Mapping Active Gene-Associated Chromatin Loops by ChIA-PET in Rice

Hierarchical chromatin structures are critical for transcriptional regulation and many biological processes. It has been widely known that the linear genome of many plants and animals is partitioned into various chromatin interacting domains or gene regulatory modules with specific chromatin features, such as H3K4me3-related active interacting domains, H3K27me3 or Polycomb-related repressive domains, and H3K9me2-related heterochromatin domains. ChIA-PET, which combines chromatin immunoprecipitation (ChIP) assay with proximity ligation, can detect gene contact networks that are connected by co-regulated genes by pulling down specific chromatin complexes using an antibody of interest. Here, we describe a detailed, long-read ChIA-PET protocol for mapping promoter-centered active gene modules in plants.