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Dynamic chromatin remodelling of ciliate macronuclear DNA as determined by an optimized chromatin immunoprecipitation (ChIP) method for Paramecium tetraurelia

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Abstract

We report the detailed evaluation of crucial parameters for chromatin immunoprecipitation (ChIP) of macronuclear DNA in the unicellular eukaryote Paramecium tetraurelia. Optimized parameters include crosslinking conditions, chromatin sonication and antibody titration thus providing a detailed protocol for successful ChIP in P. tetraurelia. As this ciliate is bacterivorous and RNAi by feeding represents a powerful tool for analysis of gene function, we moreover determined the effects of ingested nucleic acids by food bacteria. Feasibility of our protocol is demonstrated by characterisation of chromatin remodelling at promoters of cytosolic HSP70 isoforms during transcriptional activation under heat shock conditions by analyzing RNA abundance, nucleosome occupancy and levels of H3 lysine 9 acetylation.

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Acknowledgments

We are grateful to Daniela Strenkert, Michael Schroda and Alexandra Nitzsche for stimulation discussions. Further thanks for their support go to Sophie Malinsky and Mireille Bétermier. This work was supported by the Deutsche Forschungsgemeinschaft (SI 1397–2) to MS. MC receives an excellence graduate fellowship by the University of Kaiserslautern.

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  1. Faculty of Biology, Molecular Protistology, University of Kaiserslautern, Gottlieb-Daimler Straße Building 14, 67663, Kaiserslautern, Germany

    Miriam Cheaib & Martin Simon

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  1. Miriam Cheaib
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  2. Martin Simon
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Correspondence to Martin Simon.

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Cheaib, M., Simon, M. Dynamic chromatin remodelling of ciliate macronuclear DNA as determined by an optimized chromatin immunoprecipitation (ChIP) method for Paramecium tetraurelia . Appl Microbiol Biotechnol 97, 2661–2670 (2013). https://doi.org/10.1007/s00253-013-4708-1

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