Feature Review

ATAC-seq Reveals Chromatin Accessibility Changes During Maize Seed Development  

Minghua Li
Biotechnology Research Center, Cuixi Academy of Biotechnology, Zhuji, 311800, China
Author    Correspondence author
Maize Genomics and Genetics, 2025, Vol. 16, No. 4   
Received: 15 May, 2025    Accepted: 30 Jun., 2025    Published: 20 Jul., 2025
© 2025 BioPublisher Publishing Platform
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.
Abstract

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.

Keywords
Maize; ATAC-seq; Chromatin accessibility; Seed development; Regulatory network
[Full-Flipping PDF] [Full-Text HTML]
Maize Genomics and Genetics
• Volume 16
View Options
. PDF
. FPDF(win)
. FPDF(mac)
. HTML
. Online fPDF
Associated material
. Readers' comments
Other articles by authors
. Minghua Li
Related articles
. Maize
. ATAC-seq
. Chromatin accessibility
. Seed development
. Regulatory network
Tools
. Post a comment