[Pao-Yang Chen/Chung-Ju Rachel Wang] Establishing an optimized ATAC-seq protocol for the maize

 Hsieh et al., 2024 Frontiers in Plant Science

ATAC-seq (flashlight) identifies the open chromatin where genes tend to be active (singing sparrows)

【Illustration: @Nien Illustration

The advent of next-generation sequencing in crop improvement offers unprecedented insights into the chromatin landscape closely linked to gene activity governing key traits in plant development and adaptation. Particularly in maize, its dynamic chromatin structure is found to collaborate with massive transcriptional variations across tissues and developmental stages, implying intricate regulatory mechanisms, which highlights the importance of integrating chromatin information into breeding strategies for precise gene controls. The depiction of maize chromatin architecture using Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) provides great opportunities to investigate cis-regulatory elements, which is crucial for crop improvement. In this context, we developed an easy-to-implement ATAC-seq protocol for maize with fewer nuclei and simple equipment. We demonstrate a streamlined ATAC-seq protocol with four key steps for maize in which nuclei purification can be achieved without cell sorting and using only a standard bench-top centrifuge. Our protocol, coupled with the bioinformatic analysis, including validation by read length periodicity, key metrics, and correlation with transcript abundance, provides a precise and efficient assessment of the maize chromatin landscape. Beyond its application to maize, our testing design holds the potential to be applied to other crops or other tissues, especially for those with limited size and amount, establishing a robust foundation for chromatin structure studies in diverse crop species.

This article is a joint effort between Pao-Yang Chen's and Chung-Ju Rachel Wang 's labs. The two co-first authors, Dr. Jo-Wei Allison Hsieh and Pei-Yu Lin, are from Pao-Yang Chen’s lab. The study is published in Frontier in Plant Science, and the research was generously supported by both Academia Sinica and the National Science and Technology Council in Taiwan.

Jo-Wei Allison Hsieh+, Pei-Yu Lin+, Chi-Ting Wang, Yi-Jing Lee, Pearl Chang, Rita Jui-Hsien Lu, Pao-Yang Chen* and Chung-Ju Rachel Wang* (2024) Establishing an optimized ATAC-seq protocol for the maize. Frontier in Plant Science 15: 1370618. doi: 10.3389/fpls.2024.1370618 (+ co-first; * co-corresponding)