Minghua Li

Biotechnology Research Center, Cuixi Academy of Biotechnology, Zhuji, 311800, China
Author    Correspondence author
Maize Genomics and Genetics, 2025, Vol. 16, No. 4   doi: 10.5376/mgg.2025.16.0017
Received: 15 May, 2025    Accepted: 30 Jun., 2025    Published: 20 Jul., 2025

This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Li M.H., 2025, ATAC-seq reveals chromatin accessibility changes during maize seed development, Maize Genomics and Genetics, 16(4): 182-201 (doi: 10.5376/mgg.2025.16.0017)

 

Chromatin accessibility plays a key role in regulating gene expression during plant development. While transcriptional changes during maize seed development have been well studied, how chromatin accessibility shifts over time is still not fully understood. This study used ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) to examine open chromatin regions (OCRs) across the maize genome at several seed developmental stages. By combining these data with RNA-seq results, we tracked how accessibility patterns change as seeds grow and found that these changes are closely tied to gene activity. Most OCRs were located near promoters or enhancers. Motif analysis pointed to several transcription factor families—such as bZIP, MYB, and NAC—as likely players in developmental control. Functional annotation showed that OCR-associated genes are highly enriched in pathways like starch biosynthesis, hormone signaling, and embryo development. This study maps how chromatin opens and closes across maize seed development, identifies potential regulatory elements and key TFs, and offers useful insights and targets for epigenetic studies and molecular breeding in maize.

Maize; ATAC-seq; Chromatin accessibility; Seed development; Regulatory network