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.

染色质免疫沉淀和测序 (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，由于其坚固的细胞壁和复杂的成分，其在经济上重要的植物器官（EIPO）（例如种子、果实和花朵）中的应用具有挑战性。在这里，我们介绍先进的 ChIP (aChIP)，这是一种优化方法，可以有效地从植物组织中分离染色质，同时去除细胞壁和细胞成分。 aChIP 精确分析所有 14 个测试 EIPO 中的组蛋白修饰，并识别转录因子和染色质修饰酶结合位点。此外，aChIP 提高了 ChIP 效率，与之前的营养组织方法相比，揭示了许多新的修饰位点。 aChIP 揭示了油菜干种子的组蛋白修饰景观，突出了染色质动态在种子休眠和发芽过程中的复杂作用。总而言之，aChIP 是一种强大、高效且灵敏的方法，可对几乎所有植物组织（尤其是 EIPO）进行全面的染色质分析。