SimpleChIP^® - ChIP Assay Kits

Sonication or Enzymatic Digestion: We have kits to support both experimental methods

Sonication is a popular choice for preparing chromatin for ChIP. However, most protocols require subjecting the chromatin to harsh, denaturing conditions (i.e., high heat, detergent, and shearing force) that can damage both antibody epitopes and the integrity of the chromatin.

CST provides multiple options for avoiding the problems of traditional sonication protocols:

• Sonication: Our sonication protocol uses specially formulated cell and nuclear lysis buffers. This approach protects chromatin integrity and antibody epitopes, resulting in increased ChIP efficiency and making it more compatible for use with transcription factors and cofactors, which are labile and have less stable DNA interactions.
• Enzymatic digestion: Enzymatic digestion is an alternative method of chromatin fragmentation that is compatible with all target types and highly amenable to the immunoprecipitation of transcription factors and cofactors. This approach uses micrococcal nuclease to cut the linker region between nucleosomes. Additionally, it is simple to control and protects chromatin and antibody epitopes from shearing or denaturation, making it an ideal option for users who are new to performing ChIP.

The CST SimpleChIP kits for sonication or enzymatic digestion, work as well as traditional sonication for assessing histones, and both outperform traditional sonication when assessing either transcription factors or cofactors.

Chromatin was cross-linked and then fragmented with micrococcal nuclease (CST-enzymatic; blue track), CST sonication buffer (red track) or traditional sonication buffer (green track) and immunoprecipitated using the indicated antibodies. DNA was prepared for sequencing as outlined in the protocol for the SimpleChIP^® Plus Enzymatic Chromatin IP Kit (Magnetic Beads) #9005.