Laboratory methods to decipher epigenetic signatures: a comparative review

Table 1 General information of different ChIP assays including their advantages and disadvantages are summarized

Technique	Scale	Cells	Advantages	Limitations	References
nChIP (1988)	High throughput	10⁶ ~ 10⁷	Recommended for high-affinity DNA binding proteins Proteins remain intact Good chromatin and protein recovery efficiency Bead-based immunoprecipitation	Time consuming (several days) Labor intensive (several precipitation steps) High variability in results Not recommended for non-histone proteins	[89, 90]
XchIP (1984)	High throughput	10⁶ ~ 10⁷	Recommended for any weakly chromatin-associated proteins such as TFs Recommended where native protein is hard to prepare	Time consuming (several days)	[90]
CChIP	Low throughput	100	Requires as few as 100 cells It takes two to three days	It takes two to three days Highly specific primers are required	[91]
Q2 CHIP	Low throughput	100,000	Reduced steps Enhanced signal to noise ratio	Time consuming (several days)	[92]
MicroChIP/μChIP (2007)	Low throughput	10,000	Applicable for genome-wide studies	Time consuming (several days)	[93]
Fast CHIP (2006)	High throughput	10⁶ ~ 10⁷	The incubation time is decreased Several steps are reduced in protocol Preparation of PCR-ready template is reduced to 1 h	Suitable if only for large cell samples are available	[94]
Matrix ChIP (2008)	High throughput		Enhanced antibody binding capacity Requires minimal sampling Very Fast (1 day) Can detect both Low and High-affinity proteins Automation is possible Includes high sensitivity High reproducibility		[95]

ISSN: 1689-1392