ChIA-PET
ChIA-PET is dependent on identification of sequences that can be mapped to the reference sequence (ref).
ChIA-PET requires the use of peak-calling computer algorithms to organize and map PET reads to the reference genome. Because of variations between software platforms, results can vary depending on which program is used.
Although repetitive DNA regions can be associated with gene regulation (Polak & Domany, 200), they need to be removed as they can affect the data (Fullwood et al., 2009).
ChIA-PET is applicable to many different protein factors involved in transcriptional regulation or chromatin structural conformation.
ChIA-PET analysis can be applied to chromatin interactions involved in a particular nuclear process. By using general TFs such as RNA Polymerase II, it may be possible to identify all chromatin interactions involved in transcription regulation. Further, the use of protein factors involved in DNA replication or chromatin structure would allow identification of all interactions due to DNA replication and chromatin structural modification (Fullwood et al., 2009).
It is well established that cis and trans-regulatory complexes contain unique combinations of proteins based on cell and tissue specific conditions (Dekker et al., 2006). While identification of single, functional TFBS is a significant advancement, the use of ChIA-PET to identify individual proteins in a complex would require guess work and multiple experiments to identify each interacting protein. This would be a costly and time consuming endevour.
ChIA-PET is limited by the quality, purity, and specificity of the antibodies used (Fullwood et al., 2009).