Capturing Environmental Plant Memories in DNA, with a Little Help from Chromatin

Plants are eukaryotes living mostly immotile in harsh environments. On occasion, it is beneficial for their survival to maintain a transcriptional response to an environmental stress longer than the stress lasts (transcriptional memory) and even to reiterate such a response more quickly or more strongly when the same stress is re-encountered (priming memory). In eukaryotes, transcription takes place in the context of chromatin, the packaging material of DNA. Chromatin regulation is often invoked when it comes to environmental transcriptional and priming memory in plants, but rarely chromatin-based regulation can be accurately assigned to a given aspect of transcription in vivo. The conserved eukaryotic chromatin-modifying system Polycomb/Trithorax can support both long-term stability and flexibility of gene expression in Drosophila. The main principles of Polycomb/Trithorax regulation will be outlined and illustrated with the best-studied case of environmental memory from Arabidopsis. Despite being complex, the Polycomb/Trithorax system relies on experimentally tractable elements in the form of DNA, termed Polycomb/Trithorax Responsive Elements. PREs/TREs are essentially memory DNA elements. Here, relevant information to identify PRE/TRE-like elements in plants is highlighted. Examples of priming memory in plants are discussed in relation to the first two reported putative memory DNA elements. Arguably, similar cases from plants can be conducive in dissecting the contribution of DNA-based from chromatin-based regulation of transcription, when two types of DNA elements are defined: those representing binding sites for the transcription factors determining the environmental response and those controlling memory by regulating chromatin modification dynamics, ultimately maintaining the corresponding transcriptional state.