A chromatin-driven mechanism of transcription in ammonia-oxidizing archaea under environmental stress [MNase-seq]

Ammonia-oxidizing archaea (AOA) play a significant role in global nitrogen and carbon cycling. AOA can survive under fluctuating environmental conditions by modulating gene expression. Little is known about how AOA regulate gene expression to adapt environmental stress. Here, we report a chromatin-driven mechanism of transcription in Nitrososphaera Viennensis (EN76) to adapt to temperature stress. Using computational and biochemical assays, we found EN76 contains an archaeasome structure. We found that several residues, including G20, K57, and T58 of histone, are important to form archaea chromatin structures. In vitro transcription assays revealed that AOA chromatin efficiently controls gene expression, similar to eukaryote chromatin. Furthermore, we identified AOA histone acetylation, which activates gene expression. Moreover, by integrating chromatin-based gene expression analyses, we revealed that AOA differentially regulate gene expression in response to temperature stress by altering archaeasome occupancy. Our study provides unprecedented documentation that AOA fine-tunes gene expression through a chromatin-driven epigenetic mechanism. Overall design: Cells were collected by centrifugation and washed twice with MNase digestion buffer. The pellet was resuspended in MNase buffer and incubated with 50 mU of micrococcal nuclease (MNase) at 37 °C for 15 min to partially digest chromatin. The reaction was quenched with 10 mM EDTA, and DNA was extracted using phenol:chloroform:isoamyl alcohol, followed by ethanol precipitation. Purified DNA was quantified, and sequencing libraries were prepared and subjected to high-throughput sequencing on an Illumina platform (single read 75bp sequencing using HigSeq 2500).