染色质转座酶可及性测定(assay for transposase-accessible chromatin with high-throughput sequencing, ATAC-seq)技术自2013年诞生以来,凭借其超低样本需求、单碱基级别的高分辨率及操作高效性等特点,已成为植物表观遗传研究的核心工具。该技术利用工程化改造的Tn5转座酶,特异性识别并捕获全基因组范围内染色质开放区域,为解析植物发育可塑性、环境适应性及基因精准调控网络提供了全新视角。在植物研究领域中,该技术不仅突破传统方法的局限性,更在基因调控网络解析、作物遗传改良及环境适应性研究中展现出革命性潜力。笔者系统综述ATAC-seq技术的原理及其在植物研究应用中的发展历程,重点从逆境胁迫响应、生长发育调控及分子机制等角度,深入分析其在揭示染色质动态重塑、远程互作网络构建等方向的前沿进展,并探讨该技术在作物遗传改良和功能基因组学研究中的应用潜力。

Epigenomics have significantly advanced our understanding of regulatory mechanisms governing plant growth, development, stress responses, and adaptive evolution by elucidating heritable changes in gene expression that occur independently of DNA sequence alterations. Chromatin accessibility, a key component of epigenetic regulation, directly modulates the binding efficiency of transcription factors and other regulatory proteins to DNA, thereby establishing the spatiotemporal specificity of gene expression patterns. The assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) has emerged as the method of choice for mapping open chromatin regions due to its technical advantages including minimal cell input requirements, simplicity in protocol execution, superior signal-to-noise ratio, and genome-wide coverage. This technique utilizes an engineered Tn5 transposase enzyme that preferentially cleaves accessible chromatin regions while simultaneously incorporating sequencing adapters, facilitating the generation of chromatin accessibility maps through high-throughput sequencing. Since its introduction in 2013, ATAC-seq has been employed in studies; however, fewer of these investigations have focused on plant systems, with research efforts predominantly concentrated in limited model species such as Arabidopsis thaliana, rice (Oryza sativa), and maize (Zea mays). This distribution highlights the need for broader and deeper applications within plant sciences to fully realize the potential of this transformative technology. In plant stress research, integrating ATAC-seq with multi-omics approaches including RNA-seq has enabled identification of transcription factors mediating pear responses to Penicillium expansum infection, characterization of a critical promoter deletion linked to reduced cold sensitivity in tomato, elucidation of an MdRAD5B-regulated drought tolerance module in apple, pinpointing of OsbZIP14 as a central regulator during heat stress in rice, and revelation of HSFA1a-mediated enhancer-promoter conformational dynamics in tomato. These studies collectively establish chromatin dynamics as fundamental components in stress signal transduction pathways. Within growth and development research, this methodology has advanced understanding through construction of an epigenetic atlas for wheat spike development, delineation of early regulatory networks in maize embryogenesis, mapping of regulatory interaction modules controlling rice glume morphology, dissection of methylation-accessibility coupling mechanisms associated with poplar growth, and identification of chromosomal spatial organization transitions correlating with flavonoid biosynthesis in peanut, thereby comprehensively illustrating the regulatory influence of chromatin accessibility on organogenesis and yield determination processes. Nevertheless, plant ATAC-seq research faces significant challenges: the presence of cell walls and chloroplasts complicates nuclear isolation, and standardized protocols remain underdeveloped; ATAC-seq data alone cannot directly resolve transcription factor binding or histone modification patterns, whereas multi-omics integration requires substantial financial and technical resources; plant genomes contain abundant repetitive sequences with incomplete annotations, limiting the efficacy of animal-derived analytical tools for peak calling and repeat masking; additionally, insufficient genomic resources and transformation systems in non-model species hinder widespread implementation. Future advancements should prioritize developing efficient plant-specific nuclear extraction methodologies, establishing cost-effective multi-omics frameworks, creating dedicated bioinformatics pipelines, and enhancing genomic tools and transformation platforms for major crops. Overcoming these limitations will position ATAC-seq as a pivotal tool for elucidating chromatin dynamics in regulatory networks underlying complex agronomic traits, thereby advancing crop genetic improvement through novel mechanistic insights and theoretical foundations.