An integrative multi‐omics analysis of histone modifications and DNA methylation reveals the epigenomic landscape in apple under drought stress

IF 10.5 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Plant Biotechnology Journal Pub Date : 2025-07-08 DOI:10.1111/pbi.70173

Shicong Wang, Jieqiang He, Bichun Hu, Mengting Deng, Wenjie Li, Junxing Guo, Yi Song, Qianming Zheng, Xiaolin Song, Fengwang Ma, Jiangbo Wang, Qingmei Guan, Jidi Xu

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引用次数: 0

Abstract

SummaryEpigenetic regulation plays a key role in plant development and stress response processes. Although previous studies have found that epigenetic modifications are involved in the drought response in apple, a comprehensive epigenomic profile of the response of apple to drought is needed. To characterize epigenomic profiles during the response of apple to drought, we conducted transcriptome, whole‐genome bisulfite sequencing, and ChIP‐seq analyses of six histone modifications (H3ac, H3K9ac, H3K14ac, H3K4me3, H3K27me3, and H3K36me3) in Malus hupehensis at 0, 3, 6, and 9 days after drought treatment. The greatest changes in differentially expressed genes were observed after 6 days of drought treatment. However, the highest levels of DNA methylation near the gene region were observed after only 3 days of drought treatment. The global enrichment of six histone modifications slightly decreased under drought treatment. Up‐regulated drought‐responsive genes with higher fold changes were associated with the hypo‐regulation of H3K27me3, and up‐regulated genes with lower fold changes were associated with the hyper‐regulation of H3K4me3. Many drought‐responsive genes such as MYB88, NCED3, and JAZ1 are regulated by epigenetic modifications. We verified the functions of two candidate drought‐responsive genes regulated by multiple epigenetic modifications, MdABI5 (regulated by H3K14ac and H3K27me3) and MdOCP3 (regulated by H3K9ac and H3K36me3) in the drought response. The phenotypes of transgenic apple under drought showed that MdABI5 and MdOCP3 positively regulate drought tolerance in apple. Our results provide new insights t for studies of the molecular mechanism of epigenetic modifications and have implications for improving the drought resistance of apple.

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一项组蛋白修饰和DNA甲基化的综合多组学分析揭示了干旱胁迫下苹果的表观基因组景观

遗传调控在植物发育和逆境响应过程中起着关键作用。尽管已有研究发现苹果对干旱的响应涉及表观遗传修饰，但还需要对苹果对干旱的响应进行全面的表观基因组分析。为了描述苹果对干旱响应过程中的表观基因组特征，我们对干旱处理后0、3、6和9天的苹果进行了转录组、全基因组亚硫酸盐测序和ChIP - seq分析，分析了6种组蛋白修饰（H3ac、H3K9ac、H3K14ac、H3K4me3、H3K27me3和H3K36me3）。差异表达基因在干旱处理6天后变化最大。然而，仅在干旱处理3天后，在基因区域附近观察到最高水平的DNA甲基化。6种组蛋白修饰的富集程度在干旱处理下略有下降。高折叠变化的干旱响应基因上调与H3K27me3的低调控有关，低折叠变化的干旱响应基因上调与H3K4me3的高调控有关。许多干旱响应基因，如MYB88、NCED3和JAZ1，都受到表观遗传修饰的调控。我们验证了两个候选干旱响应基因MdABI5（由H3K14ac和H3K27me3调控）和MdOCP3（由H3K9ac和H3K36me3调控）在干旱响应中的功能。转基因苹果在干旱条件下的表型分析表明，MdABI5和MdOCP3正调控苹果的抗旱性。本研究结果为研究表观遗传修饰的分子机制提供了新的思路，对提高苹果抗旱性具有重要意义。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Plant Biotechnology Journal 生物-生物工程与应用微生物

CiteScore

20.50

自引率

2.90%

发文量

201

审稿时长

1 months

期刊介绍： Plant Biotechnology Journal aspires to publish original research and insightful reviews of high impact, authored by prominent researchers in applied plant science. The journal places a special emphasis on molecular plant sciences and their practical applications through plant biotechnology. Our goal is to establish a platform for showcasing significant advances in the field, encompassing curiosity-driven studies with potential applications, strategic research in plant biotechnology, scientific analysis of crucial issues for the beneficial utilization of plant sciences, and assessments of the performance of plant biotechnology products in practical applications.