Table 4 Advantages and disadvantages of ChIP techniques
From: DNA–protein interaction studies: a historical and comparative analysis
| Technique [References] | Technique | Applications | Case studies | |
|---|---|---|---|---|
| Pros | Cons | |||
| ChIP [42] |
In vivo method Enables observation of highly dynamic events |
Requires a population of cells Cannot directly indicate functional significance | Predict the location of a bound protein in a particular cell type | Liu et al. [46] |
| ChIP-chip [42, 80] |
High throughput Enables to calculate the relative binding affinity of the protein under study to each sequence |
Hybridisation noise signals from biased amplification Difficulties in comparing results from different groups | Detect the presence of a specific protein throughout a large portion of the genome | |
| ChIP-SAGE [80] | The results obtained are measured more quantitatively | It suffers from mapping ambiguity | Predict the location of a specific protein throughout a large portion or the entire genome | |
| ChIP-PET [80] |
The results obtained are measured more quantitatively Improves the mapping accuracy of short-tags and the information content | Demands a large sequencing capacity | ||
| ChIP-seq [75, 80, 83] |
Inexistence of hybridisation noise signals Obtention of rigorous and quantifiable results |
Insufficient reads can lead to a loss of sensitivity and specificity in spotting the enriched regions High cost | ||
| ChIP-exo [75] | Enables observation of highly dynamic events | Predict the location of more than one bound protein in a particular cell type | ||