Optimization of ATAC-seq in wheat seedling roots using INTACT-isolated nuclei

Area of Science:

• Plant genomics
• Epigenetics
• Molecular biology

Background:

• Genetic information in organisms is organized by genes and regulatory elements.
• Cis-regulatory elements are crucial for gene expression but remain poorly characterized in plants.
• Chromatin accessibility is a key indicator for identifying these regulatory elements.

Purpose of the Study:

• To develop a method for identifying cis-regulatory elements in tetraploid wheat.
• To characterize open chromatin regions in wheat using a novel technique.
• To improve the understanding of wheat genome functionality.

Main Methods:

• Developed a transgenic INTACT (isolation of nuclei tagged in specific cell types) system for nuclei purification in tetraploid wheat.
• Combined the INTACT system with ATAC-seq (assay for transposase-accessible chromatin with sequencing) to map open chromatin.
• Analyzed ATAC-seq data from wheat root tips.

Main Results:

• Successfully purified nuclei from wheat root tips using the INTACT system.
• Identified open chromatin regions, predominantly in intergenic and promoter areas, consistent with regulatory elements.
• Demonstrated high reproducibility and overlap of open chromatin regions between root and leaf tissues.
• Observed overlap between ATAC-seq peaks and validated cis-regulatory elements, correlating accessibility with gene expression.

Conclusions:

• Established and validated an INTACT system for efficient nuclei isolation in tetraploid wheat.
• ATAC-seq experiments using INTACT-purified nuclei revealed open chromatin regions, aiding cis-regulatory element identification.
• The INTACT system facilitates broader ATAC-seq dataset generation for a comprehensive map of accessible DNA in the wheat genome.