Chromatin immunoprecipitation (ChIP) is a technique used to study the association of proteins with distinct regions of genomic DNA using synthesis workstations. ChIP is useful in probing how the genomic location of epigenetic markers, such as histone modifications, changes between different cell types or in the same cell type grown under different conditions.
Also, it can be used to determine where transcription factors and other DNA binding proteins associate to in the genome.
In this procedure, a protein bound to a specific DNA region is crosslinked to DNA. The DNA is then sheared by sonication.
Using an antibody against the DNA-binding protein of interest, specific crosslinked protein-DNA complexes can be bound to either protein A resin, protein G resin or fixed cells with protein A or G on their cell surfaces prior to washing away contaminants and eluting the desired complex.
After elution, the protein-DNA crosslinks are reversed, and the DNA is analyzed using PCR, qPCR, microarray or nextgeneration sequencing.
Staph A cells, which are fixed cells with a high density of protein A on their surface, are commonly used in ChIP assays.
Like protein A and G affinity resins, they can bind antibodies associated with chromatin complexes prior to washing and eluting pure proteinDNA complexes.
These cells exhibit a high binding capacity of antibodies (≥2 mg human IgG per 100 mg of cells) relative to other technologies (protein A magnetic beads, for example, bind ~0.8 mg per 100 mg of beads).
Because of their high capacity, Staph A cells deliver very high sensitivity ChIP assays. Due to the possibility of aspirating cells after the equilibration, capture and wash steps, a disadvantage for Staph A cells is the difficulty in processing multiple ChIP samples in parallel with a multichannel pipette.
For this reason, each sample must be processed individually, adding significant time to the overall protocol and potentially reducing reproducibility of the technology.
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