Genome-wide occupancy studies for RNA polymerases and their basal transcription factors deliver information
about transcription dynamics and the recruitment of transcription elongation and termination
factors in eukaryotes and prokaryotes. The primary method to determine genome-wide occupancies is
chromatin immunoprecipitation combined with deep sequencing (ChIP-seq). Archaea possess a transcription
machinery that is evolutionarily closer related to its eukaryotic counterpart but it operates in a
prokaryotic cellular context. Studies on archaeal transcription brought insight into the evolution of
transcription machineries and the universality of transcription mechanisms. Because of the limited resolution
of ChIP-seq, the close spacing of promoters and transcription units found in archaeal genomes pose a
challenge for ChIP-seq and the ensuing data analysis. The extreme growth temperature of many established
archaeal model organisms necessitates further adaptations. This chapter describes a version of ChIP-seq
adapted for the basal transcription machinery of thermophilic archaea and some modifications to the data
analysis.
Blombach, F., Smollett, K.L., Werner, F. (2022). ChIP-Seq Occupancy Mapping of the Archaeal Transcription Machinery. In: Ferreira-Cerca, S. (eds) Archaea. Methods in Molecular Biology, vol 2522. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2445-6_13
Link to chapter: https://link.springer.com/protocol/10.1007/978-1-0716-2445-6_13