chromatinisation of DNA by nucleoid‐associated proteins (NAPs) in archaea ‘formats’ the genome structure in profound ways, revealing both striking differences and analogies to eukaryotic chromatin. However, the extent to which archaeal NAPs actively regulate gene expression remains poorly understood. The dawn of quantitative chromatin mapping techniques and first NAP‐specific occupancy profiles in different archaea promise a more accurate view. A picture emerges where in diverse archaea with very different NAP repertoires chromatin maintains access to regulatory motifs including the gene promoter independently of transcription activity. Our re‐analysis of genome‐wide occupancy data of the crenarchaeal NAP Cren7 shows that these chromatin‐free regions are flanked by increased Cren7 binding across the transcription start site. While bacterial NAPs often form heterochromatin‐like regions across islands with xenogeneic genes that are transcriptionally silenced, there is little evidence for similar structures in archaea and data from Haloferax show that the promoters of xenogeneic genes remain accessible. Local changes in chromatinisation causing wide‐ranging effects on transcription restricted to one chromosomal interaction domain (CID) in Saccharolobus islandicus hint at a higher‐order level of organisation between chromatin and transcription. The emerging challenge is to integrate results obtained at microscale and macroscale, reconciling molecular structure and function with dynamic genome‐wide chromatin landscapes.