Plant responses to environmental stimuli require complex gene expression reprogramming regulated at multiple levels. Cis-regulatory elements (CREs) can activate or repress gene expression through transcription factor (TF) binding. Moreover, the temporal nature of stress responses adds another layer of complexity wherein sets of genes are regulated differently based on their timing of expression during stress response. Understanding the complex cis-regulatory syntax is essential to predict when and where genes are expressed and how sequence variations lead to downstream changes in gene expression. Recent advances in deep-learning approaches have enabled predictions of gene expression from genomic DNA features (Wang et al., 2020; Meng et al., 2021). Previous studies have established the ability of computational models to predict plant spatial transcriptional response using known and novel CREs (Uygun et al., 2017). However, a global model to uncover regulatory elements affecting temporal responses to environmental stimuli is still lacking…