Genome-wide transcriptional changes and chromatin modifications associated with plant stress memory

As sessile organisms, plants had to develop various biochemical and physiological mechanisms to respond and adapt to abiotic stress conditions such as salt and drought and thus acquire stress tolerance. A particular interesting mechanism is the so called “priming effect”: an application of a mild short stress to plants at an early stage of development appears to enable them to cope better when stressed again at mature stage. However, the molecular effects of salt priming have not been systematically quantified and as a consequence the molecular basis of priming remains unknown. In this study an experimental procedure was established that allowed to test whether salt priming of young Arabidopsis thaliana plants had an effect on plants exposed to more severe salt stress at a later stage of development. To quantify how primed and non-primed plants responded to the second salt stress, global changes in their transcriptional expression profiles were monitored using Affymetrix GeneChip ATH1 microarray. Results showed that both primed and non-primed plants responded to the salt treatment modulating the same set of known stress responsive genes. However, primed plants differentially regulated a smaller set of genes. Furthermore, the vast majority of the stress responsive genes showed a weaker response in primed than in nonprimed plants. These results suggested that primed plants channelled the stress response using only selected genes. The next question addressed was how primed plants could “remember” the priming treatment after a period of extensive growth. Several studies had indicated that environmental stress induces changes in the chromatin structure thereby modifying the accessibility of the DNA for transcription factors and other regulatory proteins. This suggested a link between epigenetic modification and exposure of plants to stressful conditions, where the chromatin status might act as an epigenetic mark that could be maintained during plant growth and development. To investigate this hypothesis I carried out a comparative analysis of the epigenetic landscapes of primed and non-primed plants combining Chromatin Immuno-Precipitation with Illumina sequencing (ChIP-Seq). Genome-wide profiles of H3K4me2, H3K4me3, H3K9me2 and H3K27me3 were generated for roots and shoots of plants harvested immediately after the priming treatment. Roots of primed plants showed indeed numerous differences in their epigenetic profiles compared to non-primed roots, in particular at the level of H3K27me3. Therefore, I carried out an additional ChIP-Seq experiment before the application of the second stress to test if the priming induced changes in H3K27me3 were maintained over this period of extensive growth. Results showed that several epigenetic differences caused by priming were still maintained. Finally, to elucidate the relationship between epigenetic modifications and transcriptional responses the ChIP-Seq profiles were coupled with genome wide transcript profiles obtained by RNA-seq. Results shown that in the non-steady state there was no clear correlation between the differences detected at the transcriptional and at the epigenetic level. The results identified H3K27me3 as a potential mark for salt stress memory and they call for future studies extending both temporal and spatial resolution of epigenetic and transcriptional changes after salt priming.