Should I fragment my chromatin using enzymatic digestion or sonication when performing ChIP?

Both enzymatic digestion and sonication work when performing ChIP for histones, transcription factors, and cofactors. However, we have found that enzymatic ChIP gives higher levels of enrichment than sonication ChIP for transcription factors and cofactors, especially those with low expression. We have also found that some transcription factors and cofactors only work in enzymatic ChIP and not sonication ChIP. That being said, sonication ChIP kit has its advantage when dealing with fibrous or fatty tissue types. Please refer to our online video (https://www.cellsignal.com/learn-and-support/videos-and-webinars/webinar-enzymatic-or-sonication-protocol) for which kit to choose for your ChIP experiment.

Last updated: February 27, 2024