ChIA-PET

Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET or ChIA-PETS) is a technique that incorporates chromatin immunoprecipitation (ChIP)-based enrichment, chromatin proximity ligation, Paired-End Tags, and High-throughput sequencing to determine de novo long-range chromatin interactions genome-wide. Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET or ChIA-PETS) is a technique that incorporates chromatin immunoprecipitation (ChIP)-based enrichment, chromatin proximity ligation, Paired-End Tags, and High-throughput sequencing to determine de novo long-range chromatin interactions genome-wide. Genes can be regulated by regions far from the promoter such as regulatory elements, insulators and boundary elements, and transcription-factor binding sites (TFBS). Uncovering the interplay between regulatory regions and gene coding regions is essential for understanding the mechanisms governing gene regulation in health and disease (Maston et al., 2006). ChIA-PET can be used to identify unique, functional chromatin interactions between distal and proximal regulatory transcription-factor binding sites and the promoters of the genes they interact with. ChIA-PET can also be used to unravel the mechanisms of genome control during processes such as cell differentiation, proliferation, and development. By creating ChIA-PET interactome maps for DNA-binding regulatory proteins and promoter regions, we can better identify unique targets for therapeutic intervention (Fullwood & Yijun, 2009). The ChIA-PET method combines ChIP-based methods (Kuo & Allis, 1999), and Chromosome conformation capture (3C), to extend the capabilities of both approaches. ChIP-Sequencing (ChIP-Seq) is a popular method used to identify TFBS while 3C has been used to identify long-range chromatin interactions (Dekker et al., 2002). However, both suffer from limitations when used independently to identify de-novo long-range interactions genome wide. While ChIP-Seq is typically used for genome-wide identification of TFBS (Barski et al., 2007; Wei et al., 2006), it provides only linear information of protein binding sites along the chromosomes (but not interactions between them), and can suffer from high genomic background noise (false positives).