Mapping open chromatin by ATAC-seq in bread wheat.

Area of Science:

• Plant genomics
• Epigenetics
• Molecular biology

Background:

• Gene transcription is regulated by cis-regulatory elements.
• Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) maps these elements but faces challenges in plants due to cell walls and chloroplasts.
• Existing ATAC-seq data analysis pipelines are insufficient, especially for wheat.

Purpose of the Study:

• To provide an all-in-one solution for mapping open chromatin in wheat.
• To develop an efficient experimental protocol for high-quality ATAC-seq data from various wheat tissues.
• To create a user-friendly online pipeline for analyzing wheat ATAC-seq data.

Main Methods:

• Optimized nuclei extraction from diverse wheat tissues, minimizing debris.
• Performed ATAC-seq on challenging tissues like young spikes and ovaries.
• Developed and validated an online data analysis pipeline for ATAC-seq data.

Main Results:

• Successfully obtained high-quality nuclei and ATAC-seq data from various wheat tissues.
• Determined the saturation sequencing depth for wheat ATAC-seq to be approximately 16 Gb.
• Established a powerful and accessible online pipeline for wheat ATAC-seq data analysis.

Conclusions:

• The developed method enables efficient mapping of open chromatin in wheat.
• The online pipeline facilitates regulatory genome studies in wheat and can be adapted for other plant species.
• This work supports advancements in plant regulatory genomics research.