BACKGROUND: Long-range chromatin interactions play an important role in 
transcription regulation. Chromatin Interaction Analysis with Paired-End-Tag 
sequencing (ChIA-PET) is an emerging technology that has unique advantages in 
chromatin interaction analysis, and thus provides insight into the study of 
transcription regulation.
RESULTS: This article introduces the experimental protocol and data analysis 
process of ChIA-PET, as well as discusses some applications using this 
technology. It also unveils the direction of future studies based on this 
technology.
CONCLUSIONS: Overall we show that ChIA-PET is the cornerstone to explore the 
three-dimensional (3D) chromatin structure, and certainly will lead the 
forthcoming wave of 3D genomics studies.