Maize Genomics and Genetics 2025, Vol.16, No.4, 182-201 http://cropscipublisher.com/index.php/mgg 182 Feature Review Open Access ATAC-seq Reveals Chromatin Accessibility Changes During Maize Seed Development Minghua Li Biotechnology Research Center, Cuixi Academy of Biotechnology, Zhuji, 311800, China Corresponding author: minghua.li@cuixi.org 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 Copyright © 2025 Li, 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. Preferred citation for this article: 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) 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 1 Introduction In the last few decades, scientists have found that maize seed development is controlled by many systems. These systems work together in different parts of the plant and at different times. At the start of seed development, the embryo begins to form. Several special types of endosperm cells also start to appear. These include aleurone cells, cells that store starch, and transfer cells. The way these cells form depends on when and where certain genes are turned on. This process is mainly controlled by transcription factors (TFs). These are proteins that help turn genes on or off. Let’s look at the endosperm as an example. Two TFs called NAKED ENDOSPERM1 and 2 (NKD1/2), which belong to the AL2/GL2-type group, are needed to make sure aleurone cells form the right way. These proteins help turn on genes related to cell identity, how the cell responds to hormones, and how it stores nutrients. In maize, NKD1/2 affect over 6% of the endosperm’s gene activity. One important gene they influence is Opaque2, which helps make storage proteins. Another TF, Opaque11, acts like a main switch. It controls other TFs such as DOF3 and Opaque2 (Gontarek et al., 2016; Zhan et al., 2018). It also helps regulate genes that produce starch and proteins. In the embryo, a set of TFs called LAFL proteins help the seed move from early growth to the mature stage. For example, a B3-type TF known as ABSCISIC ACID-INSENSITIVE 3, along with similar proteins in maize, turns on genes needed in the late stages of embryo development. It also activates genes that protect the seed from drying out. All these TFs don’t work alone. They interact closely with plant hormones. Auxin, which comes from the central cell, helps start the endosperm’s development. Later, when ABA (abscisic acid) levels go up, it helps the seed mature and prepares it for dormancy (Yang et al., 2022). Gibberellins are also part of this process. If something in this system fails, the seed might grow abnormally or end up with the wrong size or content. Apart from DNA sequences and how available TFs are, the structure of chromatin—how tightly or loosely DNA is packed—also plays a big part in whether a gene is active or silent. Chromatin that’s “open,” meaning DNA is
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