Advances and applications of ChIP-seq technologies in plants

Chromatin-associated proteins play essential roles in transcriptional regulation, plant development, and responses to environmental cues. Accurate genome-wide mapping of their binding sites is critical for elucidating their functions and regulatory networks. ChIP-seq is a cornerstone technique in epigenomics and functional genomics, widely used to profile histone modifications and binding sites of transcription factors across the genome. However, its application to economically important plant organs (EIPOs), such as seeds, fruits, tubers, and flowers, has long been hindered by the presence of rigid cell walls and complex metabolic components. The recently developed aChIP-seq has made significant advances in data quality and tissue universality, providing a new approach for epigenomic and functional genomic research in EIPOs. This review summarizes recent advances in plant ChIP-seq and related techniques, proposes standards for data quality assessment, and outlines future directions for technological innovation and their applications in decoding transcriptional regulatory networks and advancing crop genetic improvement.