67 / 2024-10-18 13:39:58

aChIP for comprehensive chromatin profiling in economically important plant organs

ChIP-seq; Economically important plant organs; Epigenetic; Epigenome

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) like 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. Additionally, aChIP enhances ChIP efficiency, revealing numerous novel modified sites compared to previous methods in vegetative tissues. Remarkably, aChIP unveils the first histone modification landscape for rapeseed dry seeds, highlighting the intricate roles of chromatin dynamics during seed dormancy and germination. Together, aChIP is a powerful, efficient, and sensitive approach for comprehensive chromatin profiling in virtually all plant tissues, especially in EIPOs.