aChIP is an efficient and sensitive ChIP-seq technique for economically important plant organs

IF 15.8 1区 生物学 Q1 PLANT SCIENCES Nature Plants Pub Date : 2024-08-23 DOI:10.1038/s41477-024-01743-7
Qing Zhang, Wenying Zhong, Guangfeng Zhu, Lulu Cheng, Caijun Yin, Li Deng, Yang Yang, Zhengjing Zhang, Jinxiong Shen, Tingdong Fu, Jian-Kang Zhu, Lun Zhao
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Abstract

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is crucial for profiling histone modifications and transcription factor binding throughout the genome. However, its application in economically important plant organs (EIPOs) such as seeds, fruits and flowers is challenging due to their sturdy cell walls and complex constituents. Here we present advanced ChIP (aChIP), an optimized method that efficiently isolates chromatin from plant tissues while simultaneously removing cell walls and cellular constituents. aChIP precisely profiles histone modifications in all 14 tested EIPOs and identifies transcription factor and chromatin-modifying enzyme binding sites. In addition, aChIP enhances ChIP efficiency, revealing numerous novel modified sites compared with previous methods in vegetative tissues. aChIP reveals the histone modification landscape for rapeseed dry seeds, highlighting the intricate roles of chromatin dynamics during seed dormancy and germination. Altogether, aChIP is a powerful, efficient and sensitive approach for comprehensive chromatin profiling in virtually all plant tissues, especially in EIPOs. This study presents an advanced ChIP-seq method, provides a valuable epigenomics resource for 14 economically important plant organs and reveals histone modification landscape dynamics and functions during rapeseed seed dormancy and germination.

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aChIP 是一种高效、灵敏的 ChIP-seq 技术,适用于具有重要经济价值的植物器官
染色质免疫沉淀测序(ChIP-seq)对于分析整个基因组的组蛋白修饰和转录因子结合至关重要。然而,由于种子、果实和花朵等具有重要经济价值的植物器官(EIPOs)的细胞壁坚固、成分复杂,因此将其应用于这些器官具有挑战性。在这里,我们介绍了先进的 ChIP(aChIP),这是一种经过优化的方法,能从植物组织中有效分离染色质,同时去除细胞壁和细胞成分。aChIP 能精确分析所有 14 种受测 EIPO 的组蛋白修饰,并确定转录因子和染色质修饰酶的结合位点。此外,aChIP 还提高了 ChIP 的效率,与以前在无性组织中使用的方法相比,它揭示了许多新的修饰位点。aChIP 揭示了油菜籽干种子的组蛋白修饰情况,突出了种子休眠和萌发过程中染色质动态的复杂作用。总之,aChIP 是一种功能强大、高效灵敏的方法,可用于几乎所有植物组织,尤其是 EIPO 的染色质全面分析。
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来源期刊
Nature Plants
Nature Plants PLANT SCIENCES-
CiteScore
25.30
自引率
2.20%
发文量
196
期刊介绍: Nature Plants is an online-only, monthly journal publishing the best research on plants — from their evolution, development, metabolism and environmental interactions to their societal significance.
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