Purification of immune-active macrophage super enhancers by chemical cross-linked chromatin immune precipitation

Abstract

Summary: Isolation of extraordinarily long-length super-enhancers (SEs) using typical chromatin immune precipitation (ChIP) techniques can lead to DNA breakage due to uncontrolled cross-linking. We present a redefined ChIP technique for SE purification. After controlled paraformaldehyde-based cross-linking, glycine was used to quench the cross-linker followed by mild sonication. The sonication produced ideal fragment length of long-length SE chromatin. Presently, miR146a-5p SE of macrophages was pulled using BRD4 protein. Our protocol can reproducibly simplify the SE element isolation issues, in a quality-controlled manner.For complete details on the use and execution of this protocol, please refer to Das et al. (2021).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Keywords

• Cell Biology
• ChIPseq
• Immunology
• Molecular Biology
• Biotechnology and Bioengineering