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Chromatin interaction analysis by paired-end tag software tools

A number of high-throughput methods based on nuclear proximity ligation have been developed to detect genome-wide chromatin interactions, including high-throughput chromosome conformation capture (Hi-C) and chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) (Lieberman-Aiden et al., 2009; Fullwood et al., 2009). While Hi-C was developed to capture all chromatin interactions and is effective for mapping large-scale structures such as chromatin compartments and topologically associated domains (Lieberman-Aiden et al., 2009; Dixon et al., 2012), ChIA-PET is emerging as an important experimental method for detecting specific protein-mediated chromatin loops genome-wide at high resolution. Source text: Li et al., 2016.

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