A modified CUT&RUN-seq technique for qPCR analysis of chromatin-protein interactions
Arvind Panday, Rajula Elango, Nicholas A. Willis, Ralph Scully
Abstract
Chromatin immunoprecipitation coupled with quantitative PCR (ChIP-qPCR) even with optimization may give low signal-to-background ratio and spatial resolution. Here, we adapted Cleavage Under Targets and Release Using Nuclease (CUT&RUN) (originally developed by the Henikoff group) to develop CUT&RUN-qPCR. By studying the recruitment of selected proteins (but amenable to other proteins), we find that CUT&RUN-qPCR is more sensitive and gives better spatial resolution than ChIP-qPCR. For complete details on the use and execution of this protocol, please refer to Skene et al. (2018) and Skene and Henikoff (2017).
Topics & Concepts
Chromatin immunoprecipitationNucleaseChromatinImmunoprecipitationComputational biologyComputer scienceCleavage (geology)ChipResolution (logic)Molecular biologyBiologyChemistryDNAGeneticsGeneGene expressionArtificial intelligenceTelecommunicationsPaleontologyFracture (geology)PromoterGenomics and Chromatin DynamicsRNA Research and SplicingMolecular Biology Techniques and Applications