ChIA-PET (Chromatin Interaction Analysis by Paired-End Tag Sequencing) was introduced in 2009 and combines ChIP with chromatin conformation capture (3C) technology (Fullwood et al., 2009). Not to be confused with Chia Pets, introduced in 1977 and combines chia seeds with animal-shaped pottery. ChIA-PET can detect when distant DNA regions interact with each other via a protein of interest.
The cross-linked chromatin is digested and then pulled down with an antibody against a protein of interest. Linker sequences are ligated to the ends of the DNA which facilitate their ligation to each other (Zhang et al., 2012). This creates hybrid DNA fragments from two different regions of the genome. The resulting library is sequenced yielding a set of DNA regions that interact with each other and the protein of interest. The ChIP based nature of ChIA-PET is both its greatest advantage and limitation: ChIA-PET requires a known protein with which to screen, so it is not applicable for all experiments (Zhang et al., 2012).
Further, ChIA-PET cannot determine if the protein of interest actually binds the DNA of either interaction, it may be present in a protein complex. ChIA-PET has been used to map the interactions of many transcription factors. For example, (Li et al., 2013) used ChIA-PET to characterize the role of the CTCF protein and DNA binding sites in separating large topological domain of chromatin. Similarly, (Chen et al., 2013) recently found that miRNA expression is coordinated in large chromatin domains using ChIA-PET.
ChIA-PET Additional Reading
de Wit, E., and de Laat, W. (2012). A decade of 3C technologies: insights into nuclear organization. Genes Dev. 26, 11-24.
Sajan, S.A., and Hawkins, R.D. (2012). Methods for Identifying Higher-Order Chromatin Structure. Annu. Rev. Genomics Hum. Genet. 13, 59-82.
These reviews examine various ChIP and 3C technologies and give a particularly good descriptions and diagrammatic representations of ChIA-pet. They also explore the pros and cons of ChIA-pet at how it fits into the larger context of chromatin analysis techniques.
- Chen, D., Fu, L.Y., Zhang, Z., Li, G., Zhang, H., Jiang, L., Harrison, A.P., Shanahan, H.P., Klukas, C., Zhang, H.Y., et al. (2013). Dissecting the chromatin interactome of microRNA genes. Nucleic Acids Res.
- Fullwood, M.J., Liu, M.H., Pan, Y.F., Liu, J., Xu, H., Mohamed, Y.B., Orlov, Y.L., Velkov, S., Ho, A., Mei, P.H., et al. (2009). An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 462, 58-64.
- Li, Y., Huang, W., Niu, L., Umbach, D.M., Covo, S., and Li, L. (2013). Characterization of constitutive CTCF/cohesin loci: a possible role in establishing topological domains in mammalian genomes. BMC Genomics 14, 553-2164-14-553.
- Zhang, J., Poh, H.M., Peh, S.Q., Sia, Y.Y., Li, G., Mulawadi, F.H., Goh, Y., Fullwood, M.J., Sung, W.K., Ruan, X., and Ruan, Y. (2012). ChIA-PET analysis of transcriptional chromatin interactions. Methods 58, 289-299.