Chromatin Immunoprecipitation (ChIP)

Chromatin Immunoprecipitation (ChIP) 

What is CHIP?

❑ ChIP is a method to investigate protein-DNA interaction in vivo.
❑ The output of ChIP is enriched fragments of DNA that were bound by a particular protein.
❑ The identity of DNA fragments need to be further determined by a second method.
❑DNA is the information carrier of almost all living organisms.
❑Protein is the major building block of life.
❑Interaction between DNA and protein play vital roles in the development 
and normal function of living organisms, and disease if something goes 
wrong.
❑An important mechanism of protein-DNA interaction is via direct binding, 
i.e., a protein binds to a particular fragment of the DNA.

Binding of DNA with protein 

DNA binds with specific proteins such as:
❑ Transcription factors 
❑ Modified histones 
❑ RNA Polymerase (survey actively transcribe portions of the genome)
❑ DNA polymerase (investigate DNA replication)
❑ DNA repair enzymes 
❑ Or fragments of DNA that are modified: e.g. CpG methylation

How does ChIP work?

The ChIP procedure consists of the following steps: 

1.Isolation of total chromatin 
2.Fragmentation of the chromatin (to achieve resolution) 
3.Immunoprecipitation of the resulting chromatin fragments 
4.Analysis of the immunoprecipitated fraction to determine the amount of a target DNA sequence (or sequences) relative to its abundance in the input chromatin.

If you cross-link your sample then the technique is termed cross linking ChiP (X-ChIP), otherwise it is referred to as native ChIP (N-ChIP).

Principal of ChIP