In regards to DNA inter-ligation, fragments that are tethered by common protein complexes have greater kinetic advantages under dilute conditions, than those freely diffusing in solution or anchored in different complexes. The ability of 3C approaches to identify long-range interactions is based on the theory of proximity ligation. The next step, which is referred to as enrichment, reduces complexity for genome-wide analysis and adds specificity to chromatin interactions bound by pre-determined TFs (transcription factors). The ChIA-PET method successfully resolves the issues of non-specific interaction noise found in ChIP-Seq by sonicating the ChIP fragments in order to separate random attachments from specific interaction complexes. Despite whole genome profiling methods for both TFBS and long range interactions, combining approaches with the ChIA-PET method allows for identification of genomic areas in which the protein of interest is bound as well as the genomic region which it interacts with. ![]() Unlike 3C which is a locus-specific interaction profiling method, alternative methods such as Hi-C have been established to profile interactions genome wide. Since the noise increases in relation to the distance between interacting regions (max 100kb), laborious and tedious controls are required for accurate characterization of chromatin interactions. While 3C is capable of analyzing non-linear, long-range chromatin interactions, it cannot be used genome wide and, like ChIP-Seq, also suffers from high levels of background noise. While ChIP-Seq is able to identify TFBS genome-wide, 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). Independently, both suffer from limitations in identifying de-novo long-range interactions genome wide. ![]() ChIP-Sequencing (ChIP-Seq) is a popular method used to identify TFBS while 3C has been used to identify long-range chromatin interactions. The ChIA-PET method combines ChIP-based methods, and Chromosome conformation capture (3C) based methods, to extend the capabilities of both approaches. 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). 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.ĬhIA-PET can also be used to unravel the mechanisms of genome control during processes such as cell differentiation, proliferation, and development. 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). Genes can be regulated by regions far from the promoter such as regulatory elements, insulators and boundary elements, and transcription-factor binding sites (TFBS). For the potted plant, see Chia Pet.Ĭhromatin 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. ![]() This article is about the chromatin interaction screening technique.
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