Cleavage Under Targets & Release Using Nuclease (CUT&RUN) Protocols for the Study of Genetic and Epigenetic Regulation in Cancer

Cancer cell malignancy is regulated by a variety of mechanisms, collectively termed the hallmarks of cancer. At the core of these regulative processes are genetic and epigenetic perturbations that play an essential role in neoplasmic formation. Advances in molecular techniques have enabled the in-depth research of the epigenome by means of epigenetic profiling, a process that has been dominated by the chromatin immunoprecipitation (ChIP) method. Even though ChIP has dominated the field, the technique is hindered by limitations such as high background noise, requirement of a large number of cells, requirement of antibodies with high pull-down efficiency, and crosslinking and solubilization-induced artifacts (e.g., epitope masking). Cleavage Under Targets and Release Under Nuclease (CUT&RUN) is a recently developed epigenomic alternative method to ChIP, offering advantages designed to overcome limitations of the ChIP method. Despite its advantages, it is not always straightforward which technique is most suitable for the job at hand. This chapter aims to provide an in-depth guide in performing CUT&RUN.