Comparative epigenomic and transcriptomic analysis of Populus roots under excess Zn

• A ChIP-Seq and RNA-Seq analysis on Populus roots under excess Zn is described.
• Datasets were integrated for understanding epigenetic and transcriptional changes.
• Genes marked with H3K4me3 histone modification were highly expressed.
• Genes marked with H3K27me3 histone modification in the 5′-UTR were low expressed.
• Zn activates genes involved in carbon catabolism and nitrogen metabolism.

Epigenetic modifications of chromatin structure are extremely important in mediating stress responses in plants. Epigenetic modifications are especially important in perennial species such as trees, where they contribute to phenotypic plasticity and adaptation to unfavourable environments. Populus is a model for physiological studies of trees, and is suitable for phytoremediation of Zn-contaminated soils. Currently, epigenetic modifications involved in Zn stress response are poorly characterized for Populus. Here, we compared changes in epigenetic modifications under excess Zn using chromatin immunoprecipitation sequencing (Chip-Seq) for two histone modifications associated with highly expressed genes (H3K4me3) and repressed genes (H3K27me3) in roots of Populus × canadensis I-214. Chip-Seq data were integrated with RNA-Seq transcript abundance data to examine how epigenetic modifications affect gene expression. These analyses showed that genes with a H3K4me3 modification are generally high-expressed, while genes with a H3K27me3 modification on the 5′-UTR are mainly low-expressed. H3K4me3 modifications in roots under excess Zn condition were enriched in genes involved in carbon (C) catabolism, nitrogen (N) metabolism, and in regulation of sub-cellular vesicular trafficking. These results are consistent with Zn redistribution at a sub-cellular level to buffer Zn-induced nutrient imbalance and osmotic stress in Zn-stressed roots. In contrast H3K27me3 modifications were enriched primarily in genes involved in photosynthetic processes. Together our results provide a useful resource for understanding epigenetic modifications in response to excess Zn in Populus roots, and constitute a starting point for the identification of epigenetic markers and improving phytoremediation potential in this species.