aChIP: efficient, sensitive, robust ChIP-seq for economically important plant organs

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. We demonstrate the widespread utility of advanced ChIP-seq (aChIP) by profiling diverse chromatin proteins in 14 representative EIPOs including the extremely challenging dry seeds. aChIP shows excellent efficiency and sensitivity in vegetative tissues compared with previous methods. Finally, we profiled the landscape of histone modifications and unveiled their potential functions in rapeseed dry seeds and germinated seeds. Collectively, the data illustrate the great potential of using aChIP to unveil the intricacies of chromatin biology and shed light on their biological functions in plants, particularly within EIPOs.