Researchers use chromatin immunoprecipitation, or ChIP, to identify and characterize protein-DNA interactions in the context of chromatin. ChIP experiments can use varying input samples, chromatin fragmentation methods, and provide ChIP-qPCR or ChIP-seq readouts.
The success of your ChIP experiment depends on the fragmentation of chromatin, a critical step in the ChIP protocol. This can be accomplished with either sonication or enzymatic digestion. But how do you decide which chromatin fragmentation protocol to use in your ChIP experiments? A number of factors can influence your choice, making a decision seem daunting. So let’s simplify!
In the video below, we walk through four questions that will help you find a protocol and the ideal ChIP kit from CST that’s suited to your experimental needs. First, what is your input sample type, cells or tissues? Second, what type of protein is being targeted for IP? Histones, transcription factors, and cofactors bind to DNA with varying strength, affecting ChIP efficiency.
Other factors to consider are the abundance of the target protein in your sample, and your preferred method for chromatin fragmentation. In many instances, you can use either sonication or enzymatic digestion. We’ll also introduce some scenarios in which one method for chromatin fragmentation outperforms the other.