ChIP-seq Experiment and Data Analysis in the Cyanobacterium Synechocystis sp. PCC 6803
Joaquín Giner-Lamia,
Miguel Hernández-Prieto,
Matthias Futschik
Affiliations
Joaquín Giner-Lamia
Systems Biology and Bioinformatics Laboratory, Centre for Biomedical Research (CBMR), University of Algarve, Faro, PortugalLaboratory of Intracellular Bacterial Pathogens, Department of Microbial Biotechnology, Centro Nacional de Biotecnología - Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
Miguel Hernández-Prieto
Systems Biology and Bioinformatics Laboratory, Centre for Biomedical Research (CBMR), University of Algarve, Faro, PortugalARC Centre of Excellence for Translational Photosynthesis and School of Life and Environmental Sciences, University of Sydney, Australia
Matthias Futschik
Systems Biology and Bioinformatics Laboratory, Centre for Biomedical Research (CBMR), University of Algarve, Faro, PortugalCentre of Marine Sciences (CCMAR), University of Algarve, Faro, Portugal, School of Biomedical Sciences, Institute of Translational and Stratified Medicine (ITSMED), Faculty of Medicine and Dentistry, University of Plymouth, Plymouth PL6 8BU, UK
Nitrogen is an essential nutrient for all living organisms. In cyanobacteria, a group of oxygenic photosynthetic bacteria, nitrogen homeostasis is maintained by an intricate regulatory network around the transcription factor NtcA. Although mechanisms controlling NtcA activity appear to be well understood, the sets of genes under its control (i.e., its regulon) remain poorly defined. In this protocol, we describe the procedure for chromatin immunoprecipitation using NtcA antibodies, followed by DNA sequencing analysis (ChIP-seq) during early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803 (hereafter Synechocystis). This protocol can be extended to analyze any DNA-binding protein in cyanobacteria for which suitable antibodies exist.
