title: Epigenetic regulation of serotype expression antagonizes transcriptome dynamics in Paramecium tetraurelia.
abstract: Phenotypic variation of a single genotype is achieved by alterations in gene expression patterns. Regulation of such alterations depends on their time scale, where short-time adaptations differ from permanently established gene expression patterns maintained by epigenetic mechanisms. In the ciliate Paramecium, serotypes were described for an epigenetically controlled gene expression pattern of an individual multigene family. Paradoxically, individual serotypes can be triggered in Paramecium by alternating environments but are then stabilized by epigenetic mechanisms, thus raising the question to which extend their expression follows environmental stimuli. To characterize environmental adaptation in the context of epigenetically controlled serotype expression, we used RNA-seq to characterize transcriptomes of serotype pure cultures. The resulting vegetative transcriptome resource is first analysed for genes involved in the adaptive response to the altered environment. Secondly, we identified groups of genes that do not follow the adaptive response but show co-regulation with the epigenetically controlled serotype system, suggesting that their gene expression pattern becomes manifested by similar mechanisms. In our experimental set-up, serotype expression and the entire group of co-regulated genes were stable among environmental changes and only heat-shock genes altered expression of these gene groups. The data suggest that the maintenance of these gene expression patterns in a lineage represents epigenetically controlled robustness counteracting short-time adaptation processes.
authors.affiliation: Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, Saarbrücken 66123, Germany.
authors.forename: Miriam
authors.initials: M
authors.lastname: Cheaib
authors.affiliation: Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, Saarbrücken 66123, Germany Cluster of Excellence for Multimodal Computing and Interaction, Saarland University and Max Planck Institute for Informatics, Saarbrücken 66123, Germany.
authors.forename: Azim
authors.initials: A
authors.lastname: Dehghani Amirabad
authors.affiliation: Epigenetics Department, Centre for Human and Molecular Biology, Saarland University, Saarbrücken 66123, Germany.
authors.forename: Karl J V
authors.initials: KJ
authors.lastname: Nordström
authors.affiliation: Cluster of Excellence for Multimodal Computing and Interaction, Saarland University and Max Planck Institute for Informatics, Saarbrücken 66123, Germany.
authors.forename: Marcel H
authors.initials: MH
authors.lastname: Schulz
authors.affiliation: Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, Saarbrücken 66123, Germany martin.simon@uni-saarland.de.
authors.forename: Martin
authors.initials: M
authors.lastname: Simon
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics; D000953:Antigens, Protozoan / Q000235:genetics; D016000:Cluster Analysis; D003080:Cold Temperature; D004247:DNA / Q000378:metabolism; D044127:Epigenesis, Genetic; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D018869:Heat-Shock Response / Q000235:genetics; D005810:Multigene Family; D016805:Paramecium tetraurelia / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D014176:Protein Biosynthesis; D065288:Serogroup; D013217:Starvation / Q000235:genetics; D059467:Transcriptome
chemical_list: D000953:Antigens, Protozoan; D004247:DNA
keywords: antigenic variation; ciliate; epigenetics; heat-shock; telomere position effect