Single-cell chromatin accessibility and cis-regulatory element analyses in plants using the scPlantReg platform

Area of Science:

• Plant biology
• Genomics
• Bioinformatics

Background:

• Gene regulation is crucial for plant improvement, but cell-type-specific insights are limited by a lack of plant-specific single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) frameworks and databases.
• Existing tools lack comprehensive support for plant scATAC-seq data analysis and cross-species comparisons.

Purpose of the Study:

• To develop 'scPlantReg', an integrated framework and database for plant scATAC-seq data analysis.
• To introduce 'scATACtor', a machine-learning tool for improved cell-type annotation in plants.
• To enable cross-species comparative regulatory analyses in plants.

Main Methods:

• Developed scPlantReg for end-to-end scATAC-seq data processing and biological interpretation.
• Implemented 'scATACtor', a supervised machine-learning model for cell-type annotation.
• Applied scPlantReg to pearl millet and reanalyzed scATAC-seq datasets from 8 plant species.

Main Results:

• Characterized cell-type-specific chromatin accessibility in pearl millet.
• Identified validated activating and repressing accessible chromatin regions (ACRs) and potential regulators like WRKY TFs for xylem development.
• Uncovered conserved regulatory programs across species, including AP2/EREBP-associated ACRs for cell wall development and conserved transcription factors (TFs) in grasses.

Conclusions:

• scPlantReg provides a robust framework and valuable resource for plant regulatory genomics.
• Facilitates detailed cell-type-specific regulatory analysis and cross-species comparisons.
• Advances understanding of conserved gene regulation in plants.