ChIAPET

ChIAPET, often written as ChIA-PET, stands for Chromatin Interaction Analysis by Paired-End Tag sequencing and is a high-throughput method for mapping chromatin interactions mediated by a specific protein.

In brief, cells are crosslinked to preserve interactions, chromatin is fragmented, and DNA bound by the target protein is enriched by immunoprecipitation. DNA fragments bound to the same protein are then ligated in proximity using specialized adapters, producing chimeric DNA molecules that join two distant genomic loci. These molecules are amplified and sequenced; the paired-end tags are mapped to the genome to reveal interacting regions and the regulatory networks they form.

ChIA-PET yields a genome-wide map of protein-mediated chromatin interactions, enabling the identification of promoter–enhancer loops and other regulatory contacts specific to the protein of interest. It has been used to study transcription factors, RNA polymerase II, and chromatin modifiers across diverse cell types and conditions, contributing to understanding of gene regulation, cell-type–specific regulatory architecture, and disease-associated regulatory changes.

Limitations include dependence on high-quality antibodies, large input material, and potential biases from crosslinking and ligation; the method can be technically demanding and relatively resource-intensive. Variants and related approaches, such as HiChIP and PLAC-seq, offer streamlined workflows by combining chromatin immunoprecipitation with Hi-C or related proximity ligation strategies.