Chromatin immunoprecipitation or ChIP is an excellent method of
investigation of the specific protein interaction and its altered forms with DNA region.
These interactions have a significant role in various cellular processes such as
replication, transcription, DNA damage repair, genome stability, gene regulation and
segregation at mitosis. This technique is therefore giving us power to study a variety of
cellular mechanisms inside the cell in terms of protein-DNA interaction. As the name
Chromatin immunoprecipitation suggests this method utilizes chromatin preparation
from cells to selectively immune-precipitate the protein of interest to identify DNA
sequence associated with it. Chromatin is an organized structure of eukaryotic DNA
which contains double-stranded DNA wrapped around nucleosomes. ChIP has been
extensively used to depict transcription factors, variants of histone, chromatin
modifying enzymes, post-translational modification of histone on the genome. In the
classical ChIP method, protein and DNA is irreversibly cross-linked by UV exposure
followed by immunoprecipitation with specific antibodies, protein-DNA complex is
then purified, treated with proteases and then analysis is done by the method of
Southern blot or dot blot using a radio-labelled probe derived from the cloned DNA
fragment of interest. Further, it was modified by using formaldehyde for reversible
cross-linking of protein-DNA complex and polymerase chain reaction for the detection
of fragments of precipitated DNA. ChIP is a cumbersome procedure to perform and
present many limitations, for example it requires many cells. Therefore, many
modifications and variations, have also developed with the time which enables us to
simplify the procedure and widen its range of applications. This chapter provides a
brief method for Chromatin immunoprecipitation (ChIP) and its applications.
Keywords: ChIP, CPG islands, DNA methylation, Genome, Gene regulation,
Immunoprecipitation, Mitosis, Protein-DNA interaction, Polymerase chain
reaction, Replication, Transcription.
