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. Cells were fixed using formaldehyde and then subjected to washing with MNase buffer. The cell pellet was subsequently mixed with 50 mU of MNase and incubated at 37°C for 15 minutes. DNA was extracted using phenol:chloroform:isoamyl. High-throughput sequencing was performed as single read 75bp sequencing using HigSeq 2500.