High-throughput capture of transcription factor-driven chromatin dynamics using PHILO ChIP-seq (RNA-Seq)

Assessing the dynamics of chromatin and transcription factor (TF) DNA binding in plants remains a significant challenge, primarily due to the lack of efficient tools for capturing these features on a larger scale. Here, we present PHILO (Plant HIgh-throughput LOw input) ChIP-seq, a high-throughput ChIP-seq platform that enables the cost-effective and extensive capture of TF DNA binding and the genome-wide distribution of histone modifications. Through the application of H3K9ac PHILO ChIP-seq to eight jasmonic acid pathway mutants, involving the parallel processing of over 100 samples, we not only substantially corroborate the previously described interplay among chromatin regulators at the target genes of the JA master TF MYC2 but also unveil previously unknown histone acetylation patterns in the regulatory regions of MYC2 target genes. Overall, our PHILO ChIP-seq platform proves to be a highly effective approach for simultaneously examining chromatin on an unprecedented scale opening the door to conducting large-scale epigenome studies in plants. To identify genes that are responsive to jasmonic acid (JA) after 2 h of JA treatment, RNA-seq with Col-0 seedlings was performed.