Chromatin structure changes in Daphnia populations upon exposure to environmental cues – or – The discovery of Wolterecks “Matrix”

Abstract

Background: This study therefore describes the classical experimental system postulated by Richard Woltereck 100 years ago: the adaptive morphological phenotypic plasticity of daphnia . Phenotypic plasticity is an important feature of biological systems that is likely to play a major role in the adaptation of organisms exposed to an environmental stimulus and it is increasingly related to epigenetic mechanisms. Several studies have started to identify the epigenetic basis of phenotypic plasticity of daphnia including non-coding RNAs, covalent modifications at the histone tails and DNA methylation however no study has yet investigated those effect on the genome-wide chromatin structure. The aim of this work was to study for the first time the overall genome-wide chromatin structure of Daphnia pulex in the context of the iconic complex defense response to predation. We developed a robust and rapid ATAC-seq technique that allows for analyzing chromatin of individual daphnia and show here (i) that this technique can be used with minimal expertise in molecular biology, and (ii) we used it to identify open chromatin structure in daphnia exposed to different environmental cues.Results: Our results encouraged the expected induction of anti-predatory morphological changes in the stress treatment was significantly higher than that of daphnia from the control treatment. The developed ATAC-seq technique can be used to characterize chromatin structures of individuals even those that are small and thus with few biological material, making it possible to determine epigenetic polymorphisms relatively easily and at reasonable cost in full populations. In addition, we deliver evidence that chromatin structure changes upon stimuli from the environment.Conclusion: We report here an extremely fast and straightforward method to map the chromatin status of individuals using small amounts of input biological material. W e show here that changes in the environment, such as predator presence the chromatin structure is profoundly reorganised confirming Woltereck ’s classical postulate.