Single-Nucleus Transcriptomics Reveals How Cell Type Shapes the Circadian Transcriptome of the Arabidopsis Leaf

Area of Science:

• Plant Biology
• Molecular Biology
• Genomics

Background:

• Circadian rhythms are crucial for plant adaptation to daily environmental changes.
• Understanding cell-type-specific circadian regulation in mature plant leaves is limited.

Purpose of the Study:

• To investigate the dynamics and hierarchy of circadian gene regulation across different cell types in the mature Arabidopsis thaliana leaf.
• To identify cell-type-specific temporal expression patterns and regulatory networks.

Main Methods:

• Performed a 24-hour single-nucleus RNA sequencing circadian time course on Arabidopsis thaliana leaves.
• Captured approximately 30,000 nuclei across seven time points, covering all major leaf cell types.
• Utilized coexpression analysis and GENIE3 to define temporal expression clades and generate single-cell gene regulatory networks.

Main Results:

• Identified over 7,400 genes with cluster-resolved circadian regulation, organized into five major temporal expression clades shared across cell types.
• Discovered cell-type-specific temporal shifts in gene expression and identified numerous shared and unique transcription factor interactions.
• Uncovered complex light and hormone signaling networks associated with core clock gene targets, showing both broad and cell-type-specific regulation.

Conclusions:

• Circadian transcriptional regulation is extensive in mature Arabidopsis leaves.
• Significant complexity exists in cell-type-specific circadian regulation, involving intricate gene networks and signaling pathways.