Multi-omic dissection of ancestral heat stress memory responses in Brachypodium distachyon

Stressful environmental conditions, including heat stress (HS), are a major limiting factor in crop yield. Understanding the molecular mechanisms of plant stress memory and resilience is important for engineering more resistant plants and improving crop yield. To study how the different gene regulatory layers change upon repeated HS and how these layers are interconnected, we performed a dense temporal atlas of gene expression, alternative splicing, small and long noncoding RNAs, and DNA methylation in Brachypodium distachyon. Results show that a second HS induces changes in coding and noncoding RNA expression and alternative splicing and that DNA demethylation is responsible for mediating differential gene expression. We identified a long noncoding RNA regulatory network and provided evidence that lncRNAs positively regulate gene expression, while miRNAs are implicated in alternative splicing events. We reconstructed the ancestral heat memory network of flowering plants by comparing the dynamic responses of Arabidopsis thaliana and Brachypodium distachyon. These findings enhance our understanding of the complex inter-layer cross-talk governing HS resilience and memory and identify novel genes essential for these processes.