Single-Nucleus Transcriptomics Reveals How Tissue Context Shapes the Circadian Transcriptome of the Arabidopsis Leaf
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Background
Circadian regulation enables plants to coordinate cellular processes with daily environmental cycles, yet the dynamics and hierarchy of the clock across cells and tissue types remains poorly understood.
Results
We developed a 24 hour single nucleus RNA-sequencing (snRNA-seq) circadian time course of the mature Arabidopsis thaliana leaf to characterize circadian regulation across tissues. We captured ∼30,000 nuclei across seven circadian time points, recovering all major leaf cell types. We identified over 7,400 genes with cluster-resolved circadian regulation, and used coexpression analysis to define five major temporal expression clades shared across all cell types. We leveraged these assignments to identify genes with cell type-specific temporal shifts in expression. Single cell gene regulatory networks (scGRNs) were generated for each cluster through GENIE3, identifying many shared and unique transcription factor (TF) target interactions across clusters. A close examination of CCA1 targets identified Photosystem II repair components in a subset of mesophyll cells and a large number of auxin-associated genes in only a handful of clusters despite robust expression in other clusters, suggestive of cell type-specific CCA1 target regulation.
Conclusions
Our results demonstrate the extent to which circadian transcriptional regulation is present in the mature Arabidopsis leaf, and highlight the immense complexity in cell type specific regulation. This dataset provides a high-resolution resource for dissecting circadian gene regulation at cellular resolution and advances our understanding of tissue-specific clock dynamics in plants.
