The Role of Archaeal Chromatin in Transcription

Abstract

Genomic organization impacts accessibility and movement of information processing systems along DNA. DNA-bound proteins dynamically dictate gene expression and provide regulatory potential to tune transcription rates to match ever-changing environmental conditions. Archaeal genomes are typically small, circular, gene dense, and organized either by histone proteins that are homologous to their eukaryotic counterparts, or small basic proteins that function analogously to bacterial nucleoid proteins. We review here how archaeal genomes are organized and how such organization impacts archaeal gene expression, focusing on conserved DNA-binding proteins within the clade and the factors that are known to impact transcription initiation and elongation within protein-bound genomes.

Keywords: Alba; RNA polymerase; archaea; histone; transcription regulation.

Figure 1.. Distribution of chromatin associated proteins identified across the Archaea.

Histone proteins and nucleoid-associated proteins (NAPs; right) encoded in each phylum according to the schematic evolutionary tree of Archaea (left).

Figure 2.. The structure of histone-based chromatin in Archaea mirrors that of the eukaryotic nucleosome.

(a) The eukaryotic nucleosome hexamer containing two H3-H4 dimers (blue, green respectively) and one H2A-H2B dimer (yellow, red respectively) with wrapped DNA (gold) from a top-down and side view. N and C terminal extensions, specific to eukaryotic histones, are shown in grey. (b) Histone based-chromatin in Archaea can form from varied numbers of histone dimers (three dimers are shown here for comparison to the eukaryotic hexasome), with wrapped DNA (silver) from a top-down and side view. The archaeal histone-based chromatin structure formed with three histone dimers is almost identical to the eukaryotic hexasome without the N- and C-terminal extensions.

Figure 3.. The archaeal chromatin landscape is dynamic.

a) Wrapping of DNA by archaeal histones forms various sizes of extended histone-based chromatin structures. The regulation and depositions of these structures is unknown, but nucleoid associated proteins (NAPs) may play a role in both looping of DNA and size restriction of extended histone polymers. b) Transcription initiation factors TFB and TBP compete with histone proteins for the promoter element in archaea allowing transcription initiation upstream of a chromatinized gene body. c) RNAP must traverse a chromatinized gene body. Spt4-Spt5 permit the transition from initiation to early elongation by displacing TFE and facilitating processive elongation through a chromatin landscape.